Starting phenix.real_space_refine
on Wed Sep 17 11:49:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j3z_61128/09_2025/9j3z_61128.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j3z_61128/09_2025/9j3z_61128.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j3z_61128/09_2025/9j3z_61128.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j3z_61128/09_2025/9j3z_61128.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j3z_61128/09_2025/9j3z_61128.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j3z_61128/09_2025/9j3z_61128.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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
     P       4      5.49       5
     S      42      5.16       5
     C    5624      2.51       5
     N    1332      2.21       5
     O    1489      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8491
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 576, 4150
          Classifications: {'peptide': 576}
          Incomplete info: {'truncation_to_alanine': 114}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 554}
          Chain breaks: 1
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 384
          Unresolved non-hydrogen angles: 493
          Unresolved non-hydrogen dihedrals: 309
          Unresolved non-hydrogen chiralities: 59
          Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 6, 'HIS:plan': 3, 'ASN:plan1': 4, 'GLU:plan': 3, 'PHE:plan': 6, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 143
    Chain: "B"
      Number of atoms: 4135
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4135
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 105}
          Link IDs: {'PTRANS': 21, 'TRANS': 548}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 353
          Unresolved non-hydrogen angles: 450
          Unresolved non-hydrogen dihedrals: 286
          Unresolved non-hydrogen chiralities: 51
          Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'ASN:plan1': 3, 'PHE:plan': 6, 'GLN:plan1': 5, 'ARG:plan': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 135
    Chain: "A"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 103
          Unusual residues: {'NAG': 1, 'POV': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 103
          Unusual residues: {'NAG': 1, 'POV': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.49, per 1000 atoms: 0.29
  Number of scatterers: 8491
  At special positions: 0
  Unit cell: (124.12, 98.44, 73.83, 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)
     S      42     16.00
     P       4     15.00
     O    1489      8.00
     N    1332      7.00
     C    5624      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
  Links applied
    NAG-ASN
      " NAG A 903 " - " ASN A 309 "
      " NAG B 903 " - " ASN B 309 "
  Time building additional restraints: 0.91
  Conformation dependent library (CDL) restraints added in 350.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2144

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 0 sheets defined
      86.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 41
      removed outlier: 3.612A  pdb=" N   ARG A  41 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 38 through 41'
    Processing helix  chain 'A' and resid 42 through 63
      removed outlier: 3.904A  pdb=" N   VAL A  53 " --> pdb=" O   CYS A  49 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ASN A  63 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 92
      removed outlier: 5.573A  pdb=" N   LEU A  82 " --> pdb=" O   SER A  78 " (cutoff:3.500A)
      Proline residue:  A  83  - end of helix
    Processing helix  chain 'A' and resid 99 through 125
      removed outlier: 3.922A  pdb=" N   LEU A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 141
      Proline residue:  A 138  - end of helix
    Processing helix  chain 'A' and resid 149 through 158
      removed outlier: 3.861A  pdb=" N   ILE A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 165
      removed outlier: 3.704A  pdb=" N   TYR A 165 " --> pdb=" O   TYR A 162 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 162 through 165'
    Processing helix  chain 'A' and resid 166 through 197
      removed outlier: 4.527A  pdb=" N   TYR A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
      Proline residue:  A 174  - end of helix
      Proline residue:  A 182  - end of helix
    Processing helix  chain 'A' and resid 202 through 216
      removed outlier: 3.878A  pdb=" N   ILE A 206 " --> pdb=" O   ASN A 202 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU A 209 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 233
      removed outlier: 3.708A  pdb=" N   PHE A 221 " --> pdb=" O   ASN A 217 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   PHE A 231 " --> pdb=" O   ILE A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 250
      removed outlier: 4.478A  pdb=" N   ASN A 243 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 264
      removed outlier: 3.807A  pdb=" N   SER A 255 " --> pdb=" O   SER A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 302
      removed outlier: 4.509A  pdb=" N   LEU A 290 " --> pdb=" O   LYS A 286 " (cutoff:3.500A)
      Proline residue:  A 291  - end of helix
    Processing helix  chain 'A' and resid 306 through 322
