Starting phenix.real_space_refine
on Thu Sep 18 04:33:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ror_19402/09_2025/8ror_19402.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ror_19402/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ror_19402/09_2025/8ror_19402.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ror_19402/09_2025/8ror_19402.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ror_19402/09_2025/8ror_19402.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ror_19402/09_2025/8ror_19402.map"
  }
  resolution = 2.39
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 5.53, per 1000 atoms: 0.39
  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: 1.45
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.76
  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: 3.87

  Time building geometry restraints manager: 1.89 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:             4.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     19.770
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.040
  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:8.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.570
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (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
 ARG   0.009   0.001   ARG 1 136 
 TYR   0.031   0.002   TYR L  51 
 PHE   0.023   0.002   PHE 1 488 
 TRP   0.018   0.002   TRP 1 709 
 HIS   0.005   0.001   HIS 1 515 

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

*********************** 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  : 0.643 
Fit side-chains
   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 1422 THR cc_start: 0.6717 (p) cc_final: 0.6508 (t)
REVERT: 1 1482 ASP cc_start: 0.0005 (OUTLIER) cc_final: -0.0407 (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: 0.5507
  time to fit residues: 123.8419
Evaluate side-chains
  83 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.4980
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    5.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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**
1 428 GLN
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**
** 11418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
11494 ASN
11507 GLN
11510 GLN
L  40 GLN
L 191 HIS
H 165 HIS
** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.150732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.112146 restraints weight = 89886.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 4.66
r_work: 0.3444 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3463
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    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 = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3462
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0615
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  14296  Z= 0.202
  Angle     :  0.775  13.196  19494  Z= 0.394
  Chirality :  0.046   0.182   2131
  Planarity :  0.006   0.060   2557
  Dihedral  :  5.960  45.481   1931
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 29.38
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.49 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 26.90 %
    Favored  : 67.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.19 (0.20), residues: 1784
  helix: -0.51 (0.31), residues: 251
  sheet: -1.59 (0.26), residues: 350
  loop : -0.54 (0.19), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG 11386 
 TYR   0.024   0.002   TYR L 142 
 PHE   0.024   0.002   PHE L  57 
 TRP   0.019   0.002   TRP 1 407 
 HIS   0.009   0.002   HIS 1 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (14292)
  covalent geometry    : angle       0.77428 (19486)
  SS BOND              : bond        0.00605 (    4)
  SS BOND              : angle       1.50069 (    8)
  hydrogen bonds       : bond        0.04728 (  415)
  hydrogen bonds       : angle       7.88526 ( 1126)

*********************** 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
  173 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 98
  time to evaluate  : 0.565 
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: 0.3791 (tttm) cc_final: 0.3322 (mmmt)
REVERT: 1 1087 SER cc_start: 0.0291 (OUTLIER) cc_final: -0.0412 (p)
REVERT: 1 1338 GLN cc_start: 0.2355 (mp10) cc_final: 0.1929 (mp10)
REVERT: 1 1427 ASP cc_start: -0.1874 (OUTLIER) cc_final: -0.2433 (t70)
REVERT: 1 1456 VAL cc_start: -0.2409 (OUTLIER) cc_final: -0.2878 (p)
REVERT: 1 1482 ASP cc_start: 0.0145 (OUTLIER) cc_final: -0.0167 (p0)
REVERT: L   12 LEU cc_start: 0.4634 (OUTLIER) cc_final: 0.4399 (mp)
REVERT: L   38 TYR cc_start: 0.0930 (m-80) cc_final: 0.0652 (m-80)
REVERT: L   50 ILE cc_start: 0.2952 (OUTLIER) cc_final: 0.2707 (tp)
REVERT: L   69 SER cc_start: 0.4993 (OUTLIER) cc_final: 0.4752 (t)
REVERT: L   94 SER cc_start: 0.3924 (OUTLIER) cc_final: 0.2931 (m)
REVERT: L  107 GLU cc_start: 0.4838 (pm20) cc_final: 0.4357 (pm20)
REVERT: L  108 ILE cc_start: 0.5862 (OUTLIER) cc_final: 0.5573 (mm)
REVERT: L  188 TYR cc_start: 0.4988 (t80) cc_final: 0.4716 (t80)
REVERT: L  207 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6359 (tt)
REVERT: H  166 THR cc_start: 0.6510 (t) cc_final: 0.6108 (p)
  outliers start: 75
  outliers final: 22
  residues processed: 162
  average time/residue: 0.4328
  time to fit residues: 80.8725
Evaluate side-chains
  112 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 80
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
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 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   -1 VAL
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   94 SER
Chi-restraints excluded: chain L residue  106 LEU
Chi-restraints excluded: chain L residue  108 ILE
Chi-restraints excluded: chain L residue  146 ILE
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  207 ILE
Chi-restraints excluded: chain H residue   29 ASN
Chi-restraints excluded: chain H residue   64 LEU
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 109 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 97 optimal weight:    0.6980
   chunk 47 optimal weight:    3.9990
   chunk 101 optimal weight:    7.9990
   chunk 19 optimal weight:   20.0000
   chunk 83 optimal weight:    0.9980
   chunk 148 optimal weight:   10.0000
   chunk 107 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0770
   overall best weight:    1.3542

