Starting phenix.real_space_refine
on Thu Jun 12 15:12:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ror_19402/06_2025/8ror_19402.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ror_19402/06_2025/8ror_19402.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ror_19402/06_2025/8ror_19402.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ror_19402/06_2025/8ror_19402.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ror_19402/06_2025/8ror_19402.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ror_19402/06_2025/8ror_19402.cif"
  }
  resolution = 2.39
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      27      5.16       5
     C    8782      2.51       5
     N    2400      2.21       5
     O    2996      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14205
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "1"
      Number of atoms: 10563
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1349, 10472
          Classifications: {'peptide': 1349}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 2, 'PTRANS': 88, 'TRANS': 1258}
          Chain breaks: 13
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
      Conformer: "B"
        Number of residues, atoms: 1349, 10472
          Classifications: {'peptide': 1349}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 2, 'PTRANS': 88, 'TRANS': 1258}
          Chain breaks: 13
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
          bond proxies already assigned to first conformer: 10629
    Chain: "L"
      Number of atoms: 1698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1698
          Classifications: {'peptide': 218}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206}
    Chain: "H"
      Number of atoms: 1675
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1675
          Classifications: {'peptide': 222}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 207}
    Chain: "1"
      Number of atoms: 267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 267
          Classifications: {'water': 267}
          Link IDs: {None: 266}
    Chain: "H"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 9
    residue:
      pdb=" N  ALYS 1 240 " occ=0.70
      ... (16 atoms not shown)
      pdb=" NZ BLYS 1 240 " occ=0.30
    residue:
      pdb=" N  AGLU 1 764 " occ=0.47
      ... (16 atoms not shown)
      pdb=" OE2BGLU 1 764 " occ=0.53
    residue:
      pdb=" N  AARG 1 789 " occ=0.71
      ... (20 atoms not shown)
      pdb=" NH2BARG 1 789 " occ=0.29
    residue:
      pdb=" N  APHE 1 850 " occ=0.48
      ... (20 atoms not shown)
      pdb=" CZ BPHE 1 850 " occ=0.52
    residue:
      pdb=" N  AASN 1 911 " occ=0.56
      ... (14 atoms not shown)
      pdb=" ND2BASN 1 911 " occ=0.44
    residue:
      pdb=" N  ATRP 11025 " occ=0.43
      ... (26 atoms not shown)
      pdb=" CH2BTRP 11025 " occ=0.57
    residue:
      pdb=" N  AGLN 11034 " occ=0.52
      ... (16 atoms not shown)
      pdb=" NE2BGLN 11034 " occ=0.48
    residue:
      pdb=" N  AARG 11172 " occ=0.67
      ... (20 atoms not shown)
      pdb=" NH2BARG 11172 " occ=0.33
    residue:
      pdb=" N  ALYS 11454 " occ=0.55
      ... (16 atoms not shown)
      pdb=" NZ BLYS 11454 " occ=0.45
  Time building chain proxies: 12.55, per 1000 atoms: 0.88
  Number of scatterers: 14205
  At special positions: 0
  Unit cell: (93, 110, 129, 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      27     16.00
     O    2996      8.00
     N    2400      7.00
     C    8782      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  20 " - pdb=" SG  CYS L  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  16 " - pdb=" SG  CYS H  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 141 " - pdb=" SG  CYS H 196 " distance=2.03

  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: 3.27
  Conformation dependent library (CDL) restraints added in 2.8 seconds
  

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3318

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 33 sheets defined
      20.1% alpha, 24.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.33
  Creating SS restraints...
    Processing helix  chain '1' and resid 112 through 124
    Processing helix  chain '1' and resid 204 through 209
      removed outlier: 3.728A  pdb=" N   VAL 1 208 " --> pdb=" O   PRO 1 204 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 210 through 214
      removed outlier: 3.625A  pdb=" N   GLN 1 214 " --> pdb=" O   GLU 1 211 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 250 through 254
    Processing helix  chain '1' and resid 328 through 333
    Processing helix  chain '1' and resid 358 through 364
    Processing helix  chain '1' and resid 365 through 370
    Processing helix  chain '1' and resid 395 through 401
    Processing helix  chain '1' and resid 404 through 409
    Processing helix  chain '1' and resid 415 through 426
      removed outlier: 3.872A  pdb=" N   ASP 1 419 " --> pdb=" O   HIS 1 415 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 438 through 442
      removed outlier: 3.522A  pdb=" N   TRP 1 441 " --> pdb=" O   HIS 1 438 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 462 through 466
    Processing helix  chain '1' and resid 483 through 490
    Processing helix  chain '1' and resid 542 through 547
    Processing helix  chain '1' and resid 550 through 554
    Processing helix  chain '1' and resid 611 through 619
    Processing helix  chain '1' and resid 641 through 645
    Processing helix  chain '1' and resid 662 through 666
    Processing helix  chain '1' and resid 670 through 678
    Processing helix  chain '1' and resid 678 through 683
      removed outlier: 4.038A  pdb=" N   ASP 1 683 " --> pdb=" O   LYS 1 679 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 686 through 688
      No H-bonds generated for 'chain '1' and resid 686 through 688'
    Processing helix  chain '1' and resid 701 through 710
    Processing helix  chain '1' and resid 739 through 746
    Processing helix  chain '1' and resid 761 through 767
    Processing helix  chain '1' and resid 779 through 785
      Proline residue:  1 785  - end of helix
    Processing helix  chain '1' and resid 797 through 808
    Processing helix  chain '1' and resid 822 through 826
    Processing helix  chain '1' and resid 867 through 871
    Processing helix  chain '1' and resid 915 through 919
    Processing helix  chain '1' and resid 988 through 1001
    Processing helix  chain '1' and resid 1026 through 1033
      removed outlier: 4.108A  pdb=" N   SER 11032 " --> pdb=" O   THR 11028 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 1034 through 1037
    Processing helix  chain '1' and resid 1049 through 1059
    Processing helix  chain '1' and resid 1059 through 1067
    Processing helix  chain '1' and resid 1146 through 1154
    Processing helix  chain '1' and resid 1179 through 1192
    Processing helix  chain '1' and resid 1220 through 1223
    Processing helix  chain '1' and resid 1237 through 1241
      removed outlier: 4.526A  pdb=" N   HIS 11241 " --> pdb=" O   PRO 11238 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 1249 through 1253
    Processing helix  chain '1' and resid 1255 through 1262
    Processing helix  chain '1' and resid 1263 through 1275
      removed outlier: 3.536A  pdb=" N   VAL 11267 " --> pdb=" O   ASP 11263 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 1302 through 1307
    Processing helix  chain '1' and resid 1326 through 1338
    Processing helix  chain '1' and resid 1418 through 1423
      removed outlier: 4.524A  pdb=" N   HIS 11423 " --> pdb=" O   ARG 11419 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 1424 through 1427
    Processing helix  chain '1' and resid 1452 through 1454
      No H-bonds generated for 'chain '1' and resid 1452 through 1454'
    Processing helix  chain 'L' and resid 123 through 129
    Processing helix  chain 'L' and resid 185 through 190
    Processing helix  chain 'H' and resid 55 through 60
      removed outlier: 4.741A  pdb=" N   GLY H  60 " --> pdb=" O   GLN H  56 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 129 through 134
    Processing sheet with id=AA1, first strand: chain '1' and resid 67 through 68
    Processing sheet with id=AA2, first strand: chain '1' and resid 67 through 68
      removed outlier: 4.139A  pdb=" N   TYR 1 139 " --> pdb=" O   ARG 1 130 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain '1' and resid 161 through 162
    Processing sheet with id=AA4, first strand: chain '1' and resid 184 through 190
      removed outlier: 6.593A  pdb=" N   VAL 1 203 " --> pdb=" O   PRO 1 185 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLU 1 187 " --> pdb=" O   LEU 1 201 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain '1' and resid 184 through 190
      removed outlier: 6.593A  pdb=" N   VAL 1 203 " --> pdb=" O   PRO 1 185 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLU 1 187 " --> pdb=" O   LEU 1 201 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   ALA 1 371 " --> pdb=" O   LEU 1 394 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain '1' and resid 245 through 246
    Processing sheet with id=AA7, first strand: chain '1' and resid 257 through 259
      removed outlier: 3.924A  pdb=" N   LYS 1 307 " --> pdb=" O   LYS 1 292 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain '1' and resid 257 through 259
    Processing sheet with id=AA9, first strand: chain '1' and resid 319 through 320
    Processing sheet with id=AB1, first strand: chain '1' and resid 494 through 497
    Processing sheet with id=AB2, first strand: chain '1' and resid 574 through 582
      removed outlier: 4.684A  pdb=" N   VAL 1 576 " --> pdb=" O   THR 1 591 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   THR 1 591 " --> pdb=" O   VAL 1 576 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   GLY 1 578 " --> pdb=" O   ALA 1 589 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL 1 582 " --> pdb=" O   GLU 1 585 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLU 1 585 " --> pdb=" O   VAL 1 582 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain '1' and resid 595 through 596
      removed outlier: 4.047A  pdb=" N   GLU 1 725 " --> pdb=" O   ASP 1 596 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain '1' and resid 862 through 864
    Processing sheet with id=AB5, first strand: chain '1' and resid 913 through 914
    Processing sheet with id=AB6, first strand: chain '1' and resid 949 through 953
    Processing sheet with id=AB7, first strand: chain '1' and resid 1006 through 1008
    Processing sheet with id=AB8, first strand: chain '1' and resid 1010 through 1011
    Processing sheet with id=AB9, first strand: chain '1' and resid 1107 through 1109
    Processing sheet with id=AC1, first strand: chain '1' and resid 1162 through 1167
      removed outlier: 6.184A  pdb=" N   VAL 11176 " --> pdb=" O   ARG 11163 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   SER 11165 " --> pdb=" O   GLU 11174 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   GLU 11174 " --> pdb=" O   SER 11165 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain '1' and resid 1384 through 1386
    Processing sheet with id=AC3, first strand: chain '1' and resid 1408 through 1409
    Processing sheet with id=AC4, first strand: chain '1' and resid 1429 through 1430
      removed outlier: 3.610A  pdb=" N   LEU 11435 " --> pdb=" O   ASP 11430 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   LEU 11458 " --> pdb=" O   VAL 11436 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   GLY 11471 " --> pdb=" O   LEU 11461 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   PHE 11463 " --> pdb=" O   SER 11469 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   SER 11469 " --> pdb=" O   PHE 11463 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain '1' and resid 1429 through 1430
      removed outlier: 3.610A  pdb=" N   LEU 11435 " --> pdb=" O   ASP 11430 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   LEU 11458 " --> pdb=" O   VAL 11436 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   GLY 11471 " --> pdb=" O   LEU 11461 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   PHE 11463 " --> pdb=" O   SER 11469 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   SER 11469 " --> pdb=" O   PHE 11463 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'L' and resid 2 through 4
      removed outlier: 3.687A  pdb=" N   THR L   2 " --> pdb=" O   ARG L  21 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'L' and resid 9 through 10
      removed outlier: 3.772A  pdb=" N   GLY L  86 " --> pdb=" O   LEU L 106 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   LEU L  35 " --> pdb=" O   TYR L  51 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   TYR L  51 " --> pdb=" O   LEU L  35 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   TRP L  37 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'L' and resid 118 through 120
      removed outlier: 3.513A  pdb=" N   VAL L 135 " --> pdb=" O   PHE L 120 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'L' and resid 155 through 157
      removed outlier: 4.341A  pdb=" N   TRP L 150 " --> pdb=" O   ARG L 157 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LYS L 209 " --> pdb=" O   CYS L 196 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'H' and resid -3 through 0
      removed outlier: 4.018A  pdb=" N   MET H  12 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'H' and resid -3 through 0
    Processing sheet with id=AD3, first strand: chain 'H' and resid 4 through 5
      removed outlier: 6.822A  pdb=" N   GLU H   4 " --> pdb=" O   THR H 111 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   MET H  28 " --> pdb=" O   LEU H  44 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   LEU H  44 " --> pdb=" O   MET H  28 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   TRP H  30 " --> pdb=" O   ILE H  42 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 5
      removed outlier: 6.822A  pdb=" N   GLU H   4 " --> pdb=" O   THR H 111 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   TYR H 103 " --> pdb=" O   ARG H  92 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ASN H  94 " --> pdb=" O   MET H 101 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   MET H 101 " --> pdb=" O   ASN H  94 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'H' and resid 121 through 125
      removed outlier: 6.548A  pdb=" N   TYR H 176 " --> pdb=" O   GLY H 145 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR H 177 " --> pdb=" O   VAL H 170 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'H' and resid 152 through 155

