Starting phenix.real_space_refine
on Sat Jul 20 01:10:38 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t13_40953/07_2024/8t13_40953_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t13_40953/07_2024/8t13_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t13_40953/07_2024/8t13_40953.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t13_40953/07_2024/8t13_40953.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t13_40953/07_2024/8t13_40953_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t13_40953/07_2024/8t13_40953_neut.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
    Residue "A GLU  445": "OE1" <-> "OE2"
    Residue "B PHE  491": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.93, per 1000 atoms: 0.64
  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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.40
  Conformation dependent library (CDL) restraints added in 1.7 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: 0.99
  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: 2.57

  Time building geometry restraints manager: 3.79 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:
      100.09 -   106.89: 245
      106.89 -   113.69: 5277
      113.69 -   120.49: 3592
      120.49 -   127.29: 3590
      127.29 -   134.09: 126
  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 2.440
  nonbonded pdb=" OD1 ASN B 322 "
            pdb=" OG1 THR B 751 "
     model   vdw
     2.236 2.440
  nonbonded pdb=" O   ASN B 227 "
            pdb=" OG  SER B 231 "
     model   vdw
     2.252 2.440
  nonbonded pdb=" O   VAL B 637 "
            pdb=" OG1 THR B 638 "
     model   vdw
     2.254 2.440
  nonbonded pdb=" OG  SER B 222 "
            pdb=" OD1 ASN B 223 "
     model   vdw
     2.269 2.440
  ... (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
========== 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:             3.120
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     29.490
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  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:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.960
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 1.115 
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: 0.2208
  time to fit residues: 38.3481
Evaluate side-chains
  99 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 90 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 575 ASN
** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6538
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9494  Z= 0.242
  Angle     :  0.553   8.072  12830  Z= 0.288
  Chirality :  0.040   0.199   1408
  Planarity :  0.003   0.033   1640
  Dihedral  :  4.216  19.613   1263
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 27.33 %
    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:  0.15 (0.25), residues: 1157
  helix:  2.07 (0.24), residues: 491
  sheet:  0.08 (0.47), residues: 138
  loop : -1.93 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 859 
 HIS   0.005   0.001   HIS B 768 
 PHE   0.011   0.001   PHE B 629 
 TYR   0.019   0.002   TYR B 758 
 ARG   0.003   0.000   ARG B 737 

*********************** 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 fitting.
    rotamer outliers: 37
    poor density    : 96
  time to evaluate  : 1.070 
Fit side-chains
REVERT: A  151 ASP cc_start: 0.7373 (p0) cc_final: 0.6866 (m-30)
REVERT: A  195 GLU cc_start: 0.4585 (pp20) cc_final: 0.3568 (tt0)
REVERT: B  125 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7761 (ttt90)
REVERT: B  169 GLU cc_start: 0.8356 (pp20) cc_final: 0.8156 (pt0)
REVERT: B  234 MET cc_start: 0.8121 (tmm) cc_final: 0.7919 (tmm)
REVERT: B  467 LYS cc_start: 0.6328 (mmtt) cc_final: 0.5869 (mttm)
REVERT: B  472 ARG cc_start: 0.6627 (ptp-170) cc_final: 0.5870 (ptp90)
REVERT: B  693 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6896 (tt0)
REVERT: B  859 TRP cc_start: 0.5764 (t60) cc_final: 0.5011 (t60)
  outliers start: 37
  outliers final: 19
  residues processed: 122
  average time/residue: 0.2290
  time to fit residues: 39.0368
Evaluate side-chains
  115 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
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   37 ASP
Chi-restraints excluded: chain B residue  211 SER
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  552 MET
Chi-restraints excluded: chain B residue  584 THR
Chi-restraints excluded: chain B residue  597 ASP
Chi-restraints excluded: chain B residue  693 GLN
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 71 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9980
   chunk 114 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 104 optimal weight:    0.6980
   chunk 35 optimal weight:    0.2980
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6528
moved from start:          0.1591

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= 0.194
  Angle     :  0.500   6.324  12830  Z= 0.263
  Chirality :  0.039   0.195   1408
  Planarity :  0.003   0.032   1640
  Dihedral  :  4.122  20.588   1261
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 27.53 %
    Favored  : 68.47 %
  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:  0.16 (0.25), residues: 1157
  helix:  2.10 (0.24), residues: 491
  sheet:  0.08 (0.46), residues: 144
  loop : -1.99 (0.24), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 859 
 HIS   0.004   0.001   HIS B 768 
 PHE   0.009   0.001   PHE B 243 
 TYR   0.023   0.001   TYR B 758 
 ARG   0.003   0.000   ARG B 842 