      removed outlier: 3.762A  pdb=" N   GLY A 321 " --> pdb=" O   ALA A 317 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   VAL A 322 " --> pdb=" O   PHE A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 337
    Processing helix  chain 'A' and resid 339 through 367
      removed outlier: 4.314A  pdb=" N   ALA A 355 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      Proline residue:  A 356  - end of helix
    Processing helix  chain 'A' and resid 373 through 404
      removed outlier: 4.294A  pdb=" N   TYR A 377 " --> pdb=" O   LYS A 373 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL A 389 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 435
      removed outlier: 3.951A  pdb=" N   PHE A 434 " --> pdb=" O   MET A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 473
      removed outlier: 3.739A  pdb=" N   GLY A 462 " --> pdb=" O   TYR A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 503
      Proline residue:  A 492  - end of helix
    Processing helix  chain 'A' and resid 511 through 515
      removed outlier: 3.684A  pdb=" N   PHE A 514 " --> pdb=" O   ASP A 511 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE A 515 " --> pdb=" O   SER A 512 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 511 through 515'
    Processing helix  chain 'A' and resid 517 through 546
      removed outlier: 3.606A  pdb=" N   MET A 521 " --> pdb=" O   GLY A 517 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ASN A 543 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 682
      removed outlier: 3.751A  pdb=" N   VAL A 659 " --> pdb=" O   LEU A 655 " (cutoff:3.500A)
      removed outlier: 4.903A  pdb=" N   LEU A 660 " --> pdb=" O   THR A 656 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A 666 " --> pdb=" O   CYS A 662 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE A 667 " --> pdb=" O   LEU A 663 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   SER A 675 " --> pdb=" O   ALA A 671 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   CYS A 676 " --> pdb=" O   ASN A 672 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   TRP A 679 " --> pdb=" O   SER A 675 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   LEU A 680 " --> pdb=" O   CYS A 676 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   PHE A 681 " --> pdb=" O   LEU A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 702
    Processing helix  chain 'A' and resid 702 through 712
      removed outlier: 3.605A  pdb=" N   ILE A 706 " --> pdb=" O   GLY A 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 41
    Processing helix  chain 'B' and resid 42 through 62
      removed outlier: 4.050A  pdb=" N   VAL B  53 " --> pdb=" O   CYS B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 80
      removed outlier: 3.991A  pdb=" N   GLY B  72 " --> pdb=" O   THR B  68 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU B  73 " --> pdb=" O   GLN B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 93
      removed outlier: 3.556A  pdb=" N   ALA B  84 " --> pdb=" O   PHE B  80 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   MET B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   VAL B  92 " --> pdb=" O   LYS B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 125
      removed outlier: 3.567A  pdb=" N   LEU B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU B 123 " --> pdb=" O   VAL B 119 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA B 125 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 128
      No H-bonds generated for 'chain 'B' and resid 126 through 128'
    Processing helix  chain 'B' and resid 129 through 141
      Proline residue:  B 138  - end of helix
    Processing helix  chain 'B' and resid 149 through 158
      removed outlier: 3.806A  pdb=" N   ILE B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 166
      removed outlier: 3.702A  pdb=" N   LEU B 166 " --> pdb=" O   PRO B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 196
      Proline residue:  B 174  - end of helix
      Proline residue:  B 182  - end of helix
      removed outlier: 3.972A  pdb=" N   PHE B 187 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASP B 195 " --> pdb=" O   GLN B 191 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   THR B 196 " --> pdb=" O   LYS B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 216
      removed outlier: 3.859A  pdb=" N   LEU B 209 " --> pdb=" O   LYS B 205 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU B 215 " --> pdb=" O   LEU B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 233
      removed outlier: 3.515A  pdb=" N   PHE B 221 " --> pdb=" O   ASN B 217 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   PHE B 231 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 250
      removed outlier: 4.434A  pdb=" N   ASN B 243 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   PHE B 244 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 264
      removed outlier: 3.658A  pdb=" N   SER B 255 " --> pdb=" O   SER B 251 " (cutoff:3.500A)
      removed outlier: 5.629A  pdb=" N   LEU B 257 " --> pdb=" O   SER B 253 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   MET B 264 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 288
    Processing helix  chain 'B' and resid 288 through 302
