Starting phenix.real_space_refine
on Fri Mar 14 01:45:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t13_40953/03_2025/8t13_40953.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t13_40953/03_2025/8t13_40953.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t13_40953/03_2025/8t13_40953.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t13_40953/03_2025/8t13_40953.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t13_40953/03_2025/8t13_40953.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t13_40953/03_2025/8t13_40953.cif"
  }
  resolution = 3.45
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.025
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: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      48      5.16       5
     C    5870      2.51       5
     N    1652      2.21       5
     O    1732      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9304
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2311
          Classifications: {'peptide': 290}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 10, 'TRANS': 279}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "B"
      Number of atoms: 6991
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 877, 6991
          Classifications: {'peptide': 877}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 30, 'TRANS': 846}
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8053  SG  CYS B 728      55.134  63.043 104.459  1.00118.78           S
  ATOM   9035  SG  CYS B 847      57.686  63.062 101.545  1.00140.61           S
  ATOM   5810  SG  CYS B 447      23.364  35.012 124.916  1.00116.02           S
  ATOM   5832  SG  CYS B 450      22.384  37.761 121.962  1.00119.26           S

  Time building chain proxies: 7.01, per 1000 atoms: 0.75
  Number of scatterers: 9304
  At special positions: 0
  Unit cell: (81.03, 96.57, 149.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      48     16.00
     O    1732      8.00
     N    1652      7.00
     C    5870      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.58
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B1001 "
        pdb="ZN    ZN B1001 " - pdb=" NE2 HIS B 712 "
        pdb="ZN    ZN B1001 " - pdb=" NE2 HIS B 714 "
        pdb="ZN    ZN B1001 " - pdb=" SG  CYS B 728 "
        pdb="ZN    ZN B1001 " - pdb=" SG  CYS B 847 "
      pdb="  ZN B1002 "
        pdb="ZN    ZN B1002 " - pdb=" NE2 HIS B 442 "
        pdb="ZN    ZN B1002 " - pdb=" SG  CYS B 450 "
        pdb="ZN    ZN B1002 " - pdb=" SG  CYS B 447 "
      Number of angles added : 2


  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2166

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 8 sheets defined
      49.4% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 140 through 184
      removed outlier: 4.054A  pdb=" N   LYS A 184 " --> pdb=" O   GLN A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 244
      removed outlier: 3.777A  pdb=" N   LEU A 214 " --> pdb=" O   ARG A 210 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ASP A 215 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ALA A 216 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU A 227 " --> pdb=" O   ARG A 223 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE A 228 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLU A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      Proline residue:  A 233  - end of helix
      removed outlier: 3.579A  pdb=" N   ALA A 240 " --> pdb=" O   GLU A 236 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLN A 241 " --> pdb=" O   GLU A 237 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN A 242 " --> pdb=" O   TRP A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 284
    Processing helix  chain 'A' and resid 292 through 315
      removed outlier: 5.130A  pdb=" N   ASP A 298 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ARG A 314 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 394
      removed outlier: 3.908A  pdb=" N   GLY A 391 " --> pdb=" O   THR A 387 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLN A 392 " --> pdb=" O   PRO A 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 19
    Processing helix  chain 'B' and resid 21 through 29
    Processing helix  chain 'B' and resid 40 through 48
      removed outlier: 3.515A  pdb=" N   GLY B  48 " --> pdb=" O   GLY B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 68
      removed outlier: 3.879A  pdb=" N   LYS B  61 " --> pdb=" O   ARG B  57 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ARG B  68 " --> pdb=" O   TRP B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 93
      removed outlier: 3.604A  pdb=" N   GLY B  93 " --> pdb=" O   TYR B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 122
      No H-bonds generated for 'chain 'B' and resid 120 through 122'
    Processing helix  chain 'B' and resid 131 through 135
      removed outlier: 3.574A  pdb=" N   PHE B 134 " --> pdb=" O   ASP B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 169
      removed outlier: 3.711A  pdb=" N   GLU B 157 " --> pdb=" O   ASN B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 202
      removed outlier: 5.099A  pdb=" N   LYS B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ALA B 196 " --> pdb=" O   GLU B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 243
      removed outlier: 3.748A  pdb=" N   SER B 231 " --> pdb=" O   ASN B 227 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   PHE B 243 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 288
      removed outlier: 3.646A  pdb=" N   ILE B 277 " --> pdb=" O   ASN B 273 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   LYS B 279 " --> pdb=" O   ASP B 275 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   ARG B 280 " --> pdb=" O   ILE B 276 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   HIS B 288 " --> pdb=" O   ILE B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 292
      removed outlier: 3.638A  pdb=" N   TRP B 292 " --> pdb=" O   GLU B 289 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 289 through 292'
    Processing helix  chain 'B' and resid 329 through 333
    Processing helix  chain 'B' and resid 335 through 341
    Processing helix  chain 'B' and resid 347 through 358
    Processing helix  chain 'B' and resid 367 through 386
    Processing helix  chain 'B' and resid 395 through 405
      removed outlier: 3.952A  pdb=" N   PHE B 399 " --> pdb=" O   THR B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 427
      removed outlier: 3.879A  pdb=" N   GLU B 427 " --> pdb=" O   ARG B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 443
