Starting phenix.real_space_refine
on Wed Sep 17 12:04:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jbm_61319/09_2025/9jbm_61319.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jbm_61319/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jbm_61319/09_2025/9jbm_61319.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jbm_61319/09_2025/9jbm_61319.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jbm_61319/09_2025/9jbm_61319.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jbm_61319/09_2025/9jbm_61319.map"
  }
  resolution = 3.83
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.70, per 1000 atoms: 0.20
  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: 0.67
  Conformation dependent library (CDL) restraints added in 348.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.39
  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: 1.46

  Time building geometry restraints manager: 0.88 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:             0.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.210
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.280
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.035   0.004   ARG A 342 
 TYR   0.051   0.005   TYR A1053 
 PHE   0.033   0.003   PHE A 200 
 TRP   0.066   0.003   TRP A 257 
 HIS   0.017   0.002   HIS A 568 

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

*********************** 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  : 0.271 
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: 0.1079
  time to fit residues: 39.6497
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  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9980
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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**
** A1175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.142177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.120404 restraints weight = 16017.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.124573 restraints weight = 8560.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.127384 restraints weight = 5378.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.129337 restraints weight = 3784.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.130593 restraints weight = 2888.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8777  Z= 0.203
  Angle     :  0.743  12.527  11925  Z= 0.383
  Chirality :  0.047   0.229   1398
  Planarity :  0.006   0.067   1511
  Dihedral  :  4.615  16.649   1185
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.64 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.25), residues: 1083
  helix:  1.33 (0.22), residues: 514
  sheet:  0.74 (0.41), residues: 159
  loop : -0.08 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 702 
 TYR   0.028   0.002   TYR A  75 
 PHE   0.025   0.002   PHE A  70 
 TRP   0.033   0.003   TRP A 257 
 HIS   0.015   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 8777)
  covalent geometry    : angle       0.74278 (11925)
  hydrogen bonds       : bond        0.05456 (  479)
  hydrogen bonds       : angle       5.41283 ( 1398)

*********************** 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
  281 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 267
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7291 (mt-10)
REVERT: A   78 TRP cc_start: 0.6824 (t60) cc_final: 0.6458 (t60)
REVERT: A  133 GLU cc_start: 0.6446 (mp0) cc_final: 0.6156 (mp0)
REVERT: A  135 ASP cc_start: 0.7116 (t70) cc_final: 0.6800 (t70)
REVERT: A  143 LYS cc_start: 0.8128 (pptt) cc_final: 0.7601 (pptt)
REVERT: A  176 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8381 (mttm)
REVERT: A  181 TYR cc_start: 0.7607 (t80) cc_final: 0.7277 (t80)
REVERT: A  214 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6764 (mt-10)
REVERT: A  215 ILE cc_start: 0.8716 (mm) cc_final: 0.8457 (mm)
REVERT: A  253 CYS cc_start: 0.7318 (m) cc_final: 0.6919 (m)
REVERT: A  312 ILE cc_start: 0.8286 (mt) cc_final: 0.8016 (mp)
REVERT: A  316 GLU cc_start: 0.7568 (mp0) cc_final: 0.7100 (mp0)
REVERT: A  337 ASP cc_start: 0.7178 (m-30) cc_final: 0.6844 (m-30)
REVERT: A  353 THR cc_start: 0.8115 (t) cc_final: 0.7881 (t)
REVERT: A  361 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7947 (mmtt)
REVERT: A  364 ILE cc_start: 0.8570 (tp) cc_final: 0.8122 (tt)
REVERT: A  389 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7858 (ttmt)
REVERT: A  392 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7462 (tm-30)
REVERT: A  423 GLN cc_start: 0.8366 (tm-30) cc_final: 0.7782 (tm-30)
REVERT: A  465 GLU cc_start: 0.7381 (tp30) cc_final: 0.7007 (tp30)
REVERT: A  480 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7316 (mt-10)
REVERT: A  568 HIS cc_start: 0.7328 (m-70) cc_final: 0.6935 (m90)
REVERT: A  632 ARG cc_start: 0.7842 (ptt90) cc_final: 0.7550 (ptt90)
REVERT: A  633 MET cc_start: 0.6844 (tmm) cc_final: 0.6064 (tmm)
REVERT: A  663 MET cc_start: 0.7730 (mtm) cc_final: 0.7233 (mtm)
REVERT: A  690 TYR cc_start: 0.8233 (t80) cc_final: 0.7720 (t80)
REVERT: A  728 ASP cc_start: 0.7357 (p0) cc_final: 0.7101 (p0)
REVERT: A  734 ARG cc_start: 0.7952 (ttm110) cc_final: 0.7682 (ttm110)
REVERT: A  801 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7861 (mmmt)
REVERT: A  846 GLU cc_start: 0.7236 (tt0) cc_final: 0.7014 (tt0)
REVERT: A  861 MET cc_start: 0.7703 (tpt) cc_final: 0.7240 (tpt)
REVERT: A  962 SER cc_start: 0.8530 (t) cc_final: 0.8170 (p)
REVERT: A 1042 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7452 (ttp80)
REVERT: A 1050 PHE cc_start: 0.7558 (m-80) cc_final: 0.7334 (m-10)
REVERT: A 1092 LYS cc_start: 0.7859 (tttm) cc_final: 0.7599 (tttm)
REVERT: A 1106 MET cc_start: 0.8078 (tmm) cc_final: 0.7864 (tmm)
REVERT: A 1126 GLU cc_start: 0.7598 (pt0) cc_final: 0.7183 (pt0)
REVERT: A 1170 LYS cc_start: 0.8724 (tttt) cc_final: 0.8135 (mtmm)
  outliers start: 14
  outliers final: 8
  residues processed: 271
  average time/residue: 0.1095
  time to fit residues: 39.2319
Evaluate side-chains
  256 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 248
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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  545 VAL
Chi-restraints excluded: chain A residue  806 GLU
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 97 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 42 optimal weight:    0.4980
   chunk 73 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 119 HIS
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 568 HIS
A 625 HIS
A 698 HIS
A1061 GLN
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.142934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.121166 restraints weight = 15651.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.125269 restraints weight = 8357.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.128025 restraints weight = 5223.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.129846 restraints weight = 3661.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.131232 restraints weight = 2819.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8777  Z= 0.176
  Angle     :  0.663  11.779  11925  Z= 0.339
  Chirality :  0.044   0.176   1398
  Planarity :  0.005   0.073   1511
  Dihedral  :  4.505  16.617   1185
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.40 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 13.79 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.25), residues: 1083
  helix:  1.29 (0.22), residues: 513
  sheet:  0.70 (0.41), residues: 151
  loop : -0.27 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 623 
 TYR   0.024   0.002   TYR A 807 
 PHE   0.022   0.002   PHE A  70 
 TRP   0.017   0.002   TRP A 257 
 HIS   0.009   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 8777)
  covalent geometry    : angle       0.66349 (11925)
  hydrogen bonds       : bond        0.04796 (  479)
  hydrogen bonds       : angle       5.03197 ( 1398)