    Processing helix  chain 'B' and resid 307 through 322
      removed outlier: 3.661A  pdb=" N   THR B 311 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLY B 321 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   VAL B 322 " --> pdb=" O   PHE B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 337
    Processing helix  chain 'B' and resid 339 through 366
      removed outlier: 3.893A  pdb=" N   PHE B 352 " --> pdb=" O   VAL B 348 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ALA B 355 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      Proline residue:  B 356  - end of helix
      removed outlier: 4.013A  pdb=" N   TYR B 359 " --> pdb=" O   ALA B 355 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   THR B 366 " --> pdb=" O   ALA B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 404
      removed outlier: 3.733A  pdb=" N   ALA B 376 " --> pdb=" O   PRO B 372 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   TYR B 377 " --> pdb=" O   LYS B 373 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL B 389 " --> pdb=" O   ASP B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 435
      removed outlier: 3.613A  pdb=" N   LEU B 414 " --> pdb=" O   LEU B 410 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   THR B 415 " --> pdb=" O   PRO B 411 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA B 421 " --> pdb=" O   ASN B 417 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   CYS B 426 " --> pdb=" O   GLN B 422 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   PHE B 434 " --> pdb=" O   MET B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 474
      removed outlier: 4.075A  pdb=" N   GLY B 462 " --> pdb=" O   TYR B 458 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU B 464 " --> pdb=" O   TRP B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 478 through 502
      removed outlier: 3.825A  pdb=" N   GLY B 482 " --> pdb=" O   GLN B 478 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE B 483 " --> pdb=" O   ILE B 479 " (cutoff:3.500A)
      Proline residue:  B 492  - end of helix
    Processing helix  chain 'B' and resid 517 through 546
      removed outlier: 3.715A  pdb=" N   MET B 521 " --> pdb=" O   GLY B 517 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ASN B 543 " --> pdb=" O   LEU B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 681
      removed outlier: 3.620A  pdb=" N   VAL B 659 " --> pdb=" O   LEU B 655 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   LEU B 660 " --> pdb=" O   THR B 656 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU B 665 " --> pdb=" O   LEU B 661 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE B 667 " --> pdb=" O   LEU B 663 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLY B 668 " --> pdb=" O   LEU B 664 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA B 671 " --> pdb=" O   ILE B 667 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   SER B 675 " --> pdb=" O   ALA B 671 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   CYS B 676 " --> pdb=" O   ASN B 672 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU B 680 " --> pdb=" O   CYS B 676 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 702
      removed outlier: 3.554A  pdb=" N   VAL B 690 " --> pdb=" O   GLY B 686 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 702 through 712
      removed outlier: 4.066A  pdb=" N   ILE B 706 " --> pdb=" O   GLY B 702 " (cutoff:3.500A)

    655 hydrogen bonds defined for protein.
    1959 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.38

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1427
        1.33 -     1.45: 2253
        1.45 -     1.57: 4917
        1.57 -     1.70: 8
        1.70 -     1.82: 68
  Bond restraints: 8673
  Sorted by residual:
  bond pdb=" C21 POV A 901 "
       pdb=" O21 POV A 901 "
    ideal  model  delta    sigma   weight residual
    1.330  1.454 -0.124 2.00e-02 2.50e+03 3.87e+01
  bond pdb=" C31 POV A 901 "
       pdb=" O31 POV A 901 "
    ideal  model  delta    sigma   weight residual
    1.327  1.450 -0.123 2.00e-02 2.50e+03 3.79e+01
  bond pdb=" C   PHE A 367 "
       pdb=" N   PRO A 368 "
    ideal  model  delta    sigma   weight residual
    1.330  1.364 -0.034 1.25e-02 6.40e+03 7.55e+00
  bond pdb=" C1  NAG B 903 "
       pdb=" O5  NAG B 903 "
    ideal  model  delta    sigma   weight residual
    1.406  1.459 -0.053 2.00e-02 2.50e+03 7.09e+00
  bond pdb=" C1  NAG A 903 "
       pdb=" O5  NAG A 903 "
    ideal  model  delta    sigma   weight residual
    1.406  1.457 -0.051 2.00e-02 2.50e+03 6.53e+00
  ... (remaining 8668 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.90: 11467
        2.90 -     5.81: 279
        5.81 -     8.71: 43
        8.71 -    11.61: 16
       11.61 -    14.52: 5
  Bond angle restraints: 11810
  Sorted by residual:
  angle pdb=" N   GLY B 462 "
        pdb=" CA  GLY B 462 "
        pdb=" C   GLY B 462 "
      ideal   model   delta    sigma   weight residual
     112.77  120.28   -7.51 1.28e+00 6.10e-01 3.44e+01
  angle pdb=" C   ALA A  62 "
        pdb=" N   ASN A  63 "
        pdb=" CA  ASN A  63 "
      ideal   model   delta    sigma   weight residual
     121.54  131.15   -9.61 1.91e+00 2.74e-01 2.53e+01
  angle pdb=" C   ALA B  62 "
        pdb=" N   ASN B  63 "
        pdb=" CA  ASN B  63 "