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

Flipped N/Q/H residues before XYZ refinement:
1 256 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
** 11101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
11265 ASN
11358 ASN
11373 ASN
** 11510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   0 GLN
H 172 GLN
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.158482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.120139 restraints weight = 90806.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 4.87
r_work: 0.3517 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3520
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3520 r_free = 0.3520    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3520 r_free = 0.3520    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3520
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0805
moved from start:          0.3564

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= 0.191
  Angle     :  0.757  11.189  19494  Z= 0.383
  Chirality :  0.047   0.256   2131
  Planarity :  0.006   0.078   2557
  Dihedral  :  5.913  43.357   1925
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 27.81
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.24 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 25.07 %
    Favored  : 69.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.24 (0.20), residues: 1784
  helix: -0.68 (0.31), residues: 256
  sheet: -1.40 (0.26), residues: 341
  loop : -0.64 (0.19), residues: 1187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG 1 527 
 TYR   0.018   0.002   TYR L 142 
 PHE   0.021   0.003   PHE 11127 
 TRP   0.017   0.002   TRP 1 665 
 HIS   0.007   0.002   HIS 11031 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 (14292)
  covalent geometry    : angle       0.75657 (19486)
  SS BOND              : bond        0.00606 (    4)
  SS BOND              : angle       0.96676 (    8)
  hydrogen bonds       : bond        0.04287 (  415)
  hydrogen bonds       : angle       7.62131 ( 1126)

*********************** 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
  174 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 101
  time to evaluate  : 0.525 
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: 0.4234 (tttm) cc_final: 0.3701 (mmmt)
REVERT: 1  768 GLN cc_start: 0.0143 (OUTLIER) cc_final: -0.0558 (mt0)
REVERT: 1 1338 GLN cc_start: 0.2309 (mp10) cc_final: 0.1743 (mp-120)
REVERT: 1 1434 MET cc_start: 0.3332 (mmm) cc_final: 0.2837 (tpp)
REVERT: 1 1456 VAL cc_start: -0.2437 (OUTLIER) cc_final: -0.2746 (p)
REVERT: 1 1493 PRO cc_start: -0.0021 (Cg_endo) cc_final: -0.0275 (Cg_exo)
REVERT: L   12 LEU cc_start: 0.4482 (OUTLIER) cc_final: 0.4100 (mp)
REVERT: L   50 ILE cc_start: 0.3317 (OUTLIER) cc_final: 0.2729 (tp)
REVERT: L   69 SER cc_start: 0.5487 (OUTLIER) cc_final: 0.5241 (t)
REVERT: L   79 ARG cc_start: 0.6958 (pmt170) cc_final: 0.6755 (pmm-80)
REVERT: L  107 GLU cc_start: 0.4472 (pm20) cc_final: 0.4192 (pm20)
REVERT: L  125 GLU cc_start: 0.6275 (pm20) cc_final: 0.5102 (tm-30)
REVERT: L  146 ILE cc_start: 0.4736 (tt) cc_final: 0.4521 (OUTLIER)
REVERT: L  188 TYR cc_start: 0.5129 (t80) cc_final: 0.4791 (t80)
  outliers start: 73
  outliers final: 24
  residues processed: 164
  average time/residue: 0.4728
  time to fit residues: 88.5845
Evaluate side-chains
  109 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 81
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  221 GLN
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  712 LYS
Chi-restraints excluded: chain 1 residue  768 GLN
Chi-restraints excluded: chain 1 residue  775 THR
Chi-restraints excluded: chain 1 residue  859 VAL
Chi-restraints excluded: chain 1 residue  940 ASP
Chi-restraints excluded: chain 1 residue  943 SER
Chi-restraints excluded: chain 1 residue 1027 TYR
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 1339 LEU
Chi-restraints excluded: chain 1 residue 1436 VAL
Chi-restraints excluded: chain 1 residue 1456 VAL
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   69 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   91 PHE
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain H residue   28 MET
Chi-restraints excluded: chain H residue   29 ASN
Chi-restraints excluded: chain H residue  111 THR
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 83 optimal weight:    9.9990
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 140 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0870
   chunk 149 optimal weight:   20.0000
   chunk 154 optimal weight:    0.0000
   overall best weight:    1.4168