*********************** 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
  302 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 268
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7301 (mt-10)
REVERT: A   78 TRP cc_start: 0.6719 (t60) cc_final: 0.6462 (t60)
REVERT: A  143 LYS cc_start: 0.8223 (pptt) cc_final: 0.7716 (pptt)
REVERT: A  144 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.7935 (p)
REVERT: A  176 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8160 (mmtp)
REVERT: A  181 TYR cc_start: 0.7703 (t80) cc_final: 0.6822 (t80)
REVERT: A  182 ASP cc_start: 0.7283 (t0) cc_final: 0.6037 (t70)
REVERT: A  214 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6609 (mt-10)
REVERT: A  215 ILE cc_start: 0.8710 (mm) cc_final: 0.8438 (mm)
REVERT: A  253 CYS cc_start: 0.7379 (m) cc_final: 0.7015 (m)
REVERT: A  316 GLU cc_start: 0.7649 (mp0) cc_final: 0.7107 (mp0)
REVERT: A  337 ASP cc_start: 0.7139 (m-30) cc_final: 0.6868 (m-30)
REVERT: A  342 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7722 (ptm160)
REVERT: A  361 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7957 (mmtt)
REVERT: A  364 ILE cc_start: 0.8825 (tp) cc_final: 0.7835 (tt)
REVERT: A  371 ARG cc_start: 0.8414 (ttp80) cc_final: 0.7982 (ptm-80)
REVERT: A  374 ASP cc_start: 0.8466 (t0) cc_final: 0.8204 (t0)
REVERT: A  392 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7561 (tm-30)
REVERT: A  423 GLN cc_start: 0.8422 (tm-30) cc_final: 0.7855 (tm-30)
REVERT: A  480 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7314 (mt-10)
REVERT: A  568 HIS cc_start: 0.7248 (m90) cc_final: 0.6767 (m90)
REVERT: A  592 LYS cc_start: 0.8538 (tppt) cc_final: 0.8154 (tptt)
REVERT: A  594 MET cc_start: 0.8397 (mmm) cc_final: 0.7730 (mmm)
REVERT: A  632 ARG cc_start: 0.7809 (ptt90) cc_final: 0.7560 (ptt90)
REVERT: A  633 MET cc_start: 0.6873 (tmm) cc_final: 0.5996 (tmm)
REVERT: A  663 MET cc_start: 0.7823 (mtm) cc_final: 0.7374 (mtm)
REVERT: A  690 TYR cc_start: 0.8278 (t80) cc_final: 0.7983 (t80)
REVERT: A  691 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8030 (mmtm)
REVERT: A  716 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.7721 (m)
REVERT: A  734 ARG cc_start: 0.7992 (ttm110) cc_final: 0.7755 (ttm110)
REVERT: A  801 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7879 (mmmt)
REVERT: A  846 GLU cc_start: 0.7243 (tt0) cc_final: 0.6991 (tt0)
REVERT: A  861 MET cc_start: 0.7621 (tpt) cc_final: 0.7267 (tpt)
REVERT: A  962 SER cc_start: 0.8413 (t) cc_final: 0.8020 (p)
REVERT: A  993 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7800 (tt)
REVERT: A 1042 ARG cc_start: 0.7626 (ttp80) cc_final: 0.7314 (ttp80)
REVERT: A 1050 PHE cc_start: 0.7660 (m-80) cc_final: 0.7396 (m-10)
REVERT: A 1060 LEU cc_start: 0.7409 (tp) cc_final: 0.7065 (tp)
REVERT: A 1090 LEU cc_start: 0.8176 (mm) cc_final: 0.7776 (mp)
REVERT: A 1106 MET cc_start: 0.8266 (tmm) cc_final: 0.7978 (tmm)
REVERT: A 1111 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7225 (tm-30)
REVERT: A 1112 MET cc_start: 0.7155 (tpp) cc_final: 0.6802 (tpp)
REVERT: A 1126 GLU cc_start: 0.7569 (pt0) cc_final: 0.7224 (pt0)
REVERT: A 1170 LYS cc_start: 0.8733 (tttt) cc_final: 0.8481 (tttt)
REVERT: A 1192 GLN cc_start: 0.8060 (tp40) cc_final: 0.7492 (tp40)
  outliers start: 34
  outliers final: 17
  residues processed: 282
  average time/residue: 0.1104
  time to fit residues: 41.3942
Evaluate side-chains
  275 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 253
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 HIS
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  342 ARG
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  625 HIS
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  852 LEU
Chi-restraints excluded: chain A residue  993 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
Chi-restraints excluded: chain A residue 1183 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0000
   chunk 109 optimal weight:    6.9990
   overall best weight:    1.9992

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

Flipped N/Q/H residues before XYZ refinement:
A 119 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.139828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.117833 restraints weight = 15915.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.121871 restraints weight = 8358.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.124586 restraints weight = 5192.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.126490 restraints weight = 3640.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.127783 restraints weight = 2790.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8777  Z= 0.221
  Angle     :  0.680  12.459  11925  Z= 0.349
  Chirality :  0.045   0.197   1398
  Planarity :  0.005   0.056   1511
  Dihedral  :  4.611  21.736   1185
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.40 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 15.95 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.25), residues: 1083
  helix:  1.13 (0.22), residues: 515
  sheet:  0.51 (0.40), residues: 157
  loop : -0.38 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 623 
 TYR   0.023   0.002   TYR A  75 
 PHE   0.023   0.002   PHE A 200 
 TRP   0.010   0.002   TRP A 257 
 HIS   0.028   0.002   HIS A 625 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 8777)
  covalent geometry    : angle       0.67995 (11925)
  hydrogen bonds       : bond        0.04916 (  479)
  hydrogen bonds       : angle       5.02473 ( 1398)