*********************** 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
  141 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 101
  time to evaluate  : 1.126 
Fit side-chains
REVERT: A  151 ASP cc_start: 0.7314 (p0) cc_final: 0.6848 (m-30)
REVERT: A  195 GLU cc_start: 0.4582 (pp20) cc_final: 0.3367 (tp30)
REVERT: B  116 MET cc_start: 0.8415 (mmp) cc_final: 0.8128 (mmm)
REVERT: B  125 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7600 (ttt90)
REVERT: B  169 GLU cc_start: 0.8359 (pp20) cc_final: 0.8141 (pt0)
REVERT: B  234 MET cc_start: 0.8093 (tmm) cc_final: 0.7860 (tmm)
REVERT: B  467 LYS cc_start: 0.6212 (mmtt) cc_final: 0.5971 (mttm)
REVERT: B  472 ARG cc_start: 0.6523 (ptp-170) cc_final: 0.5770 (ptp90)
REVERT: B  733 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5479 (mp0)
REVERT: B  842 ARG cc_start: 0.7706 (tmt170) cc_final: 0.7409 (tmt170)
REVERT: B  859 TRP cc_start: 0.6031 (t60) cc_final: 0.5811 (t60)
  outliers start: 40
  outliers final: 29
  residues processed: 128
  average time/residue: 0.2297
  time to fit residues: 40.9565
Evaluate side-chains
  126 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 96
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
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  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   37 ASP
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  523 SER
Chi-restraints excluded: chain B residue  552 MET
Chi-restraints excluded: chain B residue  584 THR
Chi-restraints excluded: chain B residue  597 ASP
Chi-restraints excluded: chain B residue  623 MET
Chi-restraints excluded: chain B residue  679 THR
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 104 optimal weight:    0.0370
   chunk 79 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0970
   chunk 105 optimal weight:    0.5980
   chunk 112 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0020
   chunk 100 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.3064

-------------------------------------------------------------------------------
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 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6480
moved from start:          0.1683

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= 0.129
  Angle     :  0.453   5.920  12830  Z= 0.238
  Chirality :  0.038   0.173   1408
  Planarity :  0.003   0.032   1640
  Dihedral  :  3.806  18.999   1261
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 29.33 %
    Favored  : 68.57 %
  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:  0.38 (0.25), residues: 1157
  helix:  2.39 (0.24), residues: 486
  sheet:  0.18 (0.46), residues: 148
  loop : -1.95 (0.24), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 859 
 HIS   0.003   0.001   HIS B 714 
 PHE   0.010   0.001   PHE B 243 
 TYR   0.015   0.001   TYR B 758 
 ARG   0.002   0.000   ARG B 125 

*********************** 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
  122 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.7361 (p0) cc_final: 0.6942 (m-30)
REVERT: A  195 GLU cc_start: 0.4676 (pp20) cc_final: 0.3618 (tt0)
REVERT: A  360 GLU cc_start: 0.5397 (OUTLIER) cc_final: 0.5123 (pm20)
REVERT: B  125 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7647 (ttt90)
REVERT: B  234 MET cc_start: 0.8136 (tmm) cc_final: 0.7913 (tmm)
REVERT: B  467 LYS cc_start: 0.6281 (mmtt) cc_final: 0.6003 (mttm)
REVERT: B  472 ARG cc_start: 0.6610 (ptp-170) cc_final: 0.5846 (ptp90)
  outliers start: 21
  outliers final: 14
  residues processed: 119
  average time/residue: 0.2132
  time to fit residues: 35.7639
Evaluate side-chains
  114 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  386 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  340 GLN
Chi-restraints excluded: chain B residue  447 CYS
Chi-restraints excluded: chain B residue  584 THR
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 93 optimal weight:    0.6980
   chunk 63 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0980
   chunk 46 optimal weight:    0.3980
   chunk 95 optimal weight:    0.8980
   chunk 77 optimal weight:    0.2980
   chunk 0 optimal weight:    9.9990
   chunk 57 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 869 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6494
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9494  Z= 0.146
  Angle     :  0.479  11.393  12830  Z= 0.248
  Chirality :  0.038   0.174   1408
  Planarity :  0.003   0.033   1640
  Dihedral  :  3.812  19.133   1261
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 26.93 %
    Favored  : 69.17 %
  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:  0.38 (0.25), residues: 1157
  helix:  2.32 (0.24), residues: 493
  sheet:  0.28 (0.46), residues: 146
  loop : -1.95 (0.24), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 859 
 HIS   0.003   0.001   HIS B 712 
 PHE   0.010   0.001   PHE B 629 
 TYR   0.016   0.001   TYR B 758 
 ARG   0.008   0.000   ARG B 842 