      ideal   model   delta    sigma   weight residual
     121.54  131.07   -9.53 1.91e+00 2.74e-01 2.49e+01
  angle pdb=" C   LEU A 103 "
        pdb=" N   TYR A 104 "
        pdb=" CA  TYR A 104 "
      ideal   model   delta    sigma   weight residual
     121.14  112.85    8.29 1.75e+00 3.27e-01 2.24e+01
  angle pdb=" CA  LYS A 303 "
        pdb=" CB  LYS A 303 "
        pdb=" CG  LYS A 303 "
      ideal   model   delta    sigma   weight residual
     114.10  123.48   -9.38 2.00e+00 2.50e-01 2.20e+01
  ... (remaining 11805 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.90: 4529
       22.90 -    45.81: 444
       45.81 -    68.71: 68
       68.71 -    91.62: 17
       91.62 -   114.52: 33
  Dihedral angle restraints: 5091
    sinusoidal: 1769
      harmonic: 3322
  Sorted by residual:
  dihedral pdb=" N2  NAG A 903 "
           pdb=" C1  NAG A 903 "
           pdb=" C2  NAG A 903 "
           pdb=" O5  NAG A 903 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -178.19  -63.67 -114.52     1      3.00e+01 1.11e-03 1.51e+01
  dihedral pdb=" N2  NAG B 903 "
           pdb=" C1  NAG B 903 "
           pdb=" C2  NAG B 903 "
           pdb=" O5  NAG B 903 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -178.19  -64.17 -114.02     1      3.00e+01 1.11e-03 1.50e+01
  dihedral pdb=" C3  NAG A 903 "
           pdb=" C1  NAG A 903 "
           pdb=" C2  NAG A 903 "
           pdb=" O5  NAG A 903 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -55.55   58.16 -113.71     1      3.00e+01 1.11e-03 1.50e+01
  ... (remaining 5088 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.139: 1374
       0.139 -    0.279: 32
       0.279 -    0.418: 3
       0.418 -    0.557: 0
       0.557 -    0.697: 1
  Chirality restraints: 1410
  Sorted by residual:
  chirality pdb=" CG  LEU A 279 "
            pdb=" CB  LEU A 279 "
            pdb=" CD1 LEU A 279 "
            pdb=" CD2 LEU A 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.89   -0.70 2.00e-01 2.50e+01 1.21e+01
  chirality pdb=" C1  NAG A 903 "
            pdb=" ND2 ASN A 309 "
            pdb=" C2  NAG A 903 "
            pdb=" O5  NAG A 903 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.15e+00
  chirality pdb=" CB  ILE A 116 "
            pdb=" CA  ILE A 116 "
            pdb=" CG1 ILE A 116 "
            pdb=" CG2 ILE A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.14e+00
  ... (remaining 1407 not shown)

  Planarity restraints: 1460
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 348 "    0.023 2.00e-02 2.50e+03   4.65e-02 2.16e+01
        pdb=" C   VAL A 348 "   -0.080 2.00e-02 2.50e+03
        pdb=" O   VAL A 348 "    0.030 2.00e-02 2.50e+03
        pdb=" N   ILE A 349 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  77 "    0.018 2.00e-02 2.50e+03   3.56e-02 1.27e+01
        pdb=" C   VAL A  77 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   VAL A  77 "    0.023 2.00e-02 2.50e+03
        pdb=" N   SER A  78 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 326 "   -0.052 5.00e-02 4.00e+02   8.06e-02 1.04e+01
        pdb=" N   PRO A 327 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 327 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 327 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 1457 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 572
        2.73 -     3.27: 8844
        3.27 -     3.81: 13940
        3.81 -     4.36: 15927
        4.36 -     4.90: 27262
  Nonbonded interactions: 66545
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 138 "
            pdb=" OG1 THR A 142 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" O   SER A 251 "
            pdb=" OG  SER A 255 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ILE B 331 "
            pdb=" OG1 THR B 334 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   LEU A 300 "
            pdb=" NZ  LYS A 303 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" O   VAL B 117 "
            pdb=" OG1 THR B 121 "
     model   vdw
     2.272 3.040
  ... (remaining 66540 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 36 through 194 or (resid 195 through 196 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 202 through 368 or (resid 369 t \ 
hrough 371 and (name N or name CA or name C or name O or name CB )) or resid 372 \ 
 through 714 or (resid 715 through 717 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 901 through 903))
  selection = (chain 'B' and (resid 36 through 406 or (resid 407 through 421 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 422 through 447 or (resid 448 t \ 
hrough 450 and (name N or name CA or name C or name O or name CB )) or resid 451 \ 
 through 666 or (resid 667 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 668 through 903))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.800
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.124   8675  Z= 0.262
  Angle     :  1.141  14.516  11816  Z= 0.629
  Chirality :  0.061   0.697   1410
  Planarity :  0.007   0.081   1458
  Dihedral  : 21.166 114.522   2947
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.08 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 32.26 %
    Favored  : 66.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.36 (0.22), residues: 1136
  helix: -0.55 (0.15), residues: 885