*********************** 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
  314 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 278
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TRP cc_start: 0.6806 (t60) cc_final: 0.6598 (t60)
REVERT: A  143 LYS cc_start: 0.8260 (pptt) cc_final: 0.7776 (pptt)
REVERT: A  144 VAL cc_start: 0.8245 (t) cc_final: 0.7925 (p)
REVERT: A  154 GLU cc_start: 0.7562 (tt0) cc_final: 0.7282 (tt0)
REVERT: A  176 LYS cc_start: 0.8719 (mtmm) cc_final: 0.8284 (mttm)
REVERT: A  182 ASP cc_start: 0.7360 (t0) cc_final: 0.7072 (t0)
REVERT: A  200 PHE cc_start: 0.6329 (t80) cc_final: 0.5689 (t80)
REVERT: A  214 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6623 (mt-10)
REVERT: A  215 ILE cc_start: 0.8724 (mm) cc_final: 0.8405 (mm)
REVERT: A  229 MET cc_start: 0.5470 (tpt) cc_final: 0.4070 (tpt)
REVERT: A  240 GLU cc_start: 0.7593 (tp30) cc_final: 0.7123 (tp30)
REVERT: A  316 GLU cc_start: 0.7696 (mp0) cc_final: 0.7174 (mp0)
REVERT: A  337 ASP cc_start: 0.7170 (m-30) cc_final: 0.6918 (m-30)
REVERT: A  342 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7817 (ptm160)
REVERT: A  361 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8050 (mmtt)
REVERT: A  362 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7188 (mt-10)
REVERT: A  364 ILE cc_start: 0.8897 (tp) cc_final: 0.8334 (tt)
REVERT: A  371 ARG cc_start: 0.8378 (ttp80) cc_final: 0.8141 (ttp80)
REVERT: A  374 ASP cc_start: 0.8571 (t0) cc_final: 0.8340 (t0)
REVERT: A  392 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7561 (tm-30)
REVERT: A  423 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8044 (tm-30)
REVERT: A  480 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7367 (mt-10)
REVERT: A  526 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7993 (ttmt)
REVERT: A  568 HIS cc_start: 0.7357 (m90) cc_final: 0.6872 (m90)
REVERT: A  571 LEU cc_start: 0.8236 (mt) cc_final: 0.7855 (tp)
REVERT: A  592 LYS cc_start: 0.8526 (tppt) cc_final: 0.8021 (tppt)
REVERT: A  632 ARG cc_start: 0.7943 (ptt90) cc_final: 0.7678 (ptt90)
REVERT: A  633 MET cc_start: 0.6945 (tmm) cc_final: 0.5912 (tmm)
REVERT: A  654 LYS cc_start: 0.7143 (ptmm) cc_final: 0.6749 (ptmm)
REVERT: A  663 MET cc_start: 0.7909 (mtm) cc_final: 0.7482 (mtm)
REVERT: A  690 TYR cc_start: 0.8355 (t80) cc_final: 0.7962 (t80)
REVERT: A  691 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.8008 (mmtp)
REVERT: A  734 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7828 (ttm110)
REVERT: A  801 LYS cc_start: 0.8331 (mmmt) cc_final: 0.7891 (mmmt)
REVERT: A  846 GLU cc_start: 0.7314 (tt0) cc_final: 0.7055 (tt0)
REVERT: A  854 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7779 (tt0)
REVERT: A  861 MET cc_start: 0.7588 (tpt) cc_final: 0.7252 (tpt)
REVERT: A  869 VAL cc_start: 0.7018 (OUTLIER) cc_final: 0.6706 (m)
REVERT: A  962 SER cc_start: 0.8345 (t) cc_final: 0.7967 (p)
REVERT: A  993 LEU cc_start: 0.8111 (tp) cc_final: 0.7861 (tt)
REVERT: A 1042 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7236 (ttp80)
REVERT: A 1050 PHE cc_start: 0.7733 (m-80) cc_final: 0.7381 (m-10)
REVERT: A 1060 LEU cc_start: 0.7432 (tp) cc_final: 0.7089 (tp)
REVERT: A 1090 LEU cc_start: 0.8294 (mm) cc_final: 0.7891 (mp)
REVERT: A 1106 MET cc_start: 0.8331 (tmm) cc_final: 0.7799 (tmm)
REVERT: A 1111 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7160 (tm-30)
REVERT: A 1112 MET cc_start: 0.7078 (tpp) cc_final: 0.6739 (tpp)
REVERT: A 1126 GLU cc_start: 0.7633 (pt0) cc_final: 0.7303 (pt0)
REVERT: A 1170 LYS cc_start: 0.8728 (tttt) cc_final: 0.8329 (tttt)
REVERT: A 1192 GLN cc_start: 0.8125 (tp40) cc_final: 0.7613 (tp40)
  outliers start: 36
  outliers final: 20
  residues processed: 291
  average time/residue: 0.1026
  time to fit residues: 40.0004
Evaluate side-chains
  291 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 266
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 CYS
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  123 HIS
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  342 ARG
Chi-restraints excluded: chain A residue  365 GLU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  526 LYS
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  691 LYS
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  854 GLU
Chi-restraints excluded: chain A residue  869 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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**
** 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 = 0.3908 r_free = 0.3908 target = 0.141897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.120042 restraints weight = 15781.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.124157 restraints weight = 8289.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.126921 restraints weight = 5138.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.128711 restraints weight = 3594.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.130113 restraints weight = 2772.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.3731

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= 0.130
  Angle     :  0.621  15.379  11925  Z= 0.311
  Chirality :  0.042   0.181   1398
  Planarity :  0.005   0.056   1511
  Dihedral  :  4.412  20.358   1185
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.85 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.89 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.25), residues: 1083
  helix:  1.33 (0.23), residues: 517
  sheet:  0.33 (0.40), residues: 156
  loop : -0.31 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 839 
 TYR   0.014   0.002   TYR A 807 
 PHE   0.028   0.001   PHE A 252 
 TRP   0.009   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8777)
  covalent geometry    : angle       0.62142 (11925)
  hydrogen bonds       : bond        0.04234 (  479)
  hydrogen bonds       : angle       4.78080 ( 1398)