    445 hydrogen bonds defined for protein.
    1126 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: 6.66

  Time building geometry restraints manager: 3.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4596
        1.34 -     1.46: 3144
        1.46 -     1.58: 6508
        1.58 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 14292
  Sorted by residual:
  bond pdb=" CB  GLN 1 323 "
       pdb=" CG  GLN 1 323 "
    ideal  model  delta    sigma   weight residual
    1.520  1.565 -0.045 3.00e-02 1.11e+03 2.20e+00
  bond pdb=" CA  ASN 1 182 "
       pdb=" C   ASN 1 182 "
    ideal  model  delta    sigma   weight residual
    1.522  1.498  0.024 1.72e-02 3.38e+03 1.95e+00
  bond pdb=" CB  TRP 1 634 "
       pdb=" CG  TRP 1 634 "
    ideal  model  delta    sigma   weight residual
    1.498  1.459  0.039 3.10e-02 1.04e+03 1.59e+00
  bond pdb=" CG  LYS 1 749 "
       pdb=" CD  LYS 1 749 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.48e+00
  bond pdb=" CA  ASN 11351 "
       pdb=" CB  ASN 11351 "
    ideal  model  delta    sigma   weight residual
    1.532  1.549 -0.017 1.42e-02 4.96e+03 1.47e+00
  ... (remaining 14287 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 19190
        2.43 -     4.86: 259
        4.86 -     7.28: 28
        7.28 -     9.71: 7
        9.71 -    12.14: 2
  Bond angle restraints: 19486
  Sorted by residual:
  angle pdb=" N   VAL 1 448 "
        pdb=" CA  VAL 1 448 "
        pdb=" C   VAL 1 448 "
      ideal   model   delta    sigma   weight residual
     112.43  107.28    5.15 9.20e-01 1.18e+00 3.14e+01
  angle pdb=" C   ASP 1 958 "
        pdb=" CA  ASP 1 958 "
        pdb=" CB  ASP 1 958 "
      ideal   model   delta    sigma   weight residual
     116.54  110.35    6.19 1.15e+00 7.56e-01 2.89e+01
  angle pdb=" CA  GLN 1 323 "
        pdb=" CB  GLN 1 323 "
        pdb=" CG  GLN 1 323 "
      ideal   model   delta    sigma   weight residual
     114.10  122.40   -8.30 2.00e+00 2.50e-01 1.72e+01
  angle pdb=" CB  LYS 1 749 "
        pdb=" CG  LYS 1 749 "
        pdb=" CD  LYS 1 749 "
      ideal   model   delta    sigma   weight residual
     111.30  120.62   -9.32 2.30e+00 1.89e-01 1.64e+01
  angle pdb=" C   MET H 101 "
        pdb=" N   ASP H 102 "
        pdb=" CA  ASP H 102 "
      ideal   model   delta    sigma   weight residual
     121.54  129.18   -7.64 1.91e+00 2.74e-01 1.60e+01
  ... (remaining 19481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 7215
       17.97 -    35.94: 933
       35.94 -    53.92: 253
       53.92 -    71.89: 47
       71.89 -    89.86: 29
  Dihedral angle restraints: 8477
    sinusoidal: 3308
      harmonic: 5169
  Sorted by residual:
  dihedral pdb=" CA  MET 1 574 "
           pdb=" C   MET 1 574 "
           pdb=" N   ALA 1 575 "
           pdb=" CA  ALA 1 575 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.52   26.48     0      5.00e+00 4.00e-02 2.81e+01
  dihedral pdb=" CB  CYS L 136 "
           pdb=" SG  CYS L 136 "
           pdb=" SG  CYS L 196 "
           pdb=" CB  CYS L 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.01  -41.01     1      1.00e+01 1.00e-02 2.36e+01
  dihedral pdb=" CA  TRP 1 634 "
           pdb=" C   TRP 1 634 "
           pdb=" N   ALA 1 635 "
           pdb=" CA  ALA 1 635 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.26   22.74     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 8474 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1416
       0.036 -    0.072: 492
       0.072 -    0.109: 181
       0.109 -    0.145: 39
       0.145 -    0.181: 3
  Chirality restraints: 2131
  Sorted by residual:
  chirality pdb=" CA  ASN 11351 "
            pdb=" N   ASN 11351 "
            pdb=" C   ASN 11351 "
            pdb=" CB  ASN 11351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.18e-01
  chirality pdb=" CG  LEU 1 501 "
            pdb=" CB  LEU 1 501 "
            pdb=" CD1 LEU 1 501 "
            pdb=" CD2 LEU 1 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.23e-01
  chirality pdb=" CA  ILE 1 737 "
            pdb=" N   ILE 1 737 "
            pdb=" C   ILE 1 737 "
            pdb=" CB  ILE 1 737 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.75e-01
  ... (remaining 2128 not shown)