    Processing helix  chain 'B' and resid 462 through 466
    Processing helix  chain 'B' and resid 478 through 490
    Processing helix  chain 'B' and resid 490 through 495
    Processing helix  chain 'B' and resid 511 through 513
      No H-bonds generated for 'chain 'B' and resid 511 through 513'
    Processing helix  chain 'B' and resid 514 through 523
    Processing helix  chain 'B' and resid 537 through 541
    Processing helix  chain 'B' and resid 543 through 551
    Processing helix  chain 'B' and resid 552 through 557
      removed outlier: 3.683A  pdb=" N   ASN B 555 " --> pdb=" O   MET B 552 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 558 through 572
    Processing helix  chain 'B' and resid 602 through 626
    Processing helix  chain 'B' and resid 639 through 655
      removed outlier: 5.839A  pdb=" N   ARG B 652 " --> pdb=" O   VAL B 648 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   GLU B 653 " --> pdb=" O   ARG B 649 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU B 655 " --> pdb=" O   GLY B 651 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 671 through 675
      removed outlier: 3.665A  pdb=" N   ALA B 675 " --> pdb=" O   ASP B 672 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 678 through 685
      removed outlier: 3.669A  pdb=" N   ASN B 682 " --> pdb=" O   LEU B 678 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY B 685 " --> pdb=" O   LEU B 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 730 through 739
      removed outlier: 3.558A  pdb=" N   LEU B 734 " --> pdb=" O   ASN B 730 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 748 through 759
    Processing helix  chain 'B' and resid 759 through 765
      removed outlier: 4.026A  pdb=" N   SER B 763 " --> pdb=" O   ALA B 759 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 769 through 783
      removed outlier: 3.679A  pdb=" N   LEU B 774 " --> pdb=" O   ARG B 770 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ALA B 775 " --> pdb=" O   ASP B 771 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA B 776 " --> pdb=" O   LEU B 772 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASN B 777 " --> pdb=" O   ARG B 773 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA B 778 " --> pdb=" O   LEU B 774 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ILE B 779 " --> pdb=" O   ALA B 775 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 801 through 805
      removed outlier: 3.923A  pdb=" N   MET B 804 " --> pdb=" O   HIS B 801 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   THR B 805 " --> pdb=" O   GLU B 802 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 801 through 805'
    Processing helix  chain 'B' and resid 808 through 818
      removed outlier: 3.664A  pdb=" N   VAL B 812 " --> pdb=" O   ASP B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 841 through 848
    Processing helix  chain 'B' and resid 854 through 859
      removed outlier: 3.884A  pdb=" N   THR B 858 " --> pdb=" O   THR B 854 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 867 through 873
    Processing sheet with id=AA1, first strand: chain 'A' and resid 316 through 323
      removed outlier: 5.030A  pdb=" N   VAL A 318 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   ARG A 345 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG A 343 " --> pdb=" O   THR A 320 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   THR A 341 " --> pdb=" O   PRO A 322 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   VAL A 342 " --> pdb=" O   GLY A 401 " (cutoff:3.500A)
      removed outlier: 5.097A  pdb=" N   GLY A 401 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   THR A 344 " --> pdb=" O   ASP A 399 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   ASP A 399 " --> pdb=" O   THR A 344 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   LEU A 346 " --> pdb=" O   ILE A 397 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ILE A 397 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335
      removed outlier: 6.137A  pdb=" N   LEU A 334 " --> pdb=" O   ILE A 456 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386
      removed outlier: 3.618A  pdb=" N   LYS A 384 " --> pdb=" O   VAL A 359 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL A 359 " --> pdb=" O   LYS A 384 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU A 357 " --> pdb=" O   LEU A 386 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   THR A 358 " --> pdb=" O   LYS A 436 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LYS A 436 " --> pdb=" O   THR A 358 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 34 through 36
      removed outlier: 6.729A  pdb=" N   GLU B  35 " --> pdb=" O   GLU B 253 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 127
      removed outlier: 9.019A  pdb=" N   ARG B 125 " --> pdb=" O   LYS B  98 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   VAL B 100 " --> pdb=" O   ARG B 125 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   GLN B 127 " --> pdb=" O   VAL B 100 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   GLY B 102 " --> pdb=" O   GLN B 127 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   GLY B  75 " --> pdb=" O   GLU B  99 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   LYS B 101 " --> pdb=" O   GLY B  75 " (cutoff:3.500A)
      removed outlier: 6.067A  pdb=" N   VAL B  77 " --> pdb=" O   LYS B 101 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   LEU B 103 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ASP B  79 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ALA B 204 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 310
      removed outlier: 3.659A  pdb=" N   ARG B 595 " --> pdb=" O   LYS B 576 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG B 579 " --> pdb=" O   TYR B 452 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   MET B 454 " --> pdb=" O   ARG B 579 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   GLN B 581 " --> pdb=" O   MET B 454 " (cutoff:3.500A)
      removed outlier: 9.236A  pdb=" N   GLY B 456 " --> pdb=" O   GLN B 581 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   MET B 455 " --> pdb=" O   ILE B 474 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE B 474 " --> pdb=" O   MET B 455 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 658 through 660
    Processing sheet with id=AA8, first strand: chain 'B' and resid 714 through 717
      removed outlier: 3.741A  pdb=" N   VAL B 726 " --> pdb=" O   HIS B 714 " (cutoff:3.500A)

    402 hydrogen bonds defined for protein.