*********************** 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
  302 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 267
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 ASP cc_start: 0.7906 (t70) cc_final: 0.7349 (p0)
REVERT: A  143 LYS cc_start: 0.8184 (pptt) cc_final: 0.7736 (pptt)
REVERT: A  144 VAL cc_start: 0.8240 (t) cc_final: 0.7925 (p)
REVERT: A  154 GLU cc_start: 0.7566 (tt0) cc_final: 0.7321 (tt0)
REVERT: A  176 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8177 (mmtp)
REVERT: A  182 ASP cc_start: 0.7269 (t0) cc_final: 0.7034 (t0)
REVERT: A  200 PHE cc_start: 0.6194 (t80) cc_final: 0.5735 (t80)
REVERT: A  214 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6623 (mt-10)
REVERT: A  215 ILE cc_start: 0.8709 (mm) cc_final: 0.8402 (mm)
REVERT: A  229 MET cc_start: 0.5494 (tpt) cc_final: 0.4055 (tpt)
REVERT: A  288 MET cc_start: 0.7124 (tpt) cc_final: 0.6822 (tpt)
REVERT: A  316 GLU cc_start: 0.7767 (mp0) cc_final: 0.7316 (mp0)
REVERT: A  337 ASP cc_start: 0.7197 (m-30) cc_final: 0.6934 (m-30)
REVERT: A  342 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7848 (ptm160)
REVERT: A  362 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7225 (mt-10)
REVERT: A  364 ILE cc_start: 0.8888 (tp) cc_final: 0.8277 (tt)
REVERT: A  374 ASP cc_start: 0.8565 (t0) cc_final: 0.8361 (t0)
REVERT: A  392 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7408 (tm-30)
REVERT: A  423 GLN cc_start: 0.8461 (tm-30) cc_final: 0.7854 (tm-30)
REVERT: A  478 PHE cc_start: 0.7973 (t80) cc_final: 0.7756 (t80)
REVERT: A  480 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7384 (mt-10)
REVERT: A  485 LEU cc_start: 0.8508 (tp) cc_final: 0.8089 (tt)
REVERT: A  526 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7775 (ttpt)
REVERT: A  568 HIS cc_start: 0.7340 (m90) cc_final: 0.6844 (m90)
REVERT: A  592 LYS cc_start: 0.8435 (tppt) cc_final: 0.8075 (tptt)
REVERT: A  633 MET cc_start: 0.6951 (tmm) cc_final: 0.6057 (tmm)
REVERT: A  654 LYS cc_start: 0.7068 (ptmm) cc_final: 0.6737 (ptmm)
REVERT: A  658 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7861 (mm-30)
REVERT: A  663 MET cc_start: 0.7919 (mtm) cc_final: 0.7493 (mtm)
REVERT: A  690 TYR cc_start: 0.8283 (t80) cc_final: 0.8047 (t80)
REVERT: A  734 ARG cc_start: 0.8072 (ttm110) cc_final: 0.7853 (ttm110)
REVERT: A  745 MET cc_start: 0.6929 (ttt) cc_final: 0.6629 (ttt)
REVERT: A  760 GLU cc_start: 0.8200 (tp30) cc_final: 0.7950 (tp30)
REVERT: A  801 LYS cc_start: 0.8256 (mmmt) cc_final: 0.7832 (mmmt)
REVERT: A  846 GLU cc_start: 0.7163 (tt0) cc_final: 0.6895 (tt0)
REVERT: A  854 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7743 (tt0)
REVERT: A  861 MET cc_start: 0.7549 (tpt) cc_final: 0.7197 (tpt)
REVERT: A  962 SER cc_start: 0.8276 (t) cc_final: 0.7918 (p)
REVERT: A  993 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7800 (tt)
REVERT: A 1042 ARG cc_start: 0.7636 (ttp80) cc_final: 0.7251 (ttp80)
REVERT: A 1050 PHE cc_start: 0.7650 (m-80) cc_final: 0.7262 (m-10)
REVERT: A 1106 MET cc_start: 0.8343 (tmm) cc_final: 0.7774 (tmm)
REVERT: A 1111 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7023 (tm-30)
REVERT: A 1112 MET cc_start: 0.7069 (tpp) cc_final: 0.6732 (tpp)
REVERT: A 1126 GLU cc_start: 0.7615 (pt0) cc_final: 0.7233 (pt0)
REVERT: A 1170 LYS cc_start: 0.8729 (tttt) cc_final: 0.8065 (tttt)
REVERT: A 1192 GLN cc_start: 0.8065 (tp40) cc_final: 0.7526 (tp40)
  outliers start: 35
  outliers final: 25
  residues processed: 280
  average time/residue: 0.1040
  time to fit residues: 38.6000
Evaluate side-chains
  281 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 253
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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  280 LEU
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  342 ARG
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  526 LYS
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  591 GLU
Chi-restraints excluded: chain A residue  702 ARG
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  806 GLU
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue  993 LEU
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 1137 SER
Chi-restraints excluded: chain A residue 1168 GLU
Chi-restraints excluded: chain A residue 1183 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   chunk 0 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0170
   chunk 83 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    0.6420

-------------------------------------------------------------------------------
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 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.142473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.120786 restraints weight = 15729.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.124846 restraints weight = 8278.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.127604 restraints weight = 5142.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.129491 restraints weight = 3584.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.130811 restraints weight = 2740.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7187
moved from start:          0.3900

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= 0.119
  Angle     :  0.613  15.046  11925  Z= 0.302
  Chirality :  0.042   0.174   1398
  Planarity :  0.005   0.055   1511
  Dihedral  :  4.270  19.469   1185
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.03 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 18.75 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.25), residues: 1083
  helix:  1.49 (0.23), residues: 515
  sheet:  0.26 (0.39), residues: 156
  loop : -0.25 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1044 
 TYR   0.013   0.001   TYR A 807 
 PHE   0.025   0.001   PHE A 252 
 TRP   0.010   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A 756 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8777)
  covalent geometry    : angle       0.61252 (11925)
  hydrogen bonds       : bond        0.03959 (  479)
  hydrogen bonds       : angle       4.66366 ( 1398)