-------------------------------------------------------------------------------
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**
** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
11510 GLN
L  95 HIS
L 212 ASN
** H   0 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 = 0.4251 r_free = 0.4251 target = 0.158038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.120465 restraints weight = 90859.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 4.88
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3745
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3745 r_free = 0.3745    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3745 r_free = 0.3745    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3745
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0984
moved from start:          0.4464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14296  Z= 0.180
  Angle     :  0.757  13.206  19494  Z= 0.377
  Chirality :  0.047   0.200   2131
  Planarity :  0.006   0.091   2557
  Dihedral  :  5.793  25.803   1921
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 27.56
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.69 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 26.57 %
    Favored  : 69.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.20), residues: 1784
  helix: -0.66 (0.31), residues: 257
  sheet: -1.30 (0.26), residues: 346
  loop : -0.76 (0.19), residues: 1181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG 11457 
 TYR   0.017   0.002   TYR 1 728 
 PHE   0.029   0.003   PHE 11498 
 TRP   0.016   0.002   TRP 1 540 
 HIS   0.007   0.002   HIS 1 393 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (14292)
  covalent geometry    : angle       0.75705 (19486)
  SS BOND              : bond        0.00638 (    4)
  SS BOND              : angle       1.07584 (    8)
  hydrogen bonds       : bond        0.03990 (  415)
  hydrogen bonds       : angle       7.38855 ( 1126)

*********************** 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
  143 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 96
  time to evaluate  : 0.570 
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   93 ARG cc_start: 0.3656 (ptt180) cc_final: 0.2712 (ptt180)
REVERT: 1  307 LYS cc_start: 0.4709 (tttm) cc_final: 0.4078 (mmmt)
REVERT: 1 1434 MET cc_start: 0.3174 (mmm) cc_final: 0.2514 (tpp)
REVERT: 1 1456 VAL cc_start: -0.2260 (OUTLIER) cc_final: -0.2516 (p)
REVERT: 1 1493 PRO cc_start: 0.0028 (Cg_endo) cc_final: -0.0324 (Cg_exo)
REVERT: L   12 LEU cc_start: 0.4036 (OUTLIER) cc_final: 0.3765 (tp)
REVERT: L  108 ILE cc_start: 0.5812 (OUTLIER) cc_final: 0.5508 (mp)
REVERT: L  188 TYR cc_start: 0.5238 (t80) cc_final: 0.5006 (t80)
REVERT: H   29 ASN cc_start: -0.0871 (OUTLIER) cc_final: -0.1349 (m110)
REVERT: H   77 LEU cc_start: 0.4589 (OUTLIER) cc_final: 0.3999 (tm)
  outliers start: 47
  outliers final: 22
  residues processed: 138
  average time/residue: 0.4285
  time to fit residues: 68.8782
Evaluate side-chains
  112 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 85
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  221 GLN
Chi-restraints excluded: chain 1 residue  356 TRP
Chi-restraints excluded: chain 1 residue  419 ASP
Chi-restraints excluded: chain 1 residue  427 LEU
Chi-restraints excluded: chain 1 residue  640 LEU
Chi-restraints excluded: chain 1 residue  712 LYS
Chi-restraints excluded: chain 1 residue  953 ASP
Chi-restraints excluded: chain 1 residue 1109 SER
Chi-restraints excluded: chain 1 residue 1113 VAL
Chi-restraints excluded: chain 1 residue 1297 THR
Chi-restraints excluded: chain 1 residue 1339 LEU
Chi-restraints excluded: chain 1 residue 1353 LEU
Chi-restraints excluded: chain 1 residue 1436 VAL
Chi-restraints excluded: chain 1 residue 1456 VAL
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   91 PHE
Chi-restraints excluded: chain L residue  108 ILE
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain H residue   28 MET
Chi-restraints excluded: chain H residue   29 ASN
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   61 THR
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue  113 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 101 optimal weight:    0.0470
   chunk 14 optimal weight:    2.9990
   chunk 161 optimal weight:    1.9990
   chunk 123 optimal weight:   20.0000
   chunk 148 optimal weight:    7.9990
   chunk 122 optimal weight:    5.9990
   chunk 119 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0970
   overall best weight:    1.2080

-------------------------------------------------------------------------------
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**
** 1 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 611 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**
11494 ASN
L  24 GLN
** H   0 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 = 0.4304 r_free = 0.4304 target = 0.164922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.127797 restraints weight = 100402.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 5.20
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3788 r_free = 0.3788    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3788 r_free = 0.3788    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1034
moved from start:          0.5198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  14296  Z= 0.166
  Angle     :  0.728  11.636  19494  Z= 0.366
  Chirality :  0.045   0.162   2131
  Planarity :  0.005   0.051   2557
  Dihedral  :  5.691  26.021   1920
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 26.35
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.89 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 26.44 %
    Favored  : 69.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.38 (0.20), residues: 1784
  helix: -0.63 (0.31), residues: 256
  sheet: -1.33 (0.25), residues: 370
  loop : -0.80 (0.19), residues: 1158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG 11386 
 TYR   0.024   0.002   TYR H  88 
 PHE   0.034   0.002   PHE 11498 
 TRP   0.024   0.002   TRP 11334 
 HIS   0.006   0.001   HIS L  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (14292)
  covalent geometry    : angle       0.72827 (19486)
  SS BOND              : bond        0.00642 (    4)
  SS BOND              : angle       0.98260 (    8)
  hydrogen bonds       : bond        0.03746 (  415)
  hydrogen bonds       : angle       7.16697 ( 1126)