  Planarity restraints: 2557
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS 11423 "    0.038 5.00e-02 4.00e+02   5.74e-02 5.27e+00
        pdb=" N   PRO 11424 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO 11424 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO 11424 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG 1 637 "    0.036 5.00e-02 4.00e+02   5.53e-02 4.89e+00
        pdb=" N   PRO 1 638 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO 1 638 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO 1 638 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER 11514 "   -0.036 5.00e-02 4.00e+02   5.48e-02 4.80e+00
        pdb=" N   PRO 11515 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO 11515 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO 11515 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 2554 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 584
        2.59 -     3.17: 13545
        3.17 -     3.75: 29175
        3.75 -     4.32: 40494
        4.32 -     4.90: 61955
  Nonbonded interactions: 145753
  Sorted by model distance:
  nonbonded pdb=" OH  TYR 1 139 "
            pdb=" OD1 ASP 1 378 "
     model   vdw
     2.015 3.040
  nonbonded pdb=" O   GLN 1 617 "
            pdb=" OH  TYR 1 728 "
     model   vdw
     2.060 3.040
  nonbonded pdb=" O   LYS 1 285 "
            pdb=" OH  TYR 1 657 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" NZ  LYS 11088 "
            pdb=" O   LYS 11253 "
     model   vdw
     2.119 3.120
  nonbonded pdb=" OG1 THR 1 536 "
            pdb=" OD2 ASP 1 748 "
     model   vdw
     2.148 3.040
  ... (remaining 145748 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.29 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.670
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     41.850
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.080
  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:12.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0223
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   0.046  14296  Z= 0.202
  Angle     :  0.686  12.139  19494  Z= 0.355
  Chirality :  0.043   0.181   2131
  Planarity :  0.005   0.057   2557
  Dihedral  : 18.032  89.860   5147
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 29.16
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.58 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 27.55 %
    Favored  : 69.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.20), residues: 1784
  helix: -0.56 (0.30), residues: 266
  sheet: -1.74 (0.26), residues: 369
  loop : -0.27 (0.19), residues: 1149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP 1 709 
 HIS   0.005   0.001   HIS 1 515 
 PHE   0.023   0.002   PHE 1 488 
 TYR   0.031   0.002   TYR L  51 
 ARG   0.009   0.001   ARG 1 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17193 (  415)
  hydrogen bonds       : angle       9.35457 ( 1126)
  SS BOND              : bond        0.00259 (    4)
  SS BOND              : angle       0.46028 (    8)
  covalent geometry    : bond        0.00462 (14292)
  covalent geometry    : angle       0.68616 (19486)

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

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

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 164
  time to evaluate  : 1.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 1  307 LYS cc_start: 0.3520 (tttm) cc_final: 0.3214 (mmmt)
REVERT: 1 1377 MET cc_start: 0.3274 (mtm) cc_final: 0.2354 (pmm)
REVERT: 1 1422 THR cc_start: 0.6717 (p) cc_final: 0.6507 (t)
REVERT: 1 1482 ASP cc_start: 0.0005 (OUTLIER) cc_final: -0.0408 (m-30)
REVERT: 1 1507 GLN cc_start: 0.1865 (OUTLIER) cc_final: 0.1263 (pt0)
REVERT: L  179 SER cc_start: 0.2221 (OUTLIER) cc_final: 0.1983 (t)
REVERT: H   34 SER cc_start: -0.2758 (OUTLIER) cc_final: -0.3013 (m)
REVERT: H  166 THR cc_start: 0.5885 (t) cc_final: 0.5421 (p)
  outliers start: 43
  outliers final: 3
  residues processed: 200
  average time/residue: 1.0225
  time to fit residues: 232.0095
Evaluate side-chains
  85 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 1.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  351 THR
Chi-restraints excluded: chain 1 residue 1482 ASP
Chi-restraints excluded: chain 1 residue 1507 GLN
Chi-restraints excluded: chain L residue  146 ILE
Chi-restraints excluded: chain L residue  179 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue   61 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 149 optimal weight:    5.9990
   chunk 134 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 138 optimal weight:    0.0980
   chunk 53 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 103 optimal weight:    0.5980
   chunk 160 optimal weight:    9.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
1 108 GLN
** 1 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
1 551 ASN
** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
11034 GLN    A
** 11101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
11208 ASN
** 11418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
11507 GLN
11510 GLN
** H  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 165 HIS
** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.155040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.116311 restraints weight = 85353.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 4.67
r_work: 0.3467 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3470
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3470 r_free = 0.3470    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3470 r_free = 0.3470    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3470
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0597
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  14296  Z= 0.200
  Angle     :  0.775  12.247  19494  Z= 0.394
  Chirality :  0.046   0.212   2131
  Planarity :  0.006   0.059   2557
  Dihedral  :  5.993  46.021   1931
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 29.24
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.32 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 26.90 %
    Favored  : 67.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.20), residues: 1784
  helix: -0.52 (0.31), residues: 251
  sheet: -1.55 (0.26), residues: 343
  loop : -0.58 (0.19), residues: 1190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP 1 407 
 HIS   0.008   0.002   HIS 1 509 
 PHE   0.021   0.002   PHE 11421 
 TYR   0.026   0.002   TYR 1 728 
 ARG   0.009   0.001   ARG 11386 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04525 (  415)
  hydrogen bonds       : angle       7.86173 ( 1126)
  SS BOND              : bond        0.00755 (    4)
  SS BOND              : angle       1.61351 (    8)
  covalent geometry    : bond        0.00442 (14292)
  covalent geometry    : angle       0.77399 (19486)