*********************** 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
  138 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 99
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.7357 (p0) cc_final: 0.6936 (m-30)
REVERT: A  195 GLU cc_start: 0.4625 (pp20) cc_final: 0.3307 (tt0)
REVERT: B  125 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7671 (ttt90)
REVERT: B  234 MET cc_start: 0.8166 (tmm) cc_final: 0.7914 (tmm)
REVERT: B  472 ARG cc_start: 0.6624 (ptp-170) cc_final: 0.5847 (ptp90)
REVERT: B  693 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6945 (tt0)
REVERT: B  826 ASP cc_start: 0.7880 (t70) cc_final: 0.7237 (t0)
REVERT: B  842 ARG cc_start: 0.7584 (tmt170) cc_final: 0.7213 (tpt90)
  outliers start: 39
  outliers final: 25
  residues processed: 130
  average time/residue: 0.2259
  time to fit residues: 40.9365
Evaluate side-chains
  121 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
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  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  211 SER
Chi-restraints excluded: chain B residue  213 ASN
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  340 GLN
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  679 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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9990
   chunk 93 optimal weight:    0.0470
   chunk 51 optimal weight:    0.7980
   chunk 9 optimal weight:    0.4980
   chunk 58 optimal weight:    0.7980
   chunk 108 optimal weight:    2.9990
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6513
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9494  Z= 0.172
  Angle     :  0.496  10.113  12830  Z= 0.256
  Chirality :  0.039   0.183   1408
  Planarity :  0.003   0.033   1640
  Dihedral  :  3.918  20.242   1261
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 27.13 %
    Favored  : 68.87 %
  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:  0.31 (0.25), residues: 1157
  helix:  2.25 (0.24), residues: 492
  sheet:  0.22 (0.45), residues: 146
  loop : -1.95 (0.24), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 859 
 HIS   0.003   0.001   HIS B 712 
 PHE   0.010   0.001   PHE B 243 
 TYR   0.017   0.001   TYR B 758 
 ARG   0.003   0.000   ARG B 842 

*********************** 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
  138 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 98
  time to evaluate  : 1.072 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.7359 (p0) cc_final: 0.6963 (m-30)
REVERT: A  195 GLU cc_start: 0.4557 (pp20) cc_final: 0.3236 (tp30)
REVERT: A  342 VAL cc_start: 0.6355 (t) cc_final: 0.6151 (m)
REVERT: A  360 GLU cc_start: 0.5295 (OUTLIER) cc_final: 0.5087 (pm20)
REVERT: B  125 ARG cc_start: 0.8122 (ttp80) cc_final: 0.7662 (ttt90)
REVERT: B  234 MET cc_start: 0.8157 (tmm) cc_final: 0.7929 (tmm)
REVERT: B  241 ASN cc_start: 0.7353 (t0) cc_final: 0.7138 (t0)
REVERT: B  472 ARG cc_start: 0.6568 (ptp-170) cc_final: 0.5795 (ptp90)
REVERT: B  693 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6966 (tt0)
REVERT: B  826 ASP cc_start: 0.7886 (t70) cc_final: 0.7258 (t0)
REVERT: B  842 ARG cc_start: 0.7648 (tmt170) cc_final: 0.7307 (tpt90)
  outliers start: 40
  outliers final: 29
  residues processed: 128
  average time/residue: 0.2090
  time to fit residues: 38.2238
Evaluate side-chains
  128 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 97
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
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  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   37 ASP
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  325 VAL
Chi-restraints excluded: chain B residue  340 GLN
Chi-restraints excluded: chain B residue  346 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  679 THR
Chi-restraints excluded: chain B residue  693 GLN
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
Chi-restraints excluded: chain B residue  883 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 111 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 682 ASN ** 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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6528
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9494  Z= 0.195
  Angle     :  0.502   9.170  12830  Z= 0.261
  Chirality :  0.039   0.193   1408
  Planarity :  0.003   0.032   1640
  Dihedral  :  4.043  21.641   1261
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 26.63 %
    Favored  : 69.07 %
  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:  0.24 (0.25), residues: 1157
  helix:  2.17 (0.24), residues: 493
  sheet:  0.16 (0.46), residues: 146
  loop : -1.97 (0.24), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 859 
 HIS   0.003   0.001   HIS B 712 
 PHE   0.010   0.001   PHE B 243 
 TYR   0.019   0.001   TYR B 758 
 ARG   0.004   0.000   ARG A 330 