    1155 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: 3.00

  Time building geometry restraints manager: 3.03 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3086
        1.34 -     1.46: 2133
        1.46 -     1.58: 4196
        1.58 -     1.70: 0
        1.70 -     1.82: 79
  Bond restraints: 9494
  Sorted by residual:
  bond pdb=" CB  ARG B 737 "
       pdb=" CG  ARG B 737 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.44e-01
  bond pdb=" CB  ILE B  33 "
       pdb=" CG1 ILE B  33 "
    ideal  model  delta    sigma   weight residual
    1.530  1.549 -0.019 2.00e-02 2.50e+03 8.64e-01
  bond pdb=" CB  MET B 455 "
       pdb=" CG  MET B 455 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.51e-01
  bond pdb=" C   VAL A 286 "
       pdb=" O   VAL A 286 "
    ideal  model  delta    sigma   weight residual
    1.236  1.226  0.010 1.19e-02 7.06e+03 6.96e-01
  bond pdb=" CA  TRP B 859 "
       pdb=" CB  TRP B 859 "
    ideal  model  delta    sigma   weight residual
    1.524  1.534 -0.010 1.31e-02 5.83e+03 6.31e-01
  ... (remaining 9489 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 12739
        2.29 -     4.58: 72
        4.58 -     6.88: 11
        6.88 -     9.17: 6
        9.17 -    11.46: 2
  Bond angle restraints: 12830
  Sorted by residual:
  angle pdb=" N   TRP B 859 "
        pdb=" CA  TRP B 859 "
        pdb=" C   TRP B 859 "
      ideal   model   delta    sigma   weight residual
     111.81  106.23    5.58 1.44e+00 4.82e-01 1.50e+01
  angle pdb=" CB  MET B 455 "
        pdb=" CG  MET B 455 "
        pdb=" SD  MET B 455 "
      ideal   model   delta    sigma   weight residual
     112.70  124.16  -11.46 3.00e+00 1.11e-01 1.46e+01
  angle pdb=" CA  TYR B 758 "
        pdb=" CB  TYR B 758 "
        pdb=" CG  TYR B 758 "
      ideal   model   delta    sigma   weight residual
     113.90  119.84   -5.94 1.80e+00 3.09e-01 1.09e+01
  angle pdb=" C   LYS B 689 "
        pdb=" N   ASP B 690 "
        pdb=" CA  ASP B 690 "
      ideal   model   delta    sigma   weight residual
     121.54  127.44   -5.90 1.91e+00 2.74e-01 9.55e+00
  angle pdb=" CA  ARG B 737 "
        pdb=" CB  ARG B 737 "
        pdb=" CG  ARG B 737 "
      ideal   model   delta    sigma   weight residual
     114.10  119.91   -5.81 2.00e+00 2.50e-01 8.43e+00
  ... (remaining 12825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4817
       17.95 -    35.90: 660
       35.90 -    53.86: 181
       53.86 -    71.81: 39
       71.81 -    89.76: 16
  Dihedral angle restraints: 5713
    sinusoidal: 2357
      harmonic: 3356
  Sorted by residual:
  dihedral pdb=" CA  TYR B 758 "
           pdb=" C   TYR B 758 "
           pdb=" N   ALA B 759 "
           pdb=" CA  ALA B 759 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.31   17.69     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  ASP B 664 "
           pdb=" CB  ASP B 664 "
           pdb=" CG  ASP B 664 "
           pdb=" OD1 ASP B 664 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.86   57.86     1      2.00e+01 2.50e-03 1.12e+01
  dihedral pdb=" CG  ARG B 579 "
           pdb=" CD  ARG B 579 "
           pdb=" NE  ARG B 579 "
           pdb=" CZ  ARG B 579 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.52   44.52     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 5710 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1044
       0.037 -    0.073: 269
       0.073 -    0.110: 81
       0.110 -    0.146: 12
       0.146 -    0.183: 2
  Chirality restraints: 1408
  Sorted by residual:
  chirality pdb=" CA  TYR B 758 "
            pdb=" N   TYR B 758 "
            pdb=" C   TYR B 758 "
            pdb=" CB  TYR B 758 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.35e-01
  chirality pdb=" CA  ASP B 690 "
            pdb=" N   ASP B 690 "
            pdb=" C   ASP B 690 "
            pdb=" CB  ASP B 690 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.43e-01
  chirality pdb=" CB  THR B 790 "
            pdb=" CA  THR B 790 "
            pdb=" OG1 THR B 790 "
            pdb=" CG2 THR B 790 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.48e-01
  ... (remaining 1405 not shown)

  Planarity restraints: 1640
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 347 "    0.021 5.00e-02 4.00e+02   3.14e-02 1.58e+00
        pdb=" N   PRO B 348 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 348 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 348 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 168 "    0.006 2.00e-02 2.50e+03   1.25e-02 1.55e+00
        pdb=" CG  ASP A 168 "   -0.022 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 168 "    0.008 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 168 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 584 "    0.021 5.00e-02 4.00e+02   3.10e-02 1.54e+00
        pdb=" N   PRO B 585 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 585 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 585 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1637 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 776
        2.74 -     3.28: 8870
        3.28 -     3.82: 14616
        3.82 -     4.36: 15587
        4.36 -     4.90: 28359
  Nonbonded interactions: 68208
  Sorted by model distance:
  nonbonded pdb=" O   ASN B 241 "
            pdb=" OG1 THR B 244 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OD1 ASN B 322 "
            pdb=" OG1 THR B 751 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   ASN B 227 "
            pdb=" OG  SER B 231 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   VAL B 637 "
            pdb=" OG1 THR B 638 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG  SER B 222 "