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

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

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 102
  time to evaluate  : 2.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 1  307 LYS cc_start: 0.3753 (tttm) cc_final: 0.3257 (mmmt)
REVERT: 1 1087 SER cc_start: 0.0193 (OUTLIER) cc_final: -0.0477 (p)
REVERT: 1 1338 GLN cc_start: 0.2360 (mp10) cc_final: 0.1939 (mp10)
REVERT: 1 1427 ASP cc_start: -0.1922 (OUTLIER) cc_final: -0.2523 (t70)
REVERT: 1 1456 VAL cc_start: -0.2418 (OUTLIER) cc_final: -0.2829 (p)
REVERT: 1 1482 ASP cc_start: 0.0155 (OUTLIER) cc_final: -0.0141 (p0)
REVERT: L   12 LEU cc_start: 0.4610 (OUTLIER) cc_final: 0.4389 (mp)
REVERT: L   50 ILE cc_start: 0.2958 (OUTLIER) cc_final: 0.2671 (tp)
REVERT: L   69 SER cc_start: 0.5017 (OUTLIER) cc_final: 0.4769 (t)
REVERT: L  107 GLU cc_start: 0.5025 (pm20) cc_final: 0.4378 (pm20)
REVERT: L  108 ILE cc_start: 0.5878 (OUTLIER) cc_final: 0.5580 (mm)
REVERT: H   37 LYS cc_start: 0.4492 (mptt) cc_final: 0.3550 (tmtt)
REVERT: H  166 THR cc_start: 0.6430 (t) cc_final: 0.6015 (p)
  outliers start: 74
  outliers final: 21
  residues processed: 165
  average time/residue: 1.2234
  time to fit residues: 235.2115
Evaluate side-chains
  108 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 1.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  351 THR
Chi-restraints excluded: chain 1 residue  356 TRP
Chi-restraints excluded: chain 1 residue  640 LEU
Chi-restraints excluded: chain 1 residue  657 TYR
Chi-restraints excluded: chain 1 residue  775 THR
Chi-restraints excluded: chain 1 residue  859 VAL
Chi-restraints excluded: chain 1 residue 1037 LEU
Chi-restraints excluded: chain 1 residue 1087 SER
Chi-restraints excluded: chain 1 residue 1099 THR
Chi-restraints excluded: chain 1 residue 1109 SER
Chi-restraints excluded: chain 1 residue 1113 VAL
Chi-restraints excluded: chain 1 residue 1339 LEU
Chi-restraints excluded: chain 1 residue 1427 ASP
Chi-restraints excluded: chain 1 residue 1436 VAL
Chi-restraints excluded: chain 1 residue 1456 VAL
Chi-restraints excluded: chain 1 residue 1482 ASP
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   63 ARG
Chi-restraints excluded: chain L residue   69 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   87 VAL
Chi-restraints excluded: chain L residue  106 LEU
Chi-restraints excluded: chain L residue  108 ILE
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain H residue   29 ASN
Chi-restraints excluded: chain H residue   75 MET
Chi-restraints excluded: chain H residue  113 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 119 optimal weight:   10.0000
   chunk 153 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9980
   chunk 141 optimal weight:   20.0000
   chunk 86 optimal weight:    8.9990
   chunk 82 optimal weight:    3.9990
   chunk 176 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
1 256 GLN
** 1 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
1 428 GLN
1 551 ASN
** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
1 964 ASN
** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
11494 ASN
** 11510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 191 HIS
H   0 GLN
H  29 ASN
** H  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 172 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.169730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.135024 restraints weight = 80838.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 4.75
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3878 r_free = 0.3878    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3878 r_free = 0.3878    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1453
moved from start:          0.5026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.075  14296  Z= 0.312
  Angle     :  1.012  13.556  19494  Z= 0.525
  Chirality :  0.055   0.243   2131
  Planarity :  0.008   0.089   2557
  Dihedral  :  7.302  58.848   1923
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 42.74
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.89 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 25.52 %
    Favored  : 68.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.19), residues: 1784
  helix: -1.34 (0.29), residues: 263
  sheet: -1.47 (0.26), residues: 342
  loop : -1.10 (0.18), residues: 1179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.005   TRP 11177 
 HIS   0.011   0.003   HIS 1 515 
 PHE   0.038   0.005   PHE 1 504 
 TYR   0.026   0.003   TYR 1 131 
 ARG   0.018   0.002   ARG 11473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05468 (  415)
  hydrogen bonds       : angle       8.55551 ( 1126)
  SS BOND              : bond        0.00717 (    4)
  SS BOND              : angle       1.52603 (    8)
  covalent geometry    : bond        0.00710 (14292)
  covalent geometry    : angle       1.01219 (19486)

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

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

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 129
  time to evaluate  : 1.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 1  222 GLN cc_start: -0.1585 (OUTLIER) cc_final: -0.2075 (tp40)
REVERT: 1  307 LYS cc_start: 0.5165 (tttm) cc_final: 0.4418 (mmmt)
REVERT: 1  369 TRP cc_start: 0.3829 (m100) cc_final: 0.2646 (m100)
REVERT: 1  402 ASN cc_start: -0.0887 (m-40) cc_final: -0.1204 (t0)
REVERT: 1  549 MET cc_start: 0.0019 (OUTLIER) cc_final: -0.0480 (pmt)
REVERT: 1  653 HIS cc_start: 0.3340 (m170) cc_final: 0.2505 (m90)
REVERT: 1 1027 TYR cc_start: 0.1369 (OUTLIER) cc_final: 0.1150 (t80)
REVERT: 1 1502 LEU cc_start: 0.2930 (mt) cc_final: 0.2250 (mp)
REVERT: L   40 GLN cc_start: 0.3337 (pp30) cc_final: 0.2612 (mp10)
REVERT: L   41 ARG cc_start: 0.5589 (OUTLIER) cc_final: 0.4465 (mmt-90)
REVERT: L  207 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6626 (tt)
REVERT: L  215 GLU cc_start: 0.3693 (mm-30) cc_final: 0.3425 (mm-30)
REVERT: H   77 LEU cc_start: 0.4659 (OUTLIER) cc_final: 0.4338 (tm)
  outliers start: 87
  outliers final: 25
  residues processed: 204
  average time/residue: 0.9655
  time to fit residues: 223.7651
Evaluate side-chains
  135 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 104
  time to evaluate  : 1.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  221 GLN
Chi-restraints excluded: chain 1 residue  222 GLN
Chi-restraints excluded: chain 1 residue  427 LEU
Chi-restraints excluded: chain 1 residue  549 MET
Chi-restraints excluded: chain 1 residue  657 TYR
Chi-restraints excluded: chain 1 residue  828 THR
Chi-restraints excluded: chain 1 residue  943 SER
Chi-restraints excluded: chain 1 residue  966 THR
Chi-restraints excluded: chain 1 residue 1024 LYS
Chi-restraints excluded: chain 1 residue 1027 TYR
Chi-restraints excluded: chain 1 residue 1054 VAL
Chi-restraints excluded: chain 1 residue 1109 SER
Chi-restraints excluded: chain 1 residue 1113 VAL
Chi-restraints excluded: chain 1 residue 1402 THR
Chi-restraints excluded: chain 1 residue 1436 VAL
Chi-restraints excluded: chain 1 residue 1452 ASN
Chi-restraints excluded: chain L residue   -1 VAL
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   41 ARG
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   58 SER
Chi-restraints excluded: chain L residue   87 VAL
Chi-restraints excluded: chain L residue   91 PHE
Chi-restraints excluded: chain L residue  106 LEU
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  203 SER
Chi-restraints excluded: chain L residue  207 ILE
Chi-restraints excluded: chain H residue   29 ASN
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue  113 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 148 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 139 optimal weight:    0.6980
   chunk 118 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9980
   chunk 128 optimal weight:    0.8980
   chunk 150 optimal weight:    6.9990
   chunk 111 optimal weight:    0.9980
   chunk 168 optimal weight:   50.0000
   chunk 19 optimal weight:   30.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** 1 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 980 ASN
11208 ASN
** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 HIS
** H  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 165 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.168090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.131241 restraints weight = 83918.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3838 rms_B_bonded: 4.83
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3840 r_free = 0.3840    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3840 r_free = 0.3840    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1107
moved from start:          0.5353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  14296  Z= 0.188
  Angle     :  0.764  11.072  19494  Z= 0.386
  Chirality :  0.047   0.233   2131
  Planarity :  0.006   0.068   2557
  Dihedral  :  6.071  24.810   1920
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 28.94
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.29 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 27.49 %
    Favored  : 68.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.20), residues: 1784
  helix: -0.90 (0.31), residues: 255
  sheet: -1.60 (0.25), residues: 370
  loop : -0.84 (0.19), residues: 1159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP 1 709 
 HIS   0.010   0.002   HIS 1 393 
 PHE   0.035   0.003   PHE L  57 
 TYR   0.039   0.002   TYR L  34 
 ARG   0.023   0.001   ARG 1 354 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04161 (  415)
  hydrogen bonds       : angle       7.72744 ( 1126)
  SS BOND              : bond        0.00555 (    4)
  SS BOND              : angle       1.03580 (    8)
  covalent geometry    : bond        0.00421 (14292)
  covalent geometry    : angle       0.76385 (19486)