*********************** 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
  302 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 268
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 ASP cc_start: 0.7912 (t70) cc_final: 0.7452 (p0)
REVERT: A  143 LYS cc_start: 0.8178 (pptt) cc_final: 0.7736 (pptt)
REVERT: A  144 VAL cc_start: 0.8241 (t) cc_final: 0.7928 (p)
REVERT: A  154 GLU cc_start: 0.7561 (tt0) cc_final: 0.7310 (tt0)
REVERT: A  176 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8136 (mmtp)
REVERT: A  215 ILE cc_start: 0.8719 (mm) cc_final: 0.8275 (mm)
REVERT: A  229 MET cc_start: 0.5463 (tpt) cc_final: 0.3994 (tpt)
REVERT: A  316 GLU cc_start: 0.7772 (mp0) cc_final: 0.7245 (mp0)
REVERT: A  337 ASP cc_start: 0.7095 (m-30) cc_final: 0.6830 (m-30)
REVERT: A  342 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7743 (ptm160)
REVERT: A  349 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7600 (mt-10)
REVERT: A  362 GLU cc_start: 0.7614 (mt-10) cc_final: 0.6997 (mm-30)
REVERT: A  364 ILE cc_start: 0.8909 (tp) cc_final: 0.8490 (tp)
REVERT: A  371 ARG cc_start: 0.8419 (ttp80) cc_final: 0.8001 (ttp80)
REVERT: A  392 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7424 (tm-30)
REVERT: A  423 GLN cc_start: 0.8442 (tm-30) cc_final: 0.7847 (tm-30)
REVERT: A  478 PHE cc_start: 0.7949 (t80) cc_final: 0.7744 (t80)
REVERT: A  480 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7362 (mt-10)
REVERT: A  485 LEU cc_start: 0.8464 (tp) cc_final: 0.8022 (tt)
REVERT: A  568 HIS cc_start: 0.7392 (m90) cc_final: 0.6916 (m90)
REVERT: A  592 LYS cc_start: 0.8444 (tppt) cc_final: 0.7908 (tptm)
REVERT: A  633 MET cc_start: 0.7034 (tmm) cc_final: 0.6034 (tmm)
REVERT: A  654 LYS cc_start: 0.7104 (ptmm) cc_final: 0.6703 (ptmm)
REVERT: A  663 MET cc_start: 0.7926 (mtm) cc_final: 0.7452 (mtm)
REVERT: A  734 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7769 (ttm110)
REVERT: A  745 MET cc_start: 0.6978 (ttt) cc_final: 0.6593 (ttt)
REVERT: A  760 GLU cc_start: 0.8204 (tp30) cc_final: 0.7979 (tp30)
REVERT: A  801 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7768 (mmmt)
REVERT: A  853 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8380 (ttmm)
REVERT: A  854 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7757 (tt0)
REVERT: A  861 MET cc_start: 0.7595 (tpt) cc_final: 0.7285 (tpt)
REVERT: A  873 LYS cc_start: 0.8076 (tppp) cc_final: 0.7457 (ttmm)
REVERT: A  874 HIS cc_start: 0.7127 (m-70) cc_final: 0.6911 (m90)
REVERT: A  962 SER cc_start: 0.8295 (t) cc_final: 0.7905 (p)
REVERT: A  993 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7783 (tt)
REVERT: A 1042 ARG cc_start: 0.7591 (ttp80) cc_final: 0.7218 (ttp80)
REVERT: A 1106 MET cc_start: 0.8289 (tmm) cc_final: 0.7600 (tmm)
REVERT: A 1111 GLN cc_start: 0.7920 (tm-30) cc_final: 0.6984 (tm-30)
REVERT: A 1112 MET cc_start: 0.7080 (tpp) cc_final: 0.6727 (tpp)
REVERT: A 1125 MET cc_start: 0.7436 (mtt) cc_final: 0.6906 (mmt)
REVERT: A 1126 GLU cc_start: 0.7664 (pt0) cc_final: 0.7326 (pt0)
REVERT: A 1192 GLN cc_start: 0.8069 (tp40) cc_final: 0.7509 (tp40)
  outliers start: 34
  outliers final: 23
  residues processed: 280
  average time/residue: 0.1024
  time to fit residues: 38.2293
Evaluate side-chains
  285 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 260
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
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  280 LEU
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  342 ARG
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  591 GLU
Chi-restraints excluded: chain A residue  702 ARG
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  787 ILE
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  993 LEU
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 1137 SER
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 22 optimal weight:    5.9990
   chunk 109 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   chunk 26 optimal weight:    7.9990
   chunk 94 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 393 HIS
A 625 HIS
** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 867 ASN
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.136024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.113710 restraints weight = 16003.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.117781 restraints weight = 8604.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.120527 restraints weight = 5409.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.122406 restraints weight = 3807.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.123614 restraints weight = 2925.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.4450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8777  Z= 0.272
  Angle     :  0.741  17.517  11925  Z= 0.372
  Chirality :  0.047   0.216   1398
  Planarity :  0.005   0.077   1511
  Dihedral  :  4.671  22.671   1185
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.15 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.25), residues: 1083
  helix:  1.06 (0.22), residues: 513
  sheet: -0.01 (0.37), residues: 162
  loop : -0.37 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 310 
 TYR   0.020   0.002   TYR A 304 
 PHE   0.037   0.002   PHE A 200 
 TRP   0.011   0.002   TRP A 600 
 HIS   0.006   0.001   HIS A 972 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 ( 8777)
  covalent geometry    : angle       0.74074 (11925)
  hydrogen bonds       : bond        0.05115 (  479)
  hydrogen bonds       : angle       5.02743 ( 1398)

*********************** 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
  305 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 268
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 LYS cc_start: 0.8230 (pptt) cc_final: 0.7731 (pptt)
REVERT: A  144 VAL cc_start: 0.8254 (t) cc_final: 0.8032 (m)
REVERT: A  215 ILE cc_start: 0.8594 (mm) cc_final: 0.8221 (mm)
REVERT: A  229 MET cc_start: 0.5967 (OUTLIER) cc_final: 0.4625 (tpt)
REVERT: A  308 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7721 (ttpt)
REVERT: A  316 GLU cc_start: 0.7894 (mp0) cc_final: 0.7430 (mp0)
REVERT: A  338 VAL cc_start: 0.8034 (OUTLIER) cc_final: 0.7556 (m)
REVERT: A  342 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7721 (ptm160)
REVERT: A  349 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7684 (mt-10)
REVERT: A  362 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7316 (mm-30)
REVERT: A  364 ILE cc_start: 0.8952 (tp) cc_final: 0.8619 (tp)
REVERT: A  371 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7831 (ttp80)
REVERT: A  392 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7374 (tm-30)
REVERT: A  423 GLN cc_start: 0.8622 (tm-30) cc_final: 0.7913 (tm-30)
REVERT: A  478 PHE cc_start: 0.8032 (t80) cc_final: 0.7793 (t80)
REVERT: A  480 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7360 (mt-10)
REVERT: A  568 HIS cc_start: 0.7442 (m90) cc_final: 0.6983 (m90)
REVERT: A  623 ARG cc_start: 0.6949 (mtp85) cc_final: 0.6737 (mtm180)
REVERT: A  633 MET cc_start: 0.7092 (tmm) cc_final: 0.6080 (tmm)
REVERT: A  654 LYS cc_start: 0.7274 (ptmm) cc_final: 0.6926 (ptmm)
REVERT: A  658 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8053 (mm-30)
REVERT: A  663 MET cc_start: 0.7940 (mtm) cc_final: 0.7495 (mtm)
REVERT: A  676 THR cc_start: 0.8287 (m) cc_final: 0.7881 (t)
REVERT: A  686 LEU cc_start: 0.8073 (mt) cc_final: 0.7797 (mt)
REVERT: A  734 ARG cc_start: 0.8069 (ttm110) cc_final: 0.7794 (ttm110)
REVERT: A  745 MET cc_start: 0.6922 (ttt) cc_final: 0.6716 (ttt)
REVERT: A  801 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7855 (mmmt)
REVERT: A  854 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7751 (tt0)
REVERT: A  861 MET cc_start: 0.7377 (tpt) cc_final: 0.7096 (tpt)
REVERT: A  950 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7805 (ttpp)
REVERT: A  962 SER cc_start: 0.8320 (t) cc_final: 0.7940 (p)
REVERT: A  970 ILE cc_start: 0.8520 (tp) cc_final: 0.8257 (tp)
REVERT: A  993 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7890 (tt)
REVERT: A 1035 LYS cc_start: 0.8236 (mttt) cc_final: 0.7493 (mmmm)
REVERT: A 1042 ARG cc_start: 0.7540 (ttp80) cc_final: 0.7313 (ttp80)
REVERT: A 1050 PHE cc_start: 0.7696 (m-80) cc_final: 0.7330 (m-10)
REVERT: A 1060 LEU cc_start: 0.7475 (tp) cc_final: 0.7142 (tp)
REVERT: A 1106 MET cc_start: 0.8291 (tmm) cc_final: 0.7602 (tmm)
REVERT: A 1111 GLN cc_start: 0.7933 (tm-30) cc_final: 0.6969 (tm-30)
REVERT: A 1112 MET cc_start: 0.6937 (tpp) cc_final: 0.6651 (tpp)
REVERT: A 1125 MET cc_start: 0.7663 (mtt) cc_final: 0.7173 (mmt)
REVERT: A 1126 GLU cc_start: 0.7649 (pt0) cc_final: 0.7137 (pt0)
REVERT: A 1192 GLN cc_start: 0.8196 (tp40) cc_final: 0.7625 (tp40)
  outliers start: 37
  outliers final: 25
  residues processed: 284
  average time/residue: 0.1038
  time to fit residues: 39.6684
Evaluate side-chains
  297 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 268
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  342 ARG
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain A residue  437 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  626 PHE
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  787 ILE
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  993 LEU
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 1072 LEU
Chi-restraints excluded: chain A residue 1137 SER
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 0 optimal weight:   10.0000
   chunk 99 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 737 GLN
A 759 GLN
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 874 HIS
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.139761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.117807 restraints weight = 15541.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.121874 restraints weight = 8284.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.124523 restraints weight = 5188.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.126377 restraints weight = 3662.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.127542 restraints weight = 2820.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.4505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8777  Z= 0.130
  Angle     :  0.677  17.652  11925  Z= 0.327
  Chirality :  0.043   0.191   1398
  Planarity :  0.005   0.066   1511
  Dihedral  :  4.464  21.188   1185
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.91 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.25), residues: 1083
  helix:  1.34 (0.23), residues: 512
  sheet:  0.03 (0.38), residues: 160
  loop : -0.38 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 310 
 TYR   0.014   0.002   TYR A 461 
 PHE   0.026   0.001   PHE A 200 
 TRP   0.010   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A 972 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8777)
  covalent geometry    : angle       0.67710 (11925)
  hydrogen bonds       : bond        0.04113 (  479)
  hydrogen bonds       : angle       4.76485 ( 1398)