            pdb=" OD1 ASN B 223 "
     model   vdw
     2.269 3.040
  ... (remaining 68203 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             13.780
  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:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     28.370
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6480
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      :  0.002   0.035   9494  Z= 0.138
  Angle     :  0.526  11.458  12830  Z= 0.268
  Chirality :  0.037   0.183   1408
  Planarity :  0.003   0.031   1640
  Dihedral  : 18.193  89.761   3547
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 28.33 %
    Favored  : 71.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.26), residues: 1157
  helix:  2.22 (0.25), residues: 483
  sheet:  0.46 (0.45), residues: 141
  loop : -1.90 (0.25), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 859 
 HIS   0.003   0.001   HIS B 247 
 PHE   0.006   0.001   PHE B 483 
 TYR   0.012   0.001   TYR B 758 
 ARG   0.004   0.000   ARG B  68 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 1.219 
Fit side-chains
REVERT: A  151 ASP cc_start: 0.7349 (p0) cc_final: 0.6873 (m-30)
REVERT: A  195 GLU cc_start: 0.4828 (pp20) cc_final: 0.3761 (tt0)
REVERT: B   79 ASP cc_start: 0.7625 (m-30) cc_final: 0.7394 (m-30)
REVERT: B  101 LYS cc_start: 0.7924 (tttt) cc_final: 0.7517 (tttp)
REVERT: B  125 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7943 (ttt90)
REVERT: B  169 GLU cc_start: 0.8406 (pp20) cc_final: 0.8139 (pt0)
REVERT: B  194 MET cc_start: 0.6266 (tpp) cc_final: 0.6053 (tpp)
REVERT: B  472 ARG cc_start: 0.6652 (ptp-170) cc_final: 0.6003 (ptp90)
REVERT: B  533 ASP cc_start: 0.8174 (m-30) cc_final: 0.7965 (m-30)
REVERT: B  549 ASN cc_start: 0.7552 (m-40) cc_final: 0.7313 (t0)
REVERT: B  820 GLU cc_start: 0.7762 (mp0) cc_final: 0.7512 (mp0)
  outliers start: 1
  outliers final: 1
  residues processed: 124
  average time/residue: 0.2362
  time to fit residues: 41.6116
Evaluate side-chains
  99 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0980
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 845 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.171381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.127817 restraints weight = 13540.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.90
r_work: 0.3330 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9494  Z= 0.252
  Angle     :  0.570   8.079  12830  Z= 0.299
  Chirality :  0.041   0.216   1408
  Planarity :  0.004   0.032   1640
  Dihedral  :  4.264  22.452   1263
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 26.93 %
    Favored  : 69.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.25), residues: 1157
  helix:  2.01 (0.24), residues: 489
  sheet:  0.07 (0.46), residues: 138
  loop : -1.92 (0.25), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 859 
 HIS   0.004   0.001   HIS B 768 
 PHE   0.011   0.002   PHE B 674 
 TYR   0.020   0.002   TYR B 758 
 ARG   0.005   0.000   ARG B 871 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 97
  time to evaluate  : 1.070 
Fit side-chains
REVERT: A  151 ASP cc_start: 0.7446 (p0) cc_final: 0.6879 (m-30)
REVERT: A  195 GLU cc_start: 0.4544 (pp20) cc_final: 0.3811 (tt0)
REVERT: B  467 LYS cc_start: 0.7549 (mmtt) cc_final: 0.7140 (mttm)
REVERT: B  472 ARG cc_start: 0.7888 (ptp-170) cc_final: 0.7354 (ptp90)
REVERT: B  693 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7503 (tt0)
REVERT: B  733 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6879 (mp0)
  outliers start: 36
  outliers final: 18
  residues processed: 124
  average time/residue: 0.2412
  time to fit residues: 42.1327
Evaluate side-chains
  113 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 1.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  447 CYS
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  584 THR
Chi-restraints excluded: chain B residue  693 GLN
Chi-restraints excluded: chain B residue  733 GLU
Chi-restraints excluded: chain B residue  758 TYR
Chi-restraints excluded: chain B residue  761 MET
Chi-restraints excluded: chain B residue  788 VAL
Chi-restraints excluded: chain B residue  806 THR
Chi-restraints excluded: chain B residue  883 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 88 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 19 optimal weight:   20.0000
   chunk 26 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 112 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.169012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.125806 restraints weight = 13717.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 3.31
r_work: 0.3300 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9494  Z= 0.292
  Angle     :  0.585   6.648  12830  Z= 0.309
  Chirality :  0.042   0.256   1408
  Planarity :  0.004   0.036   1640
  Dihedral  :  4.578  28.657   1261
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 26.83 %
    Favored  : 68.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.25), residues: 1157
  helix:  1.71 (0.24), residues: 492
  sheet: -0.16 (0.46), residues: 146
  loop : -2.02 (0.24), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 859 
 HIS   0.005   0.001   HIS B 768 
 PHE   0.011   0.002   PHE B 674 
 TYR   0.032   0.002   TYR B 758 
 ARG   0.003   0.000   ARG B 871 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 96
  time to evaluate  : 1.098 
Fit side-chains
REVERT: A  151 ASP cc_start: 0.7444 (p0) cc_final: 0.6883 (m-30)
REVERT: A  156 MET cc_start: 0.4882 (OUTLIER) cc_final: 0.4602 (ttt)
REVERT: A  195 GLU cc_start: 0.4828 (pp20) cc_final: 0.3911 (tp30)