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

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

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 103
  time to evaluate  : 1.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 1  307 LYS cc_start: 0.5006 (tttm) cc_final: 0.4235 (mmmt)
REVERT: L   12 LEU cc_start: 0.4277 (OUTLIER) cc_final: 0.3905 (tp)
REVERT: L   40 GLN cc_start: 0.3215 (pp30) cc_final: 0.2942 (mp10)
REVERT: L  207 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6639 (tt)
REVERT: L  215 GLU cc_start: 0.3697 (mm-30) cc_final: 0.3404 (mm-30)
REVERT: H  101 MET cc_start: 0.3978 (mpt) cc_final: 0.3025 (mpt)
  outliers start: 57
  outliers final: 21
  residues processed: 149
  average time/residue: 1.2175
  time to fit residues: 212.8681
Evaluate side-chains
  108 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 1.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  427 LEU
Chi-restraints excluded: chain 1 residue  657 TYR
Chi-restraints excluded: chain 1 residue  859 VAL
Chi-restraints excluded: chain 1 residue 1027 TYR
Chi-restraints excluded: chain 1 residue 1083 GLN
Chi-restraints excluded: chain 1 residue 1099 THR
Chi-restraints excluded: chain 1 residue 1109 SER
Chi-restraints excluded: chain 1 residue 1339 LEU
Chi-restraints excluded: chain 1 residue 1436 VAL
Chi-restraints excluded: chain 1 residue 1452 ASN
Chi-restraints excluded: chain L residue    2 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   58 SER
Chi-restraints excluded: chain L residue   87 VAL
Chi-restraints excluded: chain L residue   91 PHE
Chi-restraints excluded: chain L residue  106 LEU
Chi-restraints excluded: chain L residue  162 LEU
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  207 ILE
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   82 SER
Chi-restraints excluded: chain H residue   87 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 111 optimal weight:    6.9990
   chunk 37 optimal weight:    0.3980
   chunk 53 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 93 optimal weight:    5.9990
   chunk 19 optimal weight:   20.0000
   chunk 27 optimal weight:    0.5980
   chunk 168 optimal weight:    7.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** 1 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 967 ASN
** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   0 GLN
** H  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.168520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.131919 restraints weight = 90777.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3847 rms_B_bonded: 5.07
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3842
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3842 r_free = 0.3842    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3842 r_free = 0.3842    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3842
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1122
moved from start:          0.5763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  14296  Z= 0.170
  Angle     :  0.746  11.340  19494  Z= 0.376
  Chirality :  0.046   0.199   2131
  Planarity :  0.006   0.056   2557
  Dihedral  :  5.876  24.672   1920
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 28.11
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.58 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 27.42 %
    Favored  : 68.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.20), residues: 1784
  helix: -0.82 (0.30), residues: 258
  sheet: -1.50 (0.24), residues: 386
  loop : -0.82 (0.19), residues: 1140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP 1 709 
 HIS   0.008   0.001   HIS 1 393 
 PHE   0.032   0.002   PHE 11498 
 TYR   0.020   0.002   TYR L  38 
 ARG   0.018   0.001   ARG 1  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03996 (  415)
  hydrogen bonds       : angle       7.50738 ( 1126)
  SS BOND              : bond        0.00557 (    4)
  SS BOND              : angle       0.77761 (    8)
  covalent geometry    : bond        0.00390 (14292)
  covalent geometry    : angle       0.74551 (19486)

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

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

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 96
  time to evaluate  : 1.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 1   81 LEU cc_start: 0.1813 (OUTLIER) cc_final: 0.1569 (tp)
REVERT: 1  236 MET cc_start: 0.0921 (pmm) cc_final: -0.3894 (tpt)
REVERT: 1  307 LYS cc_start: 0.4978 (tttm) cc_final: 0.4244 (mmmt)
REVERT: 1  549 MET cc_start: -0.0658 (OUTLIER) cc_final: -0.1836 (pmt)
REVERT: 1 1434 MET cc_start: 0.1994 (OUTLIER) cc_final: 0.1172 (tpp)
REVERT: L   12 LEU cc_start: 0.4059 (OUTLIER) cc_final: 0.3719 (tp)
REVERT: L   21 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6451 (mtp85)
REVERT: L  207 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6655 (tt)
REVERT: L  215 GLU cc_start: 0.3689 (mm-30) cc_final: 0.3403 (mm-30)
REVERT: H   28 MET cc_start: 0.1961 (pmm) cc_final: 0.0988 (ppp)
REVERT: H  136 MET cc_start: 0.6211 (ppp) cc_final: 0.5469 (tpp)
  outliers start: 49
  outliers final: 20
  residues processed: 137
  average time/residue: 0.8714
  time to fit residues: 138.3272
Evaluate side-chains
  116 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue   81 LEU
Chi-restraints excluded: chain 1 residue  427 LEU
Chi-restraints excluded: chain 1 residue  438 HIS
Chi-restraints excluded: chain 1 residue  533 THR
Chi-restraints excluded: chain 1 residue  549 MET
Chi-restraints excluded: chain 1 residue  657 TYR
Chi-restraints excluded: chain 1 residue  859 VAL
Chi-restraints excluded: chain 1 residue 1027 TYR
Chi-restraints excluded: chain 1 residue 1083 GLN
Chi-restraints excluded: chain 1 residue 1099 THR
Chi-restraints excluded: chain 1 residue 1109 SER
Chi-restraints excluded: chain 1 residue 1113 VAL
Chi-restraints excluded: chain 1 residue 1339 LEU
Chi-restraints excluded: chain 1 residue 1402 THR
Chi-restraints excluded: chain 1 residue 1434 MET
Chi-restraints excluded: chain 1 residue 1436 VAL
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   21 ARG
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   87 VAL
Chi-restraints excluded: chain L residue   91 PHE
Chi-restraints excluded: chain L residue  166 THR
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  207 ILE
Chi-restraints excluded: chain H residue   77 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 75 optimal weight:    1.9990
   chunk 137 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 169 optimal weight:    6.9990
   chunk 86 optimal weight:    0.0870
   chunk 96 optimal weight:    3.9990
   chunk 130 optimal weight:    6.9990
   chunk 50 optimal weight:    8.9990
   overall best weight:    1.2164

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

Flipped N/Q/H residues before XYZ refinement:
** 1 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
11023 GLN
** 11373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
11494 ASN
** 11510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  33 GLN
** H  56 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 = 0.4383 r_free = 0.4383 target = 0.171740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.134810 restraints weight = 106367.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 5.59
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3887
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3887 r_free = 0.3887    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3887 r_free = 0.3887    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3887
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1252
moved from start:          0.6395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14296  Z= 0.170
  Angle     :  0.747   9.065  19494  Z= 0.379
  Chirality :  0.047   0.258   2131
  Planarity :  0.006   0.057   2557
  Dihedral  :  5.918  25.479   1920
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 27.23
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.75 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 27.88 %
    Favored  : 68.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.20), residues: 1784
  helix: -0.64 (0.32), residues: 247
  sheet: -1.53 (0.25), residues: 388
  loop : -0.82 (0.19), residues: 1149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP L 150 
 HIS   0.007   0.002   HIS 1 393 
 PHE   0.032   0.002   PHE 11498 
 TYR   0.023   0.002   TYR L  38 
 ARG   0.008   0.001   ARG 1  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03812 (  415)
  hydrogen bonds       : angle       7.33195 ( 1126)
  SS BOND              : bond        0.00571 (    4)
  SS BOND              : angle       0.59481 (    8)
  covalent geometry    : bond        0.00393 (14292)
  covalent geometry    : angle       0.74667 (19486)