*********************** 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
  155 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 102
  time to evaluate  : 0.581 
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   93 ARG cc_start: 0.3542 (ptt180) cc_final: 0.2652 (ptt180)
REVERT: 1  307 LYS cc_start: 0.4829 (tttm) cc_final: 0.4209 (mmmt)
REVERT: 1  549 MET cc_start: -0.0859 (ppp) cc_final: -0.2114 (pp-130)
REVERT: 1  768 GLN cc_start: 0.0693 (OUTLIER) cc_final: -0.1294 (mt0)
REVERT: 1 1456 VAL cc_start: -0.2045 (OUTLIER) cc_final: -0.2279 (p)
REVERT: 1 1473 ARG cc_start: 0.2670 (OUTLIER) cc_final: 0.1574 (ttt-90)
REVERT: L   12 LEU cc_start: 0.3744 (OUTLIER) cc_final: 0.3432 (tp)
REVERT: L  125 GLU cc_start: 0.6402 (pm20) cc_final: 0.5266 (tm-30)
REVERT: L  177 MET cc_start: 0.1385 (tmt) cc_final: 0.1127 (tmt)
REVERT: L  188 TYR cc_start: 0.5355 (t80) cc_final: 0.5114 (t80)
REVERT: L  207 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6667 (tt)
REVERT: L  215 GLU cc_start: 0.3716 (mm-30) cc_final: 0.3429 (mm-30)
REVERT: H   29 ASN cc_start: -0.0927 (OUTLIER) cc_final: -0.1542 (m110)
REVERT: H  136 MET cc_start: 0.6226 (ppp) cc_final: 0.5524 (tpp)
  outliers start: 53
  outliers final: 27
  residues processed: 147
  average time/residue: 0.4845
  time to fit residues: 81.4660
Evaluate side-chains
  124 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 91
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  110 THR
Chi-restraints excluded: chain 1 residue  221 GLN
Chi-restraints excluded: chain 1 residue  533 THR
Chi-restraints excluded: chain 1 residue  640 LEU
Chi-restraints excluded: chain 1 residue  653 HIS
Chi-restraints excluded: chain 1 residue  712 LYS
Chi-restraints excluded: chain 1 residue  768 GLN
Chi-restraints excluded: chain 1 residue  859 VAL
Chi-restraints excluded: chain 1 residue  940 ASP
Chi-restraints excluded: chain 1 residue  943 SER
Chi-restraints excluded: chain 1 residue  953 ASP
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 1137 LEU
Chi-restraints excluded: chain 1 residue 1339 LEU
Chi-restraints excluded: chain 1 residue 1353 LEU
Chi-restraints excluded: chain 1 residue 1402 THR
Chi-restraints excluded: chain 1 residue 1436 VAL
Chi-restraints excluded: chain 1 residue 1456 VAL
Chi-restraints excluded: chain 1 residue 1473 ARG
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   50 ILE
Chi-restraints excluded: chain L residue  106 LEU
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  207 ILE
Chi-restraints excluded: chain H residue   28 MET
Chi-restraints excluded: chain H residue   29 ASN
Chi-restraints excluded: chain H residue   87 VAL
Chi-restraints excluded: chain H residue  113 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 137 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 111 optimal weight:   10.0000
   chunk 102 optimal weight:    8.9990
   chunk 113 optimal weight:    2.9990
   chunk 163 optimal weight:   10.0000
   chunk 88 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 150 optimal weight:    5.9990
   overall best weight:    1.3182

-------------------------------------------------------------------------------
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**
** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
11083 GLN
11116 GLN
** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  29 ASN
** H  33 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 = 0.4346 r_free = 0.4346 target = 0.168080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.131522 restraints weight = 94639.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 5.17
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3852 r_free = 0.3852    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3852 r_free = 0.3852    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1157
moved from start:          0.5856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  14296  Z= 0.176
  Angle     :  0.734  10.705  19494  Z= 0.369
  Chirality :  0.046   0.200   2131
  Planarity :  0.005   0.052   2557
  Dihedral  :  5.703  26.235   1920
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 26.24
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.75 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 26.70 %
    Favored  : 69.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.48 (0.20), residues: 1784
  helix: -0.69 (0.31), residues: 269
  sheet: -1.41 (0.25), residues: 365
  loop : -0.88 (0.19), residues: 1150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG 1  72 
 TYR   0.032   0.002   TYR L  34 
 PHE   0.021   0.002   PHE 11498 
 TRP   0.025   0.002   TRP 1 356 
 HIS   0.008   0.001   HIS 1 782 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (14292)
  covalent geometry    : angle       0.73358 (19486)
  SS BOND              : bond        0.00561 (    4)
  SS BOND              : angle       0.76393 (    8)
  hydrogen bonds       : bond        0.03693 (  415)
  hydrogen bonds       : angle       7.06726 ( 1126)