REVERT: A  199 LEU cc_start: 0.4533 (OUTLIER) cc_final: 0.4211 (mp)
REVERT: A  324 MET cc_start: 0.1906 (pmm) cc_final: 0.1686 (pmm)
REVERT: B  374 MET cc_start: 0.8149 (mtm) cc_final: 0.7859 (ptp)
REVERT: B  472 ARG cc_start: 0.7873 (ptp-170) cc_final: 0.7343 (ptp90)
REVERT: B  693 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7469 (tt0)
REVERT: B  733 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6976 (mp0)
  outliers start: 44
  outliers final: 26
  residues processed: 127
  average time/residue: 0.2378
  time to fit residues: 42.0103
Evaluate side-chains
  122 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 92
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  447 CYS
Chi-restraints excluded: chain B residue  584 THR
Chi-restraints excluded: chain B residue  623 MET
Chi-restraints excluded: chain B residue  679 THR
Chi-restraints excluded: chain B residue  693 GLN
Chi-restraints excluded: chain B residue  733 GLU
Chi-restraints excluded: chain B residue  748 LEU
Chi-restraints excluded: chain B residue  758 TYR
Chi-restraints excluded: chain B residue  761 MET
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  788 VAL
Chi-restraints excluded: chain B residue  806 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 90 optimal weight:    0.5980
   chunk 93 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0270
   chunk 88 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0370
   chunk 103 optimal weight:    0.9980
   chunk 82 optimal weight:    0.6980
   chunk 102 optimal weight:    1.9990
   chunk 21 optimal weight:    9.9990
   chunk 114 optimal weight:    2.9990
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 ASN
** B 731 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 = 0.4116 r_free = 0.4116 target = 0.172128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.129435 restraints weight = 13733.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 3.30
r_work: 0.3343 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9494  Z= 0.163
  Angle     :  0.502   8.510  12830  Z= 0.264
  Chirality :  0.039   0.222   1408
  Planarity :  0.003   0.035   1640
  Dihedral  :  4.187  26.005   1261
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 27.83 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.25), residues: 1157
  helix:  2.05 (0.24), residues: 487
  sheet:  0.12 (0.46), residues: 146
  loop : -1.94 (0.24), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 859 
 HIS   0.003   0.001   HIS B 712 
 PHE   0.011   0.001   PHE B 629 
 TYR   0.022   0.001   TYR B 758 
 ARG   0.007   0.000   ARG B 842 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 101
  time to evaluate  : 1.093 
Fit side-chains
REVERT: A  151 ASP cc_start: 0.7417 (p0) cc_final: 0.6875 (m-30)
REVERT: A  195 GLU cc_start: 0.4856 (pp20) cc_final: 0.3824 (tp30)
REVERT: A  324 MET cc_start: 0.2200 (pmm) cc_final: 0.1999 (pmm)
REVERT: A  360 GLU cc_start: 0.5444 (OUTLIER) cc_final: 0.5177 (pm20)
REVERT: B  328 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7687 (mt)
REVERT: B  472 ARG cc_start: 0.7842 (ptp-170) cc_final: 0.7305 (ptp90)
REVERT: B  842 ARG cc_start: 0.8104 (tmt170) cc_final: 0.7794 (tpt90)
  outliers start: 32
  outliers final: 19
  residues processed: 129
  average time/residue: 0.2206
  time to fit residues: 39.9225
Evaluate side-chains
  117 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 1.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  584 THR
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  679 THR
Chi-restraints excluded: chain B residue  748 LEU
Chi-restraints excluded: chain B residue  761 MET
Chi-restraints excluded: chain B residue  783 VAL
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  788 VAL
Chi-restraints excluded: chain B residue  806 THR
Chi-restraints excluded: chain B residue  883 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 102 optimal weight:    0.9990
   chunk 114 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 ASN
** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 845 GLN
** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.167356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.123784 restraints weight = 13665.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.72
r_work: 0.3283 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9494  Z= 0.350
  Angle     :  0.627  11.718  12830  Z= 0.326
  Chirality :  0.043   0.252   1408
  Planarity :  0.004   0.041   1640
  Dihedral  :  4.711  31.564   1261
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 27.53 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.25), residues: 1157
  helix:  1.50 (0.23), residues: 498
  sheet: -0.09 (0.45), residues: 146
  loop : -2.01 (0.25), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 859 
 HIS   0.006   0.001   HIS B 768 
 PHE   0.013   0.002   PHE B 674 
 TYR   0.031   0.002   TYR B 758 
 ARG   0.003   0.000   ARG B 237 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 92
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.7283 (p0) cc_final: 0.6823 (m-30)
REVERT: A  156 MET cc_start: 0.5299 (OUTLIER) cc_final: 0.4891 (ttt)
REVERT: A  195 GLU cc_start: 0.5143 (pp20) cc_final: 0.4066 (tp30)
REVERT: A  346 LEU cc_start: 0.6805 (tp) cc_final: 0.6418 (tp)
REVERT: A  360 GLU cc_start: 0.5532 (OUTLIER) cc_final: 0.5296 (pm20)
REVERT: B  241 ASN cc_start: 0.7453 (t0) cc_final: 0.7234 (t0)
REVERT: B  328 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7979 (mt)
REVERT: B  472 ARG cc_start: 0.8006 (ptp-170) cc_final: 0.7478 (ptp90)
REVERT: B  693 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7521 (tt0)
REVERT: B  733 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7170 (mp0)