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

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

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 105
  time to evaluate  : 1.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 1   65 ARG cc_start: 0.1299 (mmp80) cc_final: 0.1046 (tpp80)
REVERT: 1   81 LEU cc_start: 0.1861 (OUTLIER) cc_final: 0.1625 (tp)
REVERT: 1  307 LYS cc_start: 0.5227 (tttm) cc_final: 0.4340 (mmmt)
REVERT: 1  374 LEU cc_start: 0.1452 (OUTLIER) cc_final: 0.0927 (pp)
REVERT: 1  768 GLN cc_start: 0.1278 (OUTLIER) cc_final: -0.1385 (mt0)
REVERT: 1 1434 MET cc_start: 0.2097 (OUTLIER) cc_final: 0.1436 (tpp)
REVERT: 1 1440 TYR cc_start: 0.3116 (m-80) cc_final: 0.2715 (m-80)
REVERT: L   12 LEU cc_start: 0.4017 (OUTLIER) cc_final: 0.3659 (tp)
REVERT: L   18 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6463 (tp)
REVERT: L  186 ASP cc_start: 0.8099 (p0) cc_final: 0.7866 (p0)
REVERT: L  207 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6621 (tt)
REVERT: L  215 GLU cc_start: 0.3678 (mm-30) cc_final: 0.3380 (mm-30)
REVERT: H   75 MET cc_start: 0.2676 (ppp) cc_final: 0.1165 (tpt)
REVERT: H   93 SER cc_start: -0.2953 (OUTLIER) cc_final: -0.4202 (t)
REVERT: H  136 MET cc_start: 0.6250 (ppp) cc_final: 0.5592 (tpp)
  outliers start: 50
  outliers final: 23
  residues processed: 147
  average time/residue: 1.2681
  time to fit residues: 213.5079
Evaluate side-chains
  124 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 93
  time to evaluate  : 1.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue   81 LEU
Chi-restraints excluded: chain 1 residue  221 GLN
Chi-restraints excluded: chain 1 residue  374 LEU
Chi-restraints excluded: chain 1 residue  438 HIS
Chi-restraints excluded: chain 1 residue  501 LEU
Chi-restraints excluded: chain 1 residue  510 VAL
Chi-restraints excluded: chain 1 residue  768 GLN
Chi-restraints excluded: chain 1 residue  859 VAL
Chi-restraints excluded: chain 1 residue  975 THR
Chi-restraints excluded: chain 1 residue 1027 TYR
Chi-restraints excluded: chain 1 residue 1099 THR
Chi-restraints excluded: chain 1 residue 1109 SER
Chi-restraints excluded: chain 1 residue 1339 LEU
Chi-restraints excluded: chain 1 residue 1387 THR
Chi-restraints excluded: chain 1 residue 1434 MET
Chi-restraints excluded: chain 1 residue 1459 LYS
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   18 ILE
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   56 ARG
Chi-restraints excluded: chain L residue   58 SER
Chi-restraints excluded: chain L residue   87 VAL
Chi-restraints excluded: chain L residue   91 PHE
Chi-restraints excluded: chain L residue  166 THR
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  207 ILE
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   82 SER
Chi-restraints excluded: chain H residue   87 VAL
Chi-restraints excluded: chain H residue   93 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 51 optimal weight:    0.0970
   chunk 39 optimal weight:    6.9990
   chunk 87 optimal weight:    4.9990
   chunk 114 optimal weight:    5.9990
   chunk 100 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 73 optimal weight:    8.9990
   chunk 67 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
1 256 GLN
** 1 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
1 469 GLN
** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 654 ASN
** 1 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 165 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.173618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.137906 restraints weight = 97001.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 5.34
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3932 r_free = 0.3932    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3932 r_free = 0.3932    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1279
moved from start:          0.6889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  14296  Z= 0.164
  Angle     :  0.742   9.791  19494  Z= 0.376
  Chirality :  0.046   0.230   2131
  Planarity :  0.006   0.054   2557
  Dihedral  :  5.795  26.119   1920
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 26.24
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.18 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 28.66 %
    Favored  : 67.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.20), residues: 1784
  helix: -0.72 (0.31), residues: 248
  sheet: -1.50 (0.24), residues: 391
  loop : -0.85 (0.19), residues: 1145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP H  41 
 HIS   0.018   0.002   HIS H 165 
 PHE   0.024   0.002   PHE 11476 
 TYR   0.017   0.002   TYR 1 728 
 ARG   0.011   0.001   ARG 1  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03759 (  415)
  hydrogen bonds       : angle       7.29316 ( 1126)
  SS BOND              : bond        0.00501 (    4)
  SS BOND              : angle       0.51215 (    8)
  covalent geometry    : bond        0.00381 (14292)
  covalent geometry    : angle       0.74233 (19486)

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

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

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 101
  time to evaluate  : 1.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 1   65 ARG cc_start: 0.1345 (mmp80) cc_final: 0.1088 (tpp80)
REVERT: 1  146 LEU cc_start: 0.5359 (OUTLIER) cc_final: 0.5131 (mt)
REVERT: 1  307 LYS cc_start: 0.5239 (tttm) cc_final: 0.4407 (mmmt)
REVERT: 1  369 TRP cc_start: 0.3624 (m100) cc_final: 0.2495 (m100)
REVERT: 1  374 LEU cc_start: 0.1499 (OUTLIER) cc_final: 0.1033 (pp)
REVERT: 1  501 LEU cc_start: 0.2195 (OUTLIER) cc_final: 0.1578 (tt)
REVERT: 1 1377 MET cc_start: 0.1277 (mtm) cc_final: 0.1009 (mtm)
REVERT: 1 1434 MET cc_start: 0.2200 (OUTLIER) cc_final: 0.1146 (tpp)
REVERT: L    1 MET cc_start: 0.4476 (tmm) cc_final: 0.4200 (mmm)
REVERT: L   12 LEU cc_start: 0.4076 (OUTLIER) cc_final: 0.3686 (tp)
REVERT: L  207 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6695 (tt)
REVERT: L  215 GLU cc_start: 0.3586 (mm-30) cc_final: 0.3310 (mm-30)
REVERT: H   28 MET cc_start: 0.3210 (ppp) cc_final: 0.2393 (pmt)
REVERT: H   75 MET cc_start: 0.2371 (ppp) cc_final: 0.1027 (tpt)
REVERT: H  136 MET cc_start: 0.6233 (ppp) cc_final: 0.5651 (tpp)
  outliers start: 49
  outliers final: 21
  residues processed: 140
  average time/residue: 0.9819
  time to fit residues: 157.4087
Evaluate side-chains
  114 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 87
  time to evaluate  : 1.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  146 LEU
Chi-restraints excluded: chain 1 residue  221 GLN
Chi-restraints excluded: chain 1 residue  236 MET
Chi-restraints excluded: chain 1 residue  374 LEU
Chi-restraints excluded: chain 1 residue  438 HIS
Chi-restraints excluded: chain 1 residue  501 LEU
Chi-restraints excluded: chain 1 residue  510 VAL
Chi-restraints excluded: chain 1 residue  549 MET
Chi-restraints excluded: chain 1 residue  859 VAL
Chi-restraints excluded: chain 1 residue 1010 ARG
Chi-restraints excluded: chain 1 residue 1027 TYR
Chi-restraints excluded: chain 1 residue 1099 THR
Chi-restraints excluded: chain 1 residue 1109 SER
Chi-restraints excluded: chain 1 residue 1113 VAL
Chi-restraints excluded: chain 1 residue 1339 LEU
Chi-restraints excluded: chain 1 residue 1387 THR
Chi-restraints excluded: chain 1 residue 1394 ASP
Chi-restraints excluded: chain 1 residue 1434 MET
Chi-restraints excluded: chain L residue    2 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   87 VAL
Chi-restraints excluded: chain L residue   91 PHE
Chi-restraints excluded: chain L residue  166 THR
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  207 ILE
Chi-restraints excluded: chain H residue   87 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 102 optimal weight:    6.9990
   chunk 85 optimal weight:    0.0670
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 108 optimal weight:    9.9990
   chunk 35 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 58 optimal weight:   10.0000
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.8520

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

Flipped N/Q/H residues before XYZ refinement:
1 190 GLN
** 1 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 654 ASN
** 1 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 924 GLN
11083 GLN
** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
11481 GLN
** 11510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 139 ASN
H 165 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.171211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.135477 restraints weight = 105485.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 5.58
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3940 r_free = 0.3940    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3940 r_free = 0.3940    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1274
moved from start:          0.7242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  14296  Z= 0.160
  Angle     :  0.763  11.859  19494  Z= 0.380
  Chirality :  0.052   1.132   2131
  Planarity :  0.006   0.055   2557
  Dihedral  :  5.739  25.765   1920
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 25.70
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.52 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 29.45 %
    Favored  : 67.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.20), residues: 1784
  helix: -0.75 (0.31), residues: 265
  sheet: -1.45 (0.25), residues: 387
  loop : -0.88 (0.19), residues: 1132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP 11334 
 HIS   0.009   0.001   HIS H 165 
 PHE   0.029   0.002   PHE 1 546 
 TYR   0.019   0.002   TYR L  34 
 ARG   0.006   0.001   ARG 11386 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03672 (  415)
  hydrogen bonds       : angle       7.14395 ( 1126)
  SS BOND              : bond        0.00482 (    4)
  SS BOND              : angle       0.54384 (    8)
  covalent geometry    : bond        0.00380 (14292)
  covalent geometry    : angle       0.76290 (19486)