*********************** 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: 52
    poor density    : 103
  time to evaluate  : 0.631 
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  307 LYS cc_start: 0.4948 (tttm) cc_final: 0.4170 (mmmt)
REVERT: 1  453 LYS cc_start: 0.3278 (OUTLIER) cc_final: 0.2193 (tmtt)
REVERT: 1 1456 VAL cc_start: -0.1985 (OUTLIER) cc_final: -0.2235 (p)
REVERT: 1 1473 ARG cc_start: 0.2911 (OUTLIER) cc_final: 0.1434 (ttt-90)
REVERT: L   12 LEU cc_start: 0.3759 (OUTLIER) cc_final: 0.3418 (tp)
REVERT: L  177 MET cc_start: 0.1435 (tmt) cc_final: 0.1061 (tmt)
REVERT: L  188 TYR cc_start: 0.5420 (t80) cc_final: 0.5197 (t80)
REVERT: L  207 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6674 (tt)
REVERT: L  215 GLU cc_start: 0.3707 (mm-30) cc_final: 0.3383 (mm-30)
REVERT: H  136 MET cc_start: 0.6190 (ppp) cc_final: 0.5576 (tpp)
  outliers start: 52
  outliers final: 28
  residues processed: 145
  average time/residue: 0.4676
  time to fit residues: 77.5209
Evaluate side-chains
  123 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 90
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  221 GLN
Chi-restraints excluded: chain 1 residue  427 LEU
Chi-restraints excluded: chain 1 residue  453 LYS
Chi-restraints excluded: chain 1 residue  510 VAL
Chi-restraints excluded: chain 1 residue  533 THR
Chi-restraints excluded: chain 1 residue  640 LEU
Chi-restraints excluded: chain 1 residue  653 HIS
Chi-restraints excluded: chain 1 residue  712 LYS
Chi-restraints excluded: chain 1 residue  943 SER
Chi-restraints excluded: chain 1 residue  953 ASP
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 1353 LEU
Chi-restraints excluded: chain 1 residue 1402 THR
Chi-restraints excluded: chain 1 residue 1456 VAL
Chi-restraints excluded: chain 1 residue 1473 ARG
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   50 ILE
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   28 MET
Chi-restraints excluded: chain H residue   29 ASN
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue  113 SER
Chi-restraints excluded: chain H residue  197 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 175 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 102 optimal weight:    0.8980
   chunk 162 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 160 optimal weight:    6.9990
   chunk 164 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 136 optimal weight:   10.0000
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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**
** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
11023 GLN
11083 GLN
11116 GLN
** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  33 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 = 0.4386 r_free = 0.4386 target = 0.171785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.135751 restraints weight = 88972.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3906 rms_B_bonded: 5.12
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3904
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3904 r_free = 0.3904    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3904 r_free = 0.3904    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3904
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1277
moved from start:          0.6480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14296  Z= 0.176
  Angle     :  0.756  11.947  19494  Z= 0.382
  Chirality :  0.046   0.204   2131
  Planarity :  0.006   0.056   2557
  Dihedral  :  5.763  27.059   1920
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 27.19
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.75 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 27.75 %
    Favored  : 68.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.51 (0.19), residues: 1784
  helix: -0.65 (0.31), residues: 263
  sheet: -1.32 (0.25), residues: 376
  loop : -0.96 (0.19), residues: 1145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG 1  72 
 TYR   0.019   0.002   TYR 1 728 
 PHE   0.020   0.002   PHE 11498 
 TRP   0.020   0.003   TRP 11334 
 HIS   0.017   0.002   HIS H 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (14292)
  covalent geometry    : angle       0.75561 (19486)
  SS BOND              : bond        0.00484 (    4)
  SS BOND              : angle       0.69313 (    8)
  hydrogen bonds       : bond        0.03864 (  415)
  hydrogen bonds       : angle       7.11920 ( 1126)