  outliers start: 43
  outliers final: 28
  residues processed: 125
  average time/residue: 0.2159
  time to fit residues: 38.1256
Evaluate side-chains
  123 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 90
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  313 GLN
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  447 CYS
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  584 THR
Chi-restraints excluded: chain B residue  623 MET
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  679 THR
Chi-restraints excluded: chain B residue  693 GLN
Chi-restraints excluded: chain B residue  733 GLU
Chi-restraints excluded: chain B residue  748 LEU
Chi-restraints excluded: chain B residue  758 TYR
Chi-restraints excluded: chain B residue  761 MET
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  806 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 83 optimal weight:    0.2980
   chunk 77 optimal weight:    0.7980
   chunk 111 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 7 optimal weight:    0.2980
   chunk 23 optimal weight:    7.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 142 GLN
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 ASN
B 869 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.170459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.126383 restraints weight = 13592.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 3.25
r_work: 0.3329 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9494  Z= 0.194
  Angle     :  0.538   9.885  12830  Z= 0.278
  Chirality :  0.039   0.227   1408
  Planarity :  0.003   0.036   1640
  Dihedral  :  4.313  28.504   1261
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 28.73 %
    Favored  : 67.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.25), residues: 1157
  helix:  1.81 (0.24), residues: 494
  sheet: -0.11 (0.45), residues: 150
  loop : -1.97 (0.25), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 859 
 HIS   0.003   0.001   HIS B 714 
 PHE   0.010   0.001   PHE B 243 
 TYR   0.025   0.001   TYR B 758 
 ARG   0.004   0.000   ARG B 237 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 96
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.7263 (p0) cc_final: 0.6793 (m-30)
REVERT: A  156 MET cc_start: 0.5032 (OUTLIER) cc_final: 0.4737 (ttt)
REVERT: A  195 GLU cc_start: 0.4935 (pp20) cc_final: 0.3878 (tp30)
REVERT: A  324 MET cc_start: 0.2229 (pmm) cc_final: 0.1842 (pmm)
REVERT: A  346 LEU cc_start: 0.6761 (tp) cc_final: 0.6379 (tp)
REVERT: B  241 ASN cc_start: 0.7356 (t0) cc_final: 0.7112 (t0)
REVERT: B  328 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7731 (mt)
REVERT: B  472 ARG cc_start: 0.7850 (ptp-170) cc_final: 0.7292 (ptp90)
REVERT: B  842 ARG cc_start: 0.8148 (tmt170) cc_final: 0.7888 (tpt90)
  outliers start: 35
  outliers final: 25
  residues processed: 123
  average time/residue: 0.2600
  time to fit residues: 45.0031
Evaluate side-chains
  119 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 1.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  447 CYS
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  584 THR
Chi-restraints excluded: chain B residue  623 MET
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  679 THR
Chi-restraints excluded: chain B residue  733 GLU
Chi-restraints excluded: chain B residue  748 LEU
Chi-restraints excluded: chain B residue  758 TYR
Chi-restraints excluded: chain B residue  761 MET
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  788 VAL
Chi-restraints excluded: chain B residue  806 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 19 optimal weight:    0.1980
   chunk 49 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0270
   chunk 35 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.171421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.125209 restraints weight = 13631.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 3.34
r_work: 0.3315 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9494  Z= 0.183
  Angle     :  0.527   9.877  12830  Z= 0.272
  Chirality :  0.039   0.222   1408
  Planarity :  0.003   0.036   1640
  Dihedral  :  4.212  27.850   1261
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 28.13 %
    Favored  : 67.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.25), residues: 1157
  helix:  1.92 (0.24), residues: 492
  sheet:  0.12 (0.46), residues: 146
  loop : -2.00 (0.24), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 859 
 HIS   0.003   0.001   HIS B 712 
 PHE   0.011   0.001   PHE B 674 
 TYR   0.024   0.001   TYR B 758 
 ARG   0.005   0.000   ARG B 237 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 97
  time to evaluate  : 1.708 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.7370 (p0) cc_final: 0.6780 (m-30)
REVERT: A  156 MET cc_start: 0.5065 (OUTLIER) cc_final: 0.4837 (ttt)
REVERT: A  195 GLU cc_start: 0.4955 (pp20) cc_final: 0.3560 (tp30)
REVERT: A  199 LEU cc_start: 0.4500 (OUTLIER) cc_final: 0.4204 (mp)
REVERT: A  299 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7031 (pp)
REVERT: A  324 MET cc_start: 0.2476 (pmm) cc_final: 0.2079 (pmm)
REVERT: A  333 ILE cc_start: 0.3346 (tp) cc_final: 0.2911 (tp)
REVERT: A  346 LEU cc_start: 0.6761 (tp) cc_final: 0.6378 (tp)
REVERT: B   84 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7826 (mtt180)
REVERT: B  241 ASN cc_start: 0.7385 (t0) cc_final: 0.7125 (t0)
REVERT: B  328 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7712 (mt)
REVERT: B  472 ARG cc_start: 0.7876 (ptp-170) cc_final: 0.7329 (ptp90)
REVERT: B  842 ARG cc_start: 0.8183 (tmt170) cc_final: 0.7950 (tpt90)
  outliers start: 39
  outliers final: 28
  residues processed: 129