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

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

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 97
  time to evaluate  : 1.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 1  307 LYS cc_start: 0.5307 (tttm) cc_final: 0.4446 (mmmt)
REVERT: 1  369 TRP cc_start: 0.3559 (m100) cc_final: 0.2457 (m100)
REVERT: 1  374 LEU cc_start: 0.1516 (OUTLIER) cc_final: 0.1115 (pp)
REVERT: 1  501 LEU cc_start: 0.2067 (OUTLIER) cc_final: 0.1351 (tt)
REVERT: 1  565 ASN cc_start: 0.0913 (p0) cc_final: 0.0354 (p0)
REVERT: 1  594 MET cc_start: 0.3350 (mpp) cc_final: 0.3032 (mpp)
REVERT: 1  768 GLN cc_start: 0.1512 (OUTLIER) cc_final: -0.1902 (mt0)
REVERT: 1  859 VAL cc_start: -0.0869 (OUTLIER) cc_final: -0.1229 (t)
REVERT: 1  907 GLN cc_start: 0.3659 (mm-40) cc_final: 0.3409 (mm110)
REVERT: 1 1377 MET cc_start: 0.1382 (mtm) cc_final: 0.1152 (mtm)
REVERT: L   12 LEU cc_start: 0.4122 (OUTLIER) cc_final: 0.3719 (tp)
REVERT: L   36 GLU cc_start: 0.7195 (mp0) cc_final: 0.6874 (mp0)
REVERT: L  207 ILE cc_start: 0.7095 (OUTLIER) cc_final: 0.6663 (tt)
REVERT: L  215 GLU cc_start: 0.3544 (mm-30) cc_final: 0.3280 (mm-30)
REVERT: H   75 MET cc_start: 0.2324 (ppp) cc_final: 0.1032 (tpt)
REVERT: H  136 MET cc_start: 0.6181 (ppp) cc_final: 0.5659 (tpp)
  outliers start: 39
  outliers final: 22
  residues processed: 127
  average time/residue: 1.0046
  time to fit residues: 145.7817
Evaluate side-chains
  119 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 91
  time to evaluate  : 1.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue   93 ARG
Chi-restraints excluded: chain 1 residue  221 GLN
Chi-restraints excluded: chain 1 residue  236 MET
Chi-restraints excluded: chain 1 residue  374 LEU
Chi-restraints excluded: chain 1 residue  438 HIS
Chi-restraints excluded: chain 1 residue  501 LEU
Chi-restraints excluded: chain 1 residue  510 VAL
Chi-restraints excluded: chain 1 residue  549 MET
Chi-restraints excluded: chain 1 residue  768 GLN
Chi-restraints excluded: chain 1 residue  859 VAL
Chi-restraints excluded: chain 1 residue 1027 TYR
Chi-restraints excluded: chain 1 residue 1099 THR
Chi-restraints excluded: chain 1 residue 1109 SER
Chi-restraints excluded: chain 1 residue 1113 VAL
Chi-restraints excluded: chain 1 residue 1339 LEU
Chi-restraints excluded: chain 1 residue 1387 THR
Chi-restraints excluded: chain 1 residue 1499 LEU
Chi-restraints excluded: chain L residue    2 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   18 ILE
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   87 VAL
Chi-restraints excluded: chain L residue  166 THR
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  207 ILE
Chi-restraints excluded: chain H residue   87 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 34 optimal weight:    7.9990
   chunk 121 optimal weight:    0.7980
   chunk 16 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0470
   chunk 47 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 115 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.7282

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

Flipped N/Q/H residues before XYZ refinement:
** 1 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.172533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.137214 restraints weight = 105720.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3965 rms_B_bonded: 5.64
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3964
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3964 r_free = 0.3964    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3964 r_free = 0.3964    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3964
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1268
moved from start:          0.7615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14296  Z= 0.151
  Angle     :  0.747  13.788  19494  Z= 0.372
  Chirality :  0.049   0.901   2131
  Planarity :  0.005   0.054   2557
  Dihedral  :  5.594  25.419   1920
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 23.43
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.46 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 29.19 %
    Favored  : 67.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.20), residues: 1784
  helix: -0.60 (0.30), residues: 277
  sheet: -1.28 (0.25), residues: 378
  loop : -0.85 (0.19), residues: 1129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  41 
 HIS   0.007   0.001   HIS 11423 
 PHE   0.027   0.002   PHE 11516 
 TYR   0.019   0.002   TYR L  34 
 ARG   0.007   0.001   ARG L  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03569 (  415)
  hydrogen bonds       : angle       7.02936 ( 1126)
  SS BOND              : bond        0.00524 (    4)
  SS BOND              : angle       0.55764 (    8)
  covalent geometry    : bond        0.00356 (14292)
  covalent geometry    : angle       0.74659 (19486)