*********************** 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
  304 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 267
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 VAL cc_start: 0.8214 (t) cc_final: 0.8006 (p)
REVERT: A  143 LYS cc_start: 0.8184 (pptt) cc_final: 0.7703 (pptt)
REVERT: A  176 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8336 (mttm)
REVERT: A  206 ASN cc_start: 0.6915 (p0) cc_final: 0.6475 (p0)
REVERT: A  215 ILE cc_start: 0.8584 (mm) cc_final: 0.8200 (mm)
REVERT: A  229 MET cc_start: 0.5959 (tpt) cc_final: 0.4640 (tpt)
REVERT: A  316 GLU cc_start: 0.7857 (mp0) cc_final: 0.7356 (mp0)
REVERT: A  342 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7791 (ptm160)
REVERT: A  349 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7512 (mt-10)
REVERT: A  361 LYS cc_start: 0.8488 (mmtt) cc_final: 0.7972 (mmmt)
REVERT: A  362 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7329 (mm-30)
REVERT: A  364 ILE cc_start: 0.8922 (tp) cc_final: 0.8662 (tp)
REVERT: A  374 ASP cc_start: 0.8583 (t0) cc_final: 0.8377 (t0)
REVERT: A  392 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7398 (tm-30)
REVERT: A  423 GLN cc_start: 0.8499 (tm-30) cc_final: 0.7665 (tm-30)
REVERT: A  465 GLU cc_start: 0.7844 (tp30) cc_final: 0.7315 (tp30)
REVERT: A  478 PHE cc_start: 0.7955 (t80) cc_final: 0.7747 (t80)
REVERT: A  480 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7361 (mt-10)
REVERT: A  485 LEU cc_start: 0.8484 (tp) cc_final: 0.8027 (tt)
REVERT: A  568 HIS cc_start: 0.7450 (m90) cc_final: 0.6988 (m90)
REVERT: A  592 LYS cc_start: 0.8403 (tppt) cc_final: 0.7958 (tppt)
REVERT: A  623 ARG cc_start: 0.6945 (mtp85) cc_final: 0.6740 (mtp85)
REVERT: A  625 HIS cc_start: 0.6772 (OUTLIER) cc_final: 0.6571 (m90)
REVERT: A  633 MET cc_start: 0.7117 (tmm) cc_final: 0.6138 (tmm)
REVERT: A  654 LYS cc_start: 0.7125 (ptmm) cc_final: 0.6722 (ptmm)
REVERT: A  658 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8003 (mm-30)
REVERT: A  663 MET cc_start: 0.7933 (mtm) cc_final: 0.7555 (mtm)
REVERT: A  671 TYR cc_start: 0.7349 (t80) cc_final: 0.7024 (t80)
REVERT: A  726 LYS cc_start: 0.6848 (ttmm) cc_final: 0.6537 (mtpp)
REVERT: A  734 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7757 (ttm110)
REVERT: A  745 MET cc_start: 0.7003 (ttt) cc_final: 0.6636 (ttt)
REVERT: A  854 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7732 (tt0)
REVERT: A  861 MET cc_start: 0.7492 (tpt) cc_final: 0.7255 (tpt)
REVERT: A  873 LYS cc_start: 0.8117 (tppp) cc_final: 0.7297 (ttmm)
REVERT: A  962 SER cc_start: 0.8291 (t) cc_final: 0.7881 (p)
REVERT: A  993 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7826 (tt)
REVERT: A 1042 ARG cc_start: 0.7568 (ttp80) cc_final: 0.7191 (ttp80)
REVERT: A 1106 MET cc_start: 0.8246 (tmm) cc_final: 0.7601 (tmm)
REVERT: A 1111 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7302 (tm-30)
REVERT: A 1125 MET cc_start: 0.7599 (mtt) cc_final: 0.7189 (mmt)
REVERT: A 1126 GLU cc_start: 0.7618 (pt0) cc_final: 0.7222 (pt0)
  outliers start: 37
  outliers final: 29
  residues processed: 284
  average time/residue: 0.1091
  time to fit residues: 40.9922
Evaluate side-chains
  292 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 260
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  342 ARG
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  426 LEU
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  625 HIS
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  787 ILE
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1001 SER
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 1072 LEU
Chi-restraints excluded: chain A residue 1128 LEU
Chi-restraints excluded: chain A residue 1137 SER
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 96 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 104 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 105 optimal weight:    5.9990
   chunk 108 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 106 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0030
   overall best weight:    0.9592