*********************** 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
  152 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 102
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 1   89 TRP cc_start: 0.0163 (OUTLIER) cc_final: -0.0124 (m100)
REVERT: 1  307 LYS cc_start: 0.4940 (tttm) cc_final: 0.4246 (mmmt)
REVERT: 1  369 TRP cc_start: 0.3658 (m100) cc_final: 0.2388 (m100)
REVERT: 1  453 LYS cc_start: 0.3587 (OUTLIER) cc_final: 0.2254 (tmtt)
REVERT: 1 1377 MET cc_start: 0.1354 (mtm) cc_final: 0.1053 (mtm)
REVERT: 1 1456 VAL cc_start: -0.1875 (OUTLIER) cc_final: -0.2086 (p)
REVERT: 1 1473 ARG cc_start: 0.2942 (OUTLIER) cc_final: 0.1530 (ttt-90)
REVERT: L   12 LEU cc_start: 0.3712 (OUTLIER) cc_final: 0.3375 (tp)
REVERT: L   36 GLU cc_start: 0.7294 (mp0) cc_final: 0.6902 (mp0)
REVERT: L   79 ARG cc_start: 0.6906 (pmm-80) cc_final: 0.6608 (mpp80)
REVERT: L  177 MET cc_start: 0.1642 (tmt) cc_final: 0.1333 (tmt)
REVERT: L  188 TYR cc_start: 0.5467 (t80) cc_final: 0.5242 (t80)
REVERT: L  207 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6697 (tt)
REVERT: L  215 GLU cc_start: 0.3651 (mm-30) cc_final: 0.3434 (mm-30)
REVERT: H   75 MET cc_start: 0.2613 (ppp) cc_final: -0.0189 (tpt)
REVERT: H  136 MET cc_start: 0.6145 (ppp) cc_final: 0.5566 (tpp)
REVERT: H  214 ARG cc_start: -0.0544 (OUTLIER) cc_final: -0.1908 (ptp90)
  outliers start: 50
  outliers final: 23
  residues processed: 144
  average time/residue: 0.5211
  time to fit residues: 84.5784
Evaluate side-chains
  121 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 91
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue   89 TRP
Chi-restraints excluded: chain 1 residue  221 GLN
Chi-restraints excluded: chain 1 residue  438 HIS
Chi-restraints excluded: chain 1 residue  453 LYS
Chi-restraints excluded: chain 1 residue  510 VAL
Chi-restraints excluded: chain 1 residue  640 LEU
Chi-restraints excluded: chain 1 residue  653 HIS
Chi-restraints excluded: chain 1 residue  712 LYS
Chi-restraints excluded: chain 1 residue  953 ASP
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 1394 ASP
Chi-restraints excluded: chain 1 residue 1402 THR
Chi-restraints excluded: chain 1 residue 1456 VAL
Chi-restraints excluded: chain 1 residue 1473 ARG
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   29 SER
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   49 LEU
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   54 TYR
Chi-restraints excluded: chain H residue   87 VAL
Chi-restraints excluded: chain H residue  113 SER
Chi-restraints excluded: chain H residue  214 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 115 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 120 optimal weight:    0.0770
   chunk 41 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 146 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 60 optimal weight:    6.9990
   overall best weight:    0.9142

-------------------------------------------------------------------------------
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**
** 1 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 964 ASN
** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
11481 GLN
** L 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  33 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 = 0.4406 r_free = 0.4406 target = 0.173181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.136898 restraints weight = 99529.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3924 rms_B_bonded: 5.42
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3925
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3925 r_free = 0.3925    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3925 r_free = 0.3925    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3925
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1232
moved from start:          0.6829

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= 0.158
  Angle     :  0.736  11.593  19494  Z= 0.373
  Chirality :  0.046   0.177   2131
  Planarity :  0.006   0.057   2557
  Dihedral  :  5.664  28.371   1920
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 25.66
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.20 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 28.34 %
    Favored  : 68.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.19), residues: 1784
  helix: -0.72 (0.30), residues: 278
  sheet: -1.32 (0.25), residues: 390
  loop : -0.97 (0.19), residues: 1116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG 11419 
 TYR   0.018   0.002   TYR 1 728 
 PHE   0.032   0.002   PHE 1 677 
 TRP   0.019   0.002   TRP L  37 
 HIS   0.015   0.001   HIS H 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (14292)
  covalent geometry    : angle       0.73558 (19486)
  SS BOND              : bond        0.00647 (    4)
  SS BOND              : angle       0.91440 (    8)
  hydrogen bonds       : bond        0.03861 (  415)
  hydrogen bonds       : angle       7.05320 ( 1126)

*********************** 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
  135 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 97
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 1   89 TRP cc_start: 0.0019 (OUTLIER) cc_final: -0.0257 (m100)
REVERT: 1  307 LYS cc_start: 0.4912 (tttm) cc_final: 0.4140 (mmmt)
REVERT: 1  453 LYS cc_start: 0.3353 (OUTLIER) cc_final: 0.2128 (tmtt)
REVERT: 1 1377 MET cc_start: 0.1345 (mtm) cc_final: 0.1097 (mtm)
REVERT: 1 1473 ARG cc_start: 0.2784 (OUTLIER) cc_final: 0.1429 (ttm170)
REVERT: L   12 LEU cc_start: 0.3548 (OUTLIER) cc_final: 0.3210 (tp)
REVERT: L   79 ARG cc_start: 0.6802 (pmm-80) cc_final: 0.6473 (mpp80)
REVERT: L  177 MET cc_start: 0.1699 (tmt) cc_final: 0.1347 (tmt)
REVERT: L  188 TYR cc_start: 0.5438 (t80) cc_final: 0.5196 (t80)
REVERT: L  207 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6681 (tt)
REVERT: L  215 GLU cc_start: 0.3633 (mm-30) cc_final: 0.3396 (mm-30)
REVERT: H   75 MET cc_start: 0.2266 (ppp) cc_final: 0.0057 (tpt)
REVERT: H  136 MET cc_start: 0.6120 (ppp) cc_final: 0.5586 (tpp)
  outliers start: 38
  outliers final: 18
  residues processed: 131
  average time/residue: 0.5108
  time to fit residues: 75.7531
Evaluate side-chains
  115 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue   89 TRP
Chi-restraints excluded: chain 1 residue  221 GLN
Chi-restraints excluded: chain 1 residue  438 HIS
Chi-restraints excluded: chain 1 residue  453 LYS
Chi-restraints excluded: chain 1 residue  712 LYS
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 1473 ARG
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   50 ILE
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   64 LEU
Chi-restraints excluded: chain H residue   87 VAL
Chi-restraints excluded: chain H residue  113 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 128 optimal weight:    0.3980
   chunk 145 optimal weight:   10.0000
   chunk 157 optimal weight:    0.8980
   chunk 171 optimal weight:   20.0000
   chunk 22 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 133 optimal weight:    0.4980
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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**
** 1 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 924 GLN
** 11423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   0 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  56 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 = 0.4417 r_free = 0.4417 target = 0.173881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.138054 restraints weight = 98093.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 5.43
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3946 r_free = 0.3946    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3946 r_free = 0.3946    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1210
moved from start:          0.7193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  14296  Z= 0.150
  Angle     :  0.730  11.862  19494  Z= 0.369
  Chirality :  0.046   0.174   2131
  Planarity :  0.005   0.052   2557
  Dihedral  :  5.585  28.521   1920
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 23.40
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.41 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 29.06 %
    Favored  : 68.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.19), residues: 1784
  helix: -0.58 (0.30), residues: 280
  sheet: -1.37 (0.25), residues: 386
  loop : -0.93 (0.19), residues: 1118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG 11473 
 TYR   0.021   0.002   TYR 1 542 
 PHE   0.032   0.002   PHE 11476 
 TRP   0.027   0.002   TRP L  37 
 HIS   0.004   0.001   HIS 1 653 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (14292)
  covalent geometry    : angle       0.72978 (19486)
  SS BOND              : bond        0.00648 (    4)
  SS BOND              : angle       1.00166 (    8)
  hydrogen bonds       : bond        0.03669 (  415)
  hydrogen bonds       : angle       6.97809 ( 1126)