*********************** 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
  144 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 101
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.7316 (p0) cc_final: 0.6934 (m-30)
REVERT: A  195 GLU cc_start: 0.4720 (pp20) cc_final: 0.3396 (tp30)
REVERT: B  125 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7649 (ttt90)
REVERT: B  234 MET cc_start: 0.8082 (tmm) cc_final: 0.7807 (tmm)
REVERT: B  241 ASN cc_start: 0.7381 (t0) cc_final: 0.7144 (t0)
REVERT: B  472 ARG cc_start: 0.6552 (ptp-170) cc_final: 0.5798 (ptp90)
REVERT: B  693 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6811 (tt0)
REVERT: B  826 ASP cc_start: 0.7940 (t70) cc_final: 0.7347 (t0)
  outliers start: 43
  outliers final: 33
  residues processed: 133
  average time/residue: 0.2297
  time to fit residues: 42.8768
Evaluate side-chains
  129 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 95
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
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  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   37 ASP
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  325 VAL
Chi-restraints excluded: chain B residue  340 GLN
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  447 CYS
Chi-restraints excluded: chain B residue  523 SER
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  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 33 optimal weight:    0.0570
   chunk 21 optimal weight:    8.9990
   chunk 71 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 55 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 107 optimal weight:    0.0370
   chunk 97 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 142 GLN
** B 682 ASN ** 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: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6517
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9494  Z= 0.173
  Angle     :  0.496   8.715  12830  Z= 0.258
  Chirality :  0.039   0.189   1408
  Planarity :  0.003   0.043   1640
  Dihedral  :  3.992  21.430   1261
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 27.33 %
    Favored  : 68.67 %
  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:  0.24 (0.25), residues: 1157
  helix:  2.19 (0.24), residues: 493
  sheet:  0.14 (0.45), residues: 146
  loop : -1.99 (0.24), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 859 
 HIS   0.003   0.001   HIS B 714 
 PHE   0.010   0.001   PHE B 674 
 TYR   0.018   0.001   TYR B 758 
 ARG   0.008   0.000   ARG B 842 

*********************** 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
  138 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 98
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.7255 (p0) cc_final: 0.6899 (m-30)
REVERT: A  195 GLU cc_start: 0.4739 (pp20) cc_final: 0.3404 (tp30)
REVERT: B  125 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7637 (ttt90)
REVERT: B  234 MET cc_start: 0.8144 (tmm) cc_final: 0.7926 (tmm)
REVERT: B  241 ASN cc_start: 0.7362 (t0) cc_final: 0.7109 (t0)
REVERT: B  472 ARG cc_start: 0.6546 (ptp-170) cc_final: 0.5793 (ptp90)
REVERT: B  693 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6838 (tt0)
REVERT: B  826 ASP cc_start: 0.7943 (t70) cc_final: 0.7359 (t0)
REVERT: B  842 ARG cc_start: 0.7571 (tmt170) cc_final: 0.7047 (tpt90)
  outliers start: 40
  outliers final: 32
  residues processed: 128
  average time/residue: 0.2345
  time to fit residues: 41.4219
Evaluate side-chains
  127 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 94
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   37 ASP
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  325 VAL
Chi-restraints excluded: chain B residue  340 GLN
Chi-restraints excluded: chain B residue  412 ILE
Chi-restraints excluded: chain B residue  447 CYS
Chi-restraints excluded: chain B residue  523 SER
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  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 107 optimal weight:    0.0770
   chunk 62 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0570
   chunk 81 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 94 optimal weight:    0.0050
   chunk 98 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 110 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.3070