-------------------------------------------------------------------------------
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 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 874 HIS
** A 972 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.139002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.117246 restraints weight = 15621.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.121314 restraints weight = 8284.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.124041 restraints weight = 5158.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.125795 restraints weight = 3613.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.127148 restraints weight = 2789.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.4615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8777  Z= 0.141
  Angle     :  0.683  16.907  11925  Z= 0.330
  Chirality :  0.044   0.196   1398
  Planarity :  0.005   0.063   1511
  Dihedral  :  4.400  20.642   1185
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 22.20 %
    Favored  : 74.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.25), residues: 1083
  helix:  1.33 (0.23), residues: 511
  sheet:  0.04 (0.38), residues: 161
  loop : -0.40 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 310 
 TYR   0.013   0.001   TYR A 671 
 PHE   0.027   0.001   PHE A 200 
 TRP   0.008   0.001   TRP A  78 
 HIS   0.007   0.001   HIS A 625 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8777)
  covalent geometry    : angle       0.68331 (11925)
  hydrogen bonds       : bond        0.04142 (  479)
  hydrogen bonds       : angle       4.75303 ( 1398)

*********************** 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
  301 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 268
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 LYS cc_start: 0.8151 (pptt) cc_final: 0.7693 (pptt)
REVERT: A  176 LYS cc_start: 0.8692 (mtmm) cc_final: 0.8329 (mttm)
REVERT: A  206 ASN cc_start: 0.6933 (p0) cc_final: 0.6486 (p0)
REVERT: A  215 ILE cc_start: 0.8590 (mm) cc_final: 0.8207 (mm)
REVERT: A  229 MET cc_start: 0.6019 (tpt) cc_final: 0.4741 (tpt)
REVERT: A  288 MET cc_start: 0.7156 (tpt) cc_final: 0.6706 (tpt)
REVERT: A  316 GLU cc_start: 0.7866 (mp0) cc_final: 0.7357 (mp0)
REVERT: A  342 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7825 (ptm160)
REVERT: A  349 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7544 (mt-10)
REVERT: A  361 LYS cc_start: 0.8492 (mmtt) cc_final: 0.7957 (mmmt)
REVERT: A  362 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7509 (mm-30)
REVERT: A  364 ILE cc_start: 0.8939 (tp) cc_final: 0.8718 (tp)
REVERT: A  371 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7836 (ttp80)
REVERT: A  374 ASP cc_start: 0.8583 (t0) cc_final: 0.8355 (t0)
REVERT: A  392 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7428 (tm-30)
REVERT: A  423 GLN cc_start: 0.8537 (tm-30) cc_final: 0.7698 (tm-30)
REVERT: A  465 GLU cc_start: 0.7852 (tp30) cc_final: 0.7322 (tp30)
REVERT: A  478 PHE cc_start: 0.7960 (t80) cc_final: 0.7749 (t80)
REVERT: A  480 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7374 (mt-10)
REVERT: A  485 LEU cc_start: 0.8532 (tp) cc_final: 0.8106 (tt)
REVERT: A  568 HIS cc_start: 0.7483 (m90) cc_final: 0.7087 (m-70)
REVERT: A  571 LEU cc_start: 0.8326 (tp) cc_final: 0.8103 (tp)
REVERT: A  591 GLU cc_start: 0.8085 (tp30) cc_final: 0.7790 (tp30)
REVERT: A  592 LYS cc_start: 0.8414 (tppt) cc_final: 0.7962 (tppt)
REVERT: A  623 ARG cc_start: 0.7005 (mtp85) cc_final: 0.6698 (mtp85)
REVERT: A  625 HIS cc_start: 0.6827 (OUTLIER) cc_final: 0.6374 (m90)
REVERT: A  633 MET cc_start: 0.7118 (tmm) cc_final: 0.6131 (tmm)
REVERT: A  654 LYS cc_start: 0.7172 (ptmm) cc_final: 0.6749 (ptmm)
REVERT: A  658 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8003 (mm-30)
REVERT: A  663 MET cc_start: 0.7926 (mtm) cc_final: 0.7557 (mtm)
REVERT: A  671 TYR cc_start: 0.7358 (t80) cc_final: 0.7046 (t80)
REVERT: A  686 LEU cc_start: 0.8031 (mt) cc_final: 0.7764 (mt)
REVERT: A  726 LYS cc_start: 0.6828 (ttmm) cc_final: 0.6148 (ttmm)
REVERT: A  734 ARG cc_start: 0.8070 (ttm110) cc_final: 0.7784 (ttm110)
REVERT: A  745 MET cc_start: 0.6965 (ttt) cc_final: 0.6738 (ttt)
REVERT: A  823 ASP cc_start: 0.7987 (t0) cc_final: 0.7462 (t0)
REVERT: A  854 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7737 (tt0)
REVERT: A  861 MET cc_start: 0.7528 (tpt) cc_final: 0.7283 (tpt)
REVERT: A  873 LYS cc_start: 0.8105 (tppp) cc_final: 0.7381 (ttmm)
REVERT: A  950 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7955 (tmtt)
REVERT: A  962 SER cc_start: 0.8273 (t) cc_final: 0.7879 (p)
REVERT: A  993 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7843 (tt)
REVERT: A 1042 ARG cc_start: 0.7526 (ttp80) cc_final: 0.7304 (ttp80)
REVERT: A 1106 MET cc_start: 0.8236 (tmm) cc_final: 0.7630 (tmm)
REVERT: A 1111 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7408 (tm-30)
REVERT: A 1125 MET cc_start: 0.7680 (mtt) cc_final: 0.7240 (mmt)
REVERT: A 1126 GLU cc_start: 0.7656 (pt0) cc_final: 0.7275 (pt0)
REVERT: A 1170 LYS cc_start: 0.8708 (tttt) cc_final: 0.8022 (tttt)
  outliers start: 33
  outliers final: 28
  residues processed: 282
  average time/residue: 0.1085
  time to fit residues: 40.6892
Evaluate side-chains
  292 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 261
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
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  280 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  342 ARG
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  426 LEU
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  625 HIS
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  787 ILE
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1001 SER
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 1128 LEU
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 27 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0040
   chunk 85 optimal weight:    0.5980
   chunk 63 optimal weight:    8.9990
   chunk 44 optimal weight:    0.4980
   chunk 103 optimal weight:    9.9990
   chunk 18 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0030
   overall best weight:    0.3602