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

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

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 106
  time to evaluate  : 1.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 1  236 MET cc_start: 0.0832 (OUTLIER) cc_final: -0.3845 (tpt)
REVERT: 1  307 LYS cc_start: 0.5296 (tttm) cc_final: 0.4450 (mmmt)
REVERT: 1  369 TRP cc_start: 0.3484 (m100) cc_final: 0.2467 (m100)
REVERT: 1  374 LEU cc_start: 0.1617 (OUTLIER) cc_final: 0.1236 (pp)
REVERT: 1  501 LEU cc_start: 0.1832 (OUTLIER) cc_final: 0.0979 (tm)
REVERT: 1  565 ASN cc_start: 0.0794 (p0) cc_final: 0.0550 (p0)
REVERT: 1  594 MET cc_start: 0.3305 (mpp) cc_final: 0.3097 (mpp)
REVERT: 1  768 GLN cc_start: 0.1534 (OUTLIER) cc_final: -0.2107 (mt0)
REVERT: 1  859 VAL cc_start: -0.1054 (OUTLIER) cc_final: -0.1352 (t)
REVERT: 1  907 GLN cc_start: 0.3677 (mm-40) cc_final: 0.3429 (mm110)
REVERT: 1 1377 MET cc_start: 0.1429 (mtm) cc_final: 0.1208 (mtm)
REVERT: 1 1439 GLN cc_start: 0.5199 (pm20) cc_final: 0.4387 (pt0)
REVERT: 1 1473 ARG cc_start: 0.3123 (OUTLIER) cc_final: 0.1163 (ttm170)
REVERT: L   12 LEU cc_start: 0.3904 (OUTLIER) cc_final: 0.3516 (tp)
REVERT: L   36 GLU cc_start: 0.7247 (mp0) cc_final: 0.6882 (mp0)
REVERT: L  207 ILE cc_start: 0.7123 (OUTLIER) cc_final: 0.6684 (tt)
REVERT: L  215 GLU cc_start: 0.3543 (mm-30) cc_final: 0.3269 (mm-30)
REVERT: H   28 MET cc_start: 0.3102 (ppp) cc_final: 0.2510 (pmm)
REVERT: H   75 MET cc_start: 0.2170 (ppp) cc_final: 0.1120 (tpt)
REVERT: H  136 MET cc_start: 0.6169 (ppp) cc_final: 0.5712 (tpp)
  outliers start: 41
  outliers final: 27
  residues processed: 138
  average time/residue: 0.8624
  time to fit residues: 138.0869
Evaluate side-chains
  133 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 98
  time to evaluate  : 1.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue   93 ARG
Chi-restraints excluded: chain 1 residue  146 LEU
Chi-restraints excluded: chain 1 residue  221 GLN
Chi-restraints excluded: chain 1 residue  236 MET
Chi-restraints excluded: chain 1 residue  374 LEU
Chi-restraints excluded: chain 1 residue  399 MET
Chi-restraints excluded: chain 1 residue  438 HIS
Chi-restraints excluded: chain 1 residue  501 LEU
Chi-restraints excluded: chain 1 residue  510 VAL
Chi-restraints excluded: chain 1 residue  549 MET
Chi-restraints excluded: chain 1 residue  768 GLN
Chi-restraints excluded: chain 1 residue  859 VAL
Chi-restraints excluded: chain 1 residue 1010 ARG
Chi-restraints excluded: chain 1 residue 1027 TYR
Chi-restraints excluded: chain 1 residue 1099 THR
Chi-restraints excluded: chain 1 residue 1109 SER
Chi-restraints excluded: chain 1 residue 1113 VAL
Chi-restraints excluded: chain 1 residue 1339 LEU
Chi-restraints excluded: chain 1 residue 1387 THR
Chi-restraints excluded: chain 1 residue 1444 PHE
Chi-restraints excluded: chain 1 residue 1473 ARG
Chi-restraints excluded: chain 1 residue 1499 LEU
Chi-restraints excluded: chain L residue    2 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   18 ILE
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   87 VAL
Chi-restraints excluded: chain L residue  106 LEU
Chi-restraints excluded: chain L residue  166 THR
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  207 ILE
Chi-restraints excluded: chain H residue   87 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 102 optimal weight:   10.0000
   chunk 40 optimal weight:    0.5980
   chunk 139 optimal weight:    0.7980
   chunk 6 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 74 optimal weight:    9.9990
   chunk 96 optimal weight:    9.9990
   chunk 156 optimal weight:    0.3980
   chunk 146 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** 1 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
11208 ASN
** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11510 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 = 0.4456 r_free = 0.4456 target = 0.174915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.139164 restraints weight = 112496.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 5.92
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3997
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3997 r_free = 0.3997    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3997 r_free = 0.3997    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3997
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1337
moved from start:          0.7997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14296  Z= 0.157
  Angle     :  0.764  13.985  19494  Z= 0.380
  Chirality :  0.048   0.683   2131
  Planarity :  0.006   0.081   2557
  Dihedral  :  5.604  25.842   1920
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 24.53
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.52 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 30.43 %
    Favored  : 67.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.19), residues: 1784
  helix: -0.63 (0.30), residues: 282
  sheet: -1.30 (0.25), residues: 373
  loop : -0.90 (0.19), residues: 1129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP 1 704 
 HIS   0.005   0.001   HIS 1 393 
 PHE   0.027   0.002   PHE L 141 
 TYR   0.016   0.002   TYR 1 728 
 ARG   0.007   0.001   ARG L  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03591 (  415)
  hydrogen bonds       : angle       7.00547 ( 1126)
  SS BOND              : bond        0.00568 (    4)
  SS BOND              : angle       0.50231 (    8)
  covalent geometry    : bond        0.00366 (14292)
  covalent geometry    : angle       0.76412 (19486)

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

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

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3568 Ramachandran restraints generated.
    1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 103
  time to evaluate  : 1.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 1  307 LYS cc_start: 0.5400 (tttm) cc_final: 0.4526 (mmmt)
REVERT: 1  369 TRP cc_start: 0.3448 (m100) cc_final: 0.2478 (m100)
REVERT: 1  374 LEU cc_start: 0.1727 (OUTLIER) cc_final: 0.1339 (pp)
REVERT: 1  501 LEU cc_start: 0.2245 (OUTLIER) cc_final: 0.1366 (tm)
REVERT: 1  594 MET cc_start: 0.3714 (mpp) cc_final: 0.3483 (mpp)
REVERT: 1  768 GLN cc_start: 0.1679 (OUTLIER) cc_final: -0.2248 (mt0)
REVERT: 1  859 VAL cc_start: -0.0926 (OUTLIER) cc_final: -0.1309 (t)
REVERT: 1  907 GLN cc_start: 0.3721 (mm-40) cc_final: 0.3478 (mm110)
REVERT: 1 1377 MET cc_start: 0.1527 (mtm) cc_final: 0.1279 (mtm)
REVERT: 1 1439 GLN cc_start: 0.5074 (pm20) cc_final: 0.4344 (pt0)
REVERT: L   12 LEU cc_start: 0.3816 (OUTLIER) cc_final: 0.3446 (tp)
REVERT: L   36 GLU cc_start: 0.7272 (mp0) cc_final: 0.6926 (mp0)
REVERT: L   47 LYS cc_start: 0.5334 (mmtp) cc_final: 0.5079 (mmtp)
REVERT: L  207 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6739 (tt)
REVERT: L  215 GLU cc_start: 0.3542 (mm-30) cc_final: 0.3253 (mm-30)
REVERT: H   28 MET cc_start: 0.3237 (ppp) cc_final: 0.2555 (pmm)
REVERT: H   75 MET cc_start: 0.2251 (ppp) cc_final: 0.1050 (tpp)
REVERT: H  136 MET cc_start: 0.6181 (ppp) cc_final: 0.5768 (tpp)
  outliers start: 31
  outliers final: 23
  residues processed: 126
  average time/residue: 0.9797
  time to fit residues: 141.4421
Evaluate side-chains
  130 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 1.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  221 GLN
Chi-restraints excluded: chain 1 residue  236 MET
Chi-restraints excluded: chain 1 residue  374 LEU
Chi-restraints excluded: chain 1 residue  438 HIS
Chi-restraints excluded: chain 1 residue  501 LEU
Chi-restraints excluded: chain 1 residue  510 VAL
Chi-restraints excluded: chain 1 residue  549 MET
Chi-restraints excluded: chain 1 residue  653 HIS
Chi-restraints excluded: chain 1 residue  768 GLN
Chi-restraints excluded: chain 1 residue  859 VAL
Chi-restraints excluded: chain 1 residue 1010 ARG
Chi-restraints excluded: chain 1 residue 1027 TYR
Chi-restraints excluded: chain 1 residue 1099 THR
Chi-restraints excluded: chain 1 residue 1109 SER
Chi-restraints excluded: chain 1 residue 1113 VAL
Chi-restraints excluded: chain 1 residue 1339 LEU
Chi-restraints excluded: chain 1 residue 1387 THR
Chi-restraints excluded: chain 1 residue 1499 LEU
Chi-restraints excluded: chain L residue    2 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   18 ILE
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   87 VAL
Chi-restraints excluded: chain L residue  166 THR
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  207 ILE
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   87 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 126 optimal weight:   10.0000
   chunk 172 optimal weight:    0.2980
   chunk 78 optimal weight:    7.9990
   chunk 64 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   chunk 157 optimal weight:    8.9990
   chunk 132 optimal weight:    6.9990
   chunk 25 optimal weight:    9.9990
   chunk 108 optimal weight:    0.3980
   chunk 52 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** 1 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
11105 ASN
11418 ASN
** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 212 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.176162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.140916 restraints weight = 104929.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.4022 rms_B_bonded: 5.70
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4021 r_free = 0.4021    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4021 r_free = 0.4021    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1334
moved from start:          0.8235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  14296  Z= 0.152
  Angle     :  0.761  16.018  19494  Z= 0.378
  Chirality :  0.048   0.662   2131
  Planarity :  0.006   0.079   2557
  Dihedral  :  5.554  26.060   1920
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 23.73
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.24 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 29.97 %
    Favored  : 67.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.19), residues: 1784
  helix: -0.61 (0.30), residues: 282
  sheet: -1.28 (0.25), residues: 370
  loop : -0.90 (0.19), residues: 1132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP 1 704 
 HIS   0.005   0.001   HIS 1 393 
 PHE   0.024   0.002   PHE L 211 
 TYR   0.015   0.002   TYR 1 728 
 ARG   0.007   0.001   ARG L  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03586 (  415)
  hydrogen bonds       : angle       6.96710 ( 1126)
  SS BOND              : bond        0.00674 (    4)
  SS BOND              : angle       0.72975 (    8)
  covalent geometry    : bond        0.00361 (14292)
  covalent geometry    : angle       0.76058 (19486)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11109.99 seconds
wall clock time: 195 minutes 14.08 seconds (11714.08 seconds total)