*********************** 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
  133 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.571 
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: 0.4882 (tttm) cc_final: 0.4124 (mmmt)
REVERT: 1  453 LYS cc_start: 0.3213 (OUTLIER) cc_final: 0.2121 (tmtt)
REVERT: 1  565 ASN cc_start: 0.0670 (p0) cc_final: 0.0158 (p0)
REVERT: 1  574 MET cc_start: 0.1923 (mpt) cc_final: 0.1378 (mpt)
REVERT: 1 1468 GLN cc_start: 0.1691 (mm-40) cc_final: 0.1479 (pm20)
REVERT: L    1 MET cc_start: 0.4813 (ttp) cc_final: 0.4221 (mmm)
REVERT: L   12 LEU cc_start: 0.3512 (OUTLIER) cc_final: 0.3139 (tp)
REVERT: L   36 GLU cc_start: 0.7391 (mp0) cc_final: 0.7110 (pm20)
REVERT: L   79 ARG cc_start: 0.6885 (pmm-80) cc_final: 0.6574 (mpp80)
REVERT: L  177 MET cc_start: 0.1803 (tmt) cc_final: 0.1368 (tmt)
REVERT: L  188 TYR cc_start: 0.5586 (t80) cc_final: 0.5343 (t80)
REVERT: L  207 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6729 (tt)
REVERT: L  215 GLU cc_start: 0.3642 (mm-30) cc_final: 0.3315 (mm-30)
REVERT: H   67 ASP cc_start: 0.4913 (t0) cc_final: 0.4456 (t0)
REVERT: H   75 MET cc_start: 0.2108 (ppp) cc_final: 0.0208 (tpt)
REVERT: H  136 MET cc_start: 0.6110 (ppp) cc_final: 0.5642 (tpp)
  outliers start: 29
  outliers final: 17
  residues processed: 131
  average time/residue: 0.4979
  time to fit residues: 74.2135
Evaluate side-chains
  120 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  221 GLN
Chi-restraints excluded: chain 1 residue  438 HIS
Chi-restraints excluded: chain 1 residue  453 LYS
Chi-restraints excluded: chain 1 residue  712 LYS
Chi-restraints excluded: chain 1 residue  943 SER
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 L residue   12 LEU
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   39 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   64 LEU
Chi-restraints excluded: chain H residue   87 VAL
Chi-restraints excluded: chain H residue  113 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 128 optimal weight:    0.8980
   chunk 107 optimal weight:   10.0000
   chunk 43 optimal weight:    0.8980
   chunk 85 optimal weight:    0.3980
   chunk 170 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9980
   chunk 116 optimal weight:    0.9980
   chunk 138 optimal weight:    1.9990
   chunk 119 optimal weight:   10.0000
   chunk 89 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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**
** 1 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
11418 ASN
** H  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  56 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 = 0.4442 r_free = 0.4442 target = 0.176071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.140483 restraints weight = 89546.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 5.26
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3980
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3980 r_free = 0.3980    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3980 r_free = 0.3980    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3980
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1263
moved from start:          0.7542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14296  Z= 0.149
  Angle     :  0.729  11.601  19494  Z= 0.370
  Chirality :  0.046   0.212   2131
  Planarity :  0.006   0.052   2557
  Dihedral  :  5.530  28.430   1920
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 22.67
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.69 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 29.78 %
    Favored  : 68.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.45 (0.19), residues: 1784
  helix: -0.47 (0.31), residues: 280
  sheet: -1.45 (0.24), residues: 385
  loop : -0.87 (0.19), residues: 1119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG 1  72 
 TYR   0.025   0.002   TYR 11134 
 PHE   0.034   0.002   PHE 11476 
 TRP   0.020   0.002   TRP L  37 
 HIS   0.004   0.001   HIS 1 653 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (14292)
  covalent geometry    : angle       0.72851 (19486)
  SS BOND              : bond        0.00762 (    4)
  SS BOND              : angle       0.97411 (    8)
  hydrogen bonds       : bond        0.03644 (  415)
  hydrogen bonds       : angle       6.93960 ( 1126)