  average time/residue: 0.2499
  time to fit residues: 45.8677
Evaluate side-chains
  126 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 94
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  447 CYS
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  584 THR
Chi-restraints excluded: chain B residue  623 MET
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  679 THR
Chi-restraints excluded: chain B residue  733 GLU
Chi-restraints excluded: chain B residue  748 LEU
Chi-restraints excluded: chain B residue  758 TYR
Chi-restraints excluded: chain B residue  761 MET
Chi-restraints excluded: chain B residue  783 VAL
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  788 VAL
Chi-restraints excluded: chain B residue  790 THR
Chi-restraints excluded: chain B residue  806 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 115 optimal weight:    0.4980
   chunk 5 optimal weight:    0.1980
   chunk 51 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 25 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 37 optimal weight:    0.4980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 ASN
** B 869 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 = 0.4108 r_free = 0.4108 target = 0.171571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.128537 restraints weight = 13821.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.99
r_work: 0.3339 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9494  Z= 0.182
  Angle     :  0.536   9.633  12830  Z= 0.277
  Chirality :  0.039   0.221   1408
  Planarity :  0.003   0.036   1640
  Dihedral  :  4.160  27.405   1261
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 27.93 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.25), residues: 1157
  helix:  1.97 (0.24), residues: 492
  sheet:  0.12 (0.46), residues: 146
  loop : -2.00 (0.24), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 332 
 HIS   0.003   0.001   HIS B 712 
 PHE   0.011   0.001   PHE B 243 
 TYR   0.023   0.001   TYR B 758 
 ARG   0.008   0.000   ARG B 237 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 92
  time to evaluate  : 1.907 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.7369 (p0) cc_final: 0.6840 (m-30)
REVERT: A  156 MET cc_start: 0.4868 (OUTLIER) cc_final: 0.4629 (ttt)
REVERT: A  195 GLU cc_start: 0.5047 (pp20) cc_final: 0.3540 (tp30)
REVERT: A  199 LEU cc_start: 0.4412 (OUTLIER) cc_final: 0.4124 (mp)
REVERT: A  299 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7020 (pp)
REVERT: A  324 MET cc_start: 0.2495 (pmm) cc_final: 0.2037 (pmm)
REVERT: A  333 ILE cc_start: 0.3366 (tp) cc_final: 0.2914 (tp)
REVERT: A  346 LEU cc_start: 0.6766 (tp) cc_final: 0.6381 (tp)
REVERT: B   84 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7798 (mtt180)
REVERT: B  241 ASN cc_start: 0.7366 (t0) cc_final: 0.7097 (t0)
REVERT: B  328 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7675 (mt)
REVERT: B  472 ARG cc_start: 0.7868 (ptp-170) cc_final: 0.7303 (ptp90)
  outliers start: 39
  outliers final: 30
  residues processed: 123
  average time/residue: 0.2914
  time to fit residues: 51.7294
Evaluate side-chains
  124 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 90
  time to evaluate  : 2.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  447 CYS
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  584 THR
Chi-restraints excluded: chain B residue  623 MET
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  679 THR
Chi-restraints excluded: chain B residue  733 GLU
Chi-restraints excluded: chain B residue  748 LEU
Chi-restraints excluded: chain B residue  758 TYR
Chi-restraints excluded: chain B residue  761 MET
Chi-restraints excluded: chain B residue  783 VAL
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  788 VAL
Chi-restraints excluded: chain B residue  790 THR
Chi-restraints excluded: chain B residue  806 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0370
   chunk 29 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 66 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 ASN
** B 869 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 = 0.4108 r_free = 0.4108 target = 0.171636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.127792 restraints weight = 13578.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.87
r_work: 0.3352 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9494  Z= 0.176
  Angle     :  0.529   9.520  12830  Z= 0.274
  Chirality :  0.039   0.219   1408
  Planarity :  0.003   0.035   1640
  Dihedral  :  4.127  27.174   1261
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 28.33 %
    Favored  : 67.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.25), residues: 1157
  helix:  2.01 (0.24), residues: 492
  sheet:  0.15 (0.46), residues: 146
  loop : -2.00 (0.24), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 332 
 HIS   0.003   0.001   HIS B 714 
 PHE   0.011   0.001   PHE B 243 
 TYR   0.023   0.001   TYR B 758 
 ARG   0.007   0.000   ARG B 842 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 96
  time to evaluate  : 1.788 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.7142 (p0) cc_final: 0.6677 (m-30)
REVERT: A  156 MET cc_start: 0.5094 (OUTLIER) cc_final: 0.4869 (ttt)
REVERT: A  195 GLU cc_start: 0.5109 (pp20) cc_final: 0.3535 (tp30)
REVERT: A  199 LEU cc_start: 0.4583 (OUTLIER) cc_final: 0.4247 (mp)
REVERT: A  299 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7033 (pp)
REVERT: A  324 MET cc_start: 0.2517 (pmm) cc_final: 0.2023 (pmm)
REVERT: A  333 ILE cc_start: 0.3579 (tp) cc_final: 0.3070 (tp)
REVERT: A  346 LEU cc_start: 0.6797 (tp) cc_final: 0.6410 (tp)
REVERT: B   84 ARG cc_start: 0.8142 (mtt180) cc_final: 0.7931 (mtt180)