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

Flipped N/Q/H residues before XYZ refinement:
** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 869 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6482
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9494  Z= 0.135
  Angle     :  0.475   8.360  12830  Z= 0.243
  Chirality :  0.038   0.170   1408
  Planarity :  0.003   0.034   1640
  Dihedral  :  3.731  19.058   1261
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 28.23 %
    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:  0.34 (0.25), residues: 1157
  helix:  2.32 (0.24), residues: 493
  sheet:  0.13 (0.45), residues: 148
  loop : -1.97 (0.24), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 859 
 HIS   0.003   0.001   HIS B 714 
 PHE   0.009   0.001   PHE B 243 
 TYR   0.013   0.001   TYR B 758 
 ARG   0.004   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
  130 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.7172 (p0) cc_final: 0.6865 (m-30)
REVERT: A  195 GLU cc_start: 0.4590 (pp20) cc_final: 0.3267 (tp30)
REVERT: B  125 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7583 (ttt90)
REVERT: B  234 MET cc_start: 0.8173 (tmm) cc_final: 0.7929 (tmm)
REVERT: B  241 ASN cc_start: 0.7302 (t0) cc_final: 0.7062 (t0)
REVERT: B  472 ARG cc_start: 0.6553 (ptp-170) cc_final: 0.5788 (ptp90)
REVERT: B  826 ASP cc_start: 0.7913 (t70) cc_final: 0.7280 (t0)
  outliers start: 30
  outliers final: 25
  residues processed: 123
  average time/residue: 0.2130
  time to fit residues: 36.7657
Evaluate side-chains
  120 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  192 GLU
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  325 VAL
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  447 CYS
Chi-restraints excluded: chain B residue  523 SER
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  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  790 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 52 optimal weight:    0.2980
   chunk 76 optimal weight:    0.7980
   chunk 115 optimal weight:    0.9990
   chunk 106 optimal weight:    0.4980
   chunk 92 optimal weight:    0.0070
   chunk 9 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9990
   chunk 28 optimal weight:   20.0000
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6504
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9494  Z= 0.155
  Angle     :  0.490   8.599  12830  Z= 0.252
  Chirality :  0.038   0.180   1408
  Planarity :  0.003   0.039   1640
  Dihedral  :  3.807  19.564   1261
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 28.33 %
    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:  0.28 (0.25), residues: 1157
  helix:  2.28 (0.24), residues: 493
  sheet:  0.05 (0.44), residues: 153
  loop : -2.03 (0.24), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 859 
 HIS   0.003   0.001   HIS B 714 
 PHE   0.011   0.001   PHE B 629 
 TYR   0.013   0.001   TYR B 758 
 ARG   0.009   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
  121 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.7169 (p0) cc_final: 0.6829 (m-30)
REVERT: A  195 GLU cc_start: 0.4644 (pp20) cc_final: 0.3312 (tp30)
REVERT: B  125 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7627 (ttt90)
REVERT: B  234 MET cc_start: 0.8166 (tmm) cc_final: 0.7922 (tmm)
REVERT: B  241 ASN cc_start: 0.7300 (t0) cc_final: 0.7051 (t0)
REVERT: B  472 ARG cc_start: 0.6494 (ptp-170) cc_final: 0.5731 (ptp90)
REVERT: B  826 ASP cc_start: 0.7911 (t70) cc_final: 0.7277 (t0)
REVERT: B  842 ARG cc_start: 0.7346 (tpt90) cc_final: 0.6983 (tpt170)
REVERT: B  846 TRP cc_start: 0.8396 (OUTLIER) cc_final: 0.6354 (m100)
  outliers start: 27
  outliers final: 25
  residues processed: 115
  average time/residue: 0.2266
  time to fit residues: 36.8649
Evaluate side-chains
  119 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  192 GLU
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  325 VAL
Chi-restraints excluded: chain B residue  346 THR
Chi-restraints excluded: chain B residue  447 CYS
Chi-restraints excluded: chain B residue  523 SER
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  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  790 THR
Chi-restraints excluded: chain B residue  846 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 25 optimal weight:    0.2980
   chunk 92 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   chunk 11 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 66 optimal weight:    0.2980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 731 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 = 0.4137 r_free = 0.4137 target = 0.173869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.130887 restraints weight = 13361.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 2.81
r_work: 0.3372 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2323

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= 0.149
  Angle     :  0.485   8.594  12830  Z= 0.248
  Chirality :  0.038   0.175   1408
  Planarity :  0.003   0.034   1640
  Dihedral  :  3.782  18.910   1261
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 28.33 %
    Favored  : 68.87 %
  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:  0.30 (0.25), residues: 1157
  helix:  2.31 (0.24), residues: 493
  sheet:  0.05 (0.44), residues: 153
  loop : -2.02 (0.24), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 859 
 HIS   0.003   0.001   HIS B 712 
 PHE   0.010   0.001   PHE B 629 
 TYR   0.013   0.001   TYR B 758 
 ARG   0.008   0.000   ARG B 842 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2317.57 seconds
wall clock time: 41 minutes 51.36 seconds (2511.36 seconds total)