********************** 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
  127 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.545 
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: 0.5116 (tttm) cc_final: 0.4262 (mmmt)
REVERT: 1  453 LYS cc_start: 0.3271 (OUTLIER) cc_final: 0.2178 (tmtt)
REVERT: 1  565 ASN cc_start: 0.0813 (p0) cc_final: 0.0464 (p0)
REVERT: 1  574 MET cc_start: 0.1965 (mpt) cc_final: 0.1430 (mpt)
REVERT: 1 1134 TYR cc_start: 0.2302 (t80) cc_final: 0.1493 (t80)
REVERT: 1 1391 GLU cc_start: 0.4196 (tt0) cc_final: 0.3565 (tp30)
REVERT: 1 1468 GLN cc_start: 0.1652 (mm-40) cc_final: 0.1399 (pm20)
REVERT: 1 1473 ARG cc_start: 0.2637 (OUTLIER) cc_final: 0.1487 (ttt-90)
REVERT: L   12 LEU cc_start: 0.3577 (OUTLIER) cc_final: 0.3176 (tp)
REVERT: L   36 GLU cc_start: 0.7459 (mp0) cc_final: 0.7023 (pm20)
REVERT: L   79 ARG cc_start: 0.6870 (pmm-80) cc_final: 0.6560 (mpp80)
REVERT: L   91 PHE cc_start: 0.6014 (t80) cc_final: 0.5732 (t80)
REVERT: L  106 LEU cc_start: 0.4762 (tt) cc_final: 0.4484 (tp)
REVERT: L  177 MET cc_start: 0.1901 (tmt) cc_final: 0.1407 (tmt)
REVERT: L  188 TYR cc_start: 0.5671 (t80) cc_final: 0.5357 (t80)
REVERT: L  215 GLU cc_start: 0.3764 (mm-30) cc_final: 0.3400 (mm-30)
REVERT: H   12 MET cc_start: 0.3791 (pmm) cc_final: 0.3397 (ppp)
REVERT: H   75 MET cc_start: 0.1926 (ppp) cc_final: 0.0302 (tpp)
REVERT: H  136 MET cc_start: 0.6190 (ppp) cc_final: 0.5677 (tpp)
  outliers start: 23
  outliers final: 17
  residues processed: 125
  average time/residue: 0.4771
  time to fit residues: 68.1135
Evaluate side-chains
  119 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 1 residue  221 GLN
Chi-restraints excluded: chain 1 residue  438 HIS
Chi-restraints excluded: chain 1 residue  453 LYS
Chi-restraints excluded: chain 1 residue  510 VAL
Chi-restraints excluded: chain 1 residue  653 HIS
Chi-restraints excluded: chain 1 residue  712 LYS
Chi-restraints excluded: chain 1 residue  943 SER
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 1473 ARG
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue  166 THR
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain H residue   64 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 97 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 156 optimal weight:    9.9990
   chunk 50 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 74 optimal weight:   20.0000
   chunk 116 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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**
** 1 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 967 ASN
11208 ASN
L  44 GLN
** H  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4497 r_free = 0.4497 target = 0.178640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.143919 restraints weight = 100194.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.4055 rms_B_bonded: 5.57
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4055
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4055 r_free = 0.4055    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4054 r_free = 0.4054    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1498
moved from start:          0.8336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  14296  Z= 0.182
  Angle     :  0.788  11.592  19494  Z= 0.401
  Chirality :  0.047   0.183   2131
  Planarity :  0.006   0.051   2557
  Dihedral  :  5.886  29.583   1920
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 26.61
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.43 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 30.30 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.19), residues: 1784
  helix: -0.63 (0.31), residues: 269
  sheet: -1.49 (0.24), residues: 399
  loop : -0.92 (0.19), residues: 1116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L 157 
 TYR   0.019   0.002   TYR 1 728 
 PHE   0.024   0.003   PHE 11476 
 TRP   0.077   0.003   TRP 1 704 
 HIS   0.005   0.001   HIS 11241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (14292)
  covalent geometry    : angle       0.78775 (19486)
  SS BOND              : bond        0.00583 (    4)
  SS BOND              : angle       1.07279 (    8)
  hydrogen bonds       : bond        0.03841 (  415)
  hydrogen bonds       : angle       7.13821 ( 1126)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5842.60 seconds
wall clock time: 100 minutes 58.56 seconds (6058.56 seconds total)