REVERT: B  241 ASN cc_start: 0.7402 (t0) cc_final: 0.7148 (t0)
REVERT: B  328 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7770 (mt)
REVERT: B  472 ARG cc_start: 0.7925 (ptp-170) cc_final: 0.7383 (ptp90)
  outliers start: 37
  outliers final: 30
  residues processed: 126
  average time/residue: 0.2522
  time to fit residues: 45.6339
Evaluate side-chains
  125 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 91
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   49 GLU
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  447 CYS
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  584 THR
Chi-restraints excluded: chain B residue  623 MET
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  679 THR
Chi-restraints excluded: chain B residue  733 GLU
Chi-restraints excluded: chain B residue  748 LEU
Chi-restraints excluded: chain B residue  758 TYR
Chi-restraints excluded: chain B residue  761 MET
Chi-restraints excluded: chain B residue  783 VAL
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  788 VAL
Chi-restraints excluded: chain B residue  790 THR
Chi-restraints excluded: chain B residue  806 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 113 optimal weight:    0.8980
   chunk 22 optimal weight:   30.0000
   chunk 39 optimal weight:    0.4980
   chunk 104 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 112 optimal weight:    0.0040
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
B 213 ASN
** B 869 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 = 0.4108 r_free = 0.4108 target = 0.171553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.128535 restraints weight = 13752.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 3.05
r_work: 0.3339 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9494  Z= 0.179
  Angle     :  0.534   9.633  12830  Z= 0.277
  Chirality :  0.039   0.219   1408
  Planarity :  0.003   0.035   1640
  Dihedral  :  4.118  27.133   1261
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 28.43 %
    Favored  : 67.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.25), residues: 1157
  helix:  2.02 (0.24), residues: 491
  sheet:  0.18 (0.46), residues: 146
  loop : -2.00 (0.24), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 332 
 HIS   0.003   0.001   HIS B 712 
 PHE   0.013   0.001   PHE B 629 
 TYR   0.023   0.001   TYR B 758 
 ARG   0.005   0.000   ARG B 842 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 93
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.7149 (p0) cc_final: 0.6761 (m-30)
REVERT: A  195 GLU cc_start: 0.5047 (pp20) cc_final: 0.3717 (tp30)
REVERT: A  199 LEU cc_start: 0.4391 (OUTLIER) cc_final: 0.4126 (mp)
REVERT: A  299 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7063 (pp)
REVERT: A  324 MET cc_start: 0.2678 (pmm) cc_final: 0.2140 (pmm)
REVERT: A  333 ILE cc_start: 0.3630 (tp) cc_final: 0.3122 (tp)
REVERT: A  346 LEU cc_start: 0.6756 (tp) cc_final: 0.6377 (tp)
REVERT: B  241 ASN cc_start: 0.7327 (t0) cc_final: 0.7072 (t0)
REVERT: B  328 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7722 (mt)
REVERT: B  472 ARG cc_start: 0.7858 (ptp-170) cc_final: 0.7287 (ptp90)
  outliers start: 36
  outliers final: 30
  residues processed: 122
  average time/residue: 0.2153
  time to fit residues: 37.7002
Evaluate side-chains
  121 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 88
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   49 GLU
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  447 CYS
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  584 THR
Chi-restraints excluded: chain B residue  623 MET
Chi-restraints excluded: chain B residue  678 LEU
Chi-restraints excluded: chain B residue  679 THR
Chi-restraints excluded: chain B residue  733 GLU
Chi-restraints excluded: chain B residue  748 LEU
Chi-restraints excluded: chain B residue  758 TYR
Chi-restraints excluded: chain B residue  761 MET
Chi-restraints excluded: chain B residue  783 VAL
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  788 VAL
Chi-restraints excluded: chain B residue  790 THR
Chi-restraints excluded: chain B residue  806 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 20 optimal weight:    0.0170
   chunk 86 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 89 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0980
   chunk 72 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 85 optimal weight:    0.3980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.3618

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

Flipped N/Q/H residues before XYZ refinement:
B 213 ASN
** B 869 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 = 0.4128 r_free = 0.4128 target = 0.173393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.130320 restraints weight = 13854.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 3.12
r_work: 0.3368 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9494  Z= 0.148
  Angle     :  0.515   9.573  12830  Z= 0.265
  Chirality :  0.038   0.204   1408
  Planarity :  0.003   0.036   1640
  Dihedral  :  3.940  25.239   1261
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 29.13 %
    Favored  : 67.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.25), residues: 1157
  helix:  2.12 (0.24), residues: 492
  sheet:  0.28 (0.46), residues: 146
  loop : -1.98 (0.24), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 332 
 HIS   0.003   0.001   HIS B 714 
 PHE   0.011   0.001   PHE B 134 
 TYR   0.018   0.001   TYR B 758 
 ARG   0.005   0.000   ARG B 842 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5040.33 seconds
wall clock time: 89 minutes 10.31 seconds (5350.31 seconds total)