-------------------------------------------------------------------------------
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 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 874 HIS
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.141096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.119386 restraints weight = 15685.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.123503 restraints weight = 8317.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.126205 restraints weight = 5173.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.128108 restraints weight = 3622.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.129287 restraints weight = 2763.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.4663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8777  Z= 0.118
  Angle     :  0.688  17.353  11925  Z= 0.327
  Chirality :  0.043   0.173   1398
  Planarity :  0.005   0.063   1511
  Dihedral  :  4.301  18.440   1185
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.94 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 22.84 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.25), residues: 1083
  helix:  1.39 (0.23), residues: 513
  sheet: -0.04 (0.38), residues: 162
  loop : -0.46 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 310 
 TYR   0.015   0.001   TYR A 857 
 PHE   0.020   0.001   PHE A 200 
 TRP   0.012   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A 625 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8777)
  covalent geometry    : angle       0.68815 (11925)
  hydrogen bonds       : bond        0.03836 (  479)
  hydrogen bonds       : angle       4.65509 ( 1398)

********************** 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
  296 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 264
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 SER cc_start: 0.7861 (t) cc_final: 0.7634 (t)
REVERT: A  143 LYS cc_start: 0.8125 (pptt) cc_final: 0.7748 (pptt)
REVERT: A  144 VAL cc_start: 0.8215 (m) cc_final: 0.7892 (p)
REVERT: A  176 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8260 (mmtp)
REVERT: A  206 ASN cc_start: 0.6796 (p0) cc_final: 0.6325 (p0)
REVERT: A  229 MET cc_start: 0.5918 (tpt) cc_final: 0.4545 (tpt)
REVERT: A  252 PHE cc_start: 0.7803 (t80) cc_final: 0.7511 (t80)
REVERT: A  277 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7571 (mm-30)
REVERT: A  288 MET cc_start: 0.7145 (tpt) cc_final: 0.6642 (tpt)
REVERT: A  316 GLU cc_start: 0.7823 (mp0) cc_final: 0.7343 (mp0)
REVERT: A  349 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7463 (mt-10)
REVERT: A  361 LYS cc_start: 0.8451 (mmtt) cc_final: 0.7868 (mmmt)
REVERT: A  362 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7365 (mm-30)
REVERT: A  364 ILE cc_start: 0.8951 (tp) cc_final: 0.8681 (tp)
REVERT: A  392 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7450 (tm-30)
REVERT: A  423 GLN cc_start: 0.8447 (tm-30) cc_final: 0.7617 (tm-30)
REVERT: A  427 LEU cc_start: 0.8321 (tt) cc_final: 0.8095 (tp)
REVERT: A  465 GLU cc_start: 0.7848 (tp30) cc_final: 0.7294 (tp30)
REVERT: A  478 PHE cc_start: 0.7926 (t80) cc_final: 0.7722 (t80)
REVERT: A  480 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7386 (mt-10)
REVERT: A  568 HIS cc_start: 0.7515 (m90) cc_final: 0.7130 (m-70)
REVERT: A  591 GLU cc_start: 0.8049 (tp30) cc_final: 0.7749 (tp30)
REVERT: A  592 LYS cc_start: 0.8370 (tppt) cc_final: 0.7920 (tppt)
REVERT: A  625 HIS cc_start: 0.6649 (m90) cc_final: 0.6368 (m90)
REVERT: A  633 MET cc_start: 0.7105 (tmm) cc_final: 0.6197 (tmm)
REVERT: A  654 LYS cc_start: 0.7116 (ptmm) cc_final: 0.6716 (ptmm)
REVERT: A  658 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7978 (mm-30)
REVERT: A  663 MET cc_start: 0.7866 (mtm) cc_final: 0.7555 (mtm)
REVERT: A  671 TYR cc_start: 0.7343 (t80) cc_final: 0.7042 (t80)
REVERT: A  690 TYR cc_start: 0.8243 (t80) cc_final: 0.7903 (t80)
REVERT: A  734 ARG cc_start: 0.8070 (ttm110) cc_final: 0.7779 (ttm110)
REVERT: A  745 MET cc_start: 0.6988 (ttt) cc_final: 0.6748 (ttt)
REVERT: A  760 GLU cc_start: 0.8189 (tp30) cc_final: 0.7906 (tp30)
REVERT: A  823 ASP cc_start: 0.7953 (t0) cc_final: 0.7471 (t0)
REVERT: A  854 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7754 (tt0)
REVERT: A  861 MET cc_start: 0.7545 (tpt) cc_final: 0.7311 (tpt)
REVERT: A  873 LYS cc_start: 0.8013 (tppp) cc_final: 0.6919 (mtpp)
REVERT: A  962 SER cc_start: 0.8233 (t) cc_final: 0.7845 (p)
REVERT: A  993 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7863 (tt)
REVERT: A 1042 ARG cc_start: 0.7522 (ttp80) cc_final: 0.7143 (ttp80)
REVERT: A 1044 ARG cc_start: 0.8474 (mtp85) cc_final: 0.8175 (ttm-80)
REVERT: A 1111 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7234 (tm-30)
REVERT: A 1125 MET cc_start: 0.7563 (mtt) cc_final: 0.7123 (mmt)
REVERT: A 1126 GLU cc_start: 0.7659 (pt0) cc_final: 0.7287 (pt0)
  outliers start: 32
  outliers final: 25
  residues processed: 277
  average time/residue: 0.1100
  time to fit residues: 40.5315
Evaluate side-chains
  287 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 261
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
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  280 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  437 VAL
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  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  787 ILE
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  993 LEU
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 1128 LEU
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 73 optimal weight:    0.0670
   chunk 91 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 60 optimal weight:   10.0000
   chunk 105 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.7318

-------------------------------------------------------------------------------
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**
** 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 = 0.3886 r_free = 0.3886 target = 0.140250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.118327 restraints weight = 15739.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.122384 restraints weight = 8353.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.125114 restraints weight = 5233.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.126921 restraints weight = 3678.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.128318 restraints weight = 2834.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.4795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8777  Z= 0.130
  Angle     :  0.695  16.906  11925  Z= 0.331
  Chirality :  0.044   0.207   1398
  Planarity :  0.005   0.062   1511
  Dihedral  :  4.228  17.200   1185
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.40 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 23.81 %
    Favored  : 72.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.25), residues: 1083
  helix:  1.48 (0.23), residues: 504
  sheet: -0.02 (0.39), residues: 152
  loop : -0.49 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 310 
 TYR   0.012   0.001   TYR A 857 
 PHE   0.018   0.001   PHE A 252 
 TRP   0.012   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8777)
  covalent geometry    : angle       0.69514 (11925)
  hydrogen bonds       : bond        0.03877 (  479)
  hydrogen bonds       : angle       4.66605 ( 1398)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1615.33 seconds
wall clock time: 28 minutes 36.68 seconds (1716.68 seconds total)