  sheet:  None (None), residues: 0
  loop : -1.66 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  61 
 TYR   0.019   0.002   TYR B 170 
 PHE   0.046   0.003   PHE B 699 
 TRP   0.015   0.001   TRP A 679 
 HIS   0.011   0.003   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 ( 8673)
  covalent geometry    : angle       1.13784 (11810)
  hydrogen bonds       : bond        0.20759 (  655)
  hydrogen bonds       : angle       6.17561 ( 1959)
  link_NAG-ASN         : bond        0.01257 (    2)
  link_NAG-ASN         : angle       4.04099 (    6)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 189
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A  280 ILE cc_start: 0.8503 (mm) cc_final: 0.8043 (mp)
REVERT: A  358 MET cc_start: 0.8958 (mmm) cc_final: 0.8751 (tpp)
REVERT: B   47 LEU cc_start: 0.8252 (mm) cc_final: 0.7915 (mt)
  outliers start: 6
  outliers final: 3
  residues processed: 191
  average time/residue: 0.0751
  time to fit residues: 21.0598
Evaluate side-chains
  179 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 176
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  711 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:   50.0000
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
A 310 HIS
B 181 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.174984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.133833 restraints weight = 12753.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.137684 restraints weight = 7362.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.139867 restraints weight = 5330.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.141267 restraints weight = 4460.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.142330 restraints weight = 4010.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   8675  Z= 0.248
  Angle     :  0.780  10.155  11816  Z= 0.397
  Chirality :  0.048   0.273   1410
  Planarity :  0.006   0.069   1458
  Dihedral  : 13.444 107.058   1385
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.64 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 25.84 %
    Favored  : 68.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.24), residues: 1136
  helix:  0.91 (0.16), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.36 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 235 
 TYR   0.021   0.002   TYR B 455 
 PHE   0.034   0.002   PHE B 332 
 TRP   0.013   0.002   TRP A 460 
 HIS   0.005   0.001   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 8673)
  covalent geometry    : angle       0.77369 (11810)
  hydrogen bonds       : bond        0.05358 (  655)
  hydrogen bonds       : angle       4.48981 ( 1959)
  link_NAG-ASN         : bond        0.00907 (    2)
  link_NAG-ASN         : angle       4.29985 (    6)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 174
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A   48 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8213 (tt0)
REVERT: A  185 PHE cc_start: 0.7796 (m-80) cc_final: 0.7555 (m-80)
REVERT: A  299 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7037 (mt-10)
  outliers start: 41
  outliers final: 21
  residues processed: 200
  average time/residue: 0.0825
  time to fit residues: 23.7576
Evaluate side-chains
  180 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 GLU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  286 LYS
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  297 MET
Chi-restraints excluded: chain B residue  339 GLU
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  460 TRP
Chi-restraints excluded: chain B residue  711 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 109 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 108 optimal weight:    6.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 216 GLN
A 310 HIS
B 181 ASN
B 216 GLN
B 310 HIS
B 412 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.179291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.138643 restraints weight = 12591.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.142723 restraints weight = 7140.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.145221 restraints weight = 5102.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.146602 restraints weight = 4195.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.147216 restraints weight = 3789.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8675  Z= 0.144
  Angle     :  0.674  10.990  11816  Z= 0.335
  Chirality :  0.044   0.191   1410
  Planarity :  0.005   0.066   1458
  Dihedral  : 12.026  96.118   1382
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.82 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 26.48 %
    Favored  : 69.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.25), residues: 1136
  helix:  1.63 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.37 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  61 
 TYR   0.019   0.001   TYR B 104 
 PHE   0.021   0.001   PHE B 332 
 TRP   0.014   0.001   TRP A 460 
 HIS   0.008   0.002   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8673)
  covalent geometry    : angle       0.66543 (11810)
  hydrogen bonds       : bond        0.04541 (  655)
  hydrogen bonds       : angle       4.12144 ( 1959)
  link_NAG-ASN         : bond        0.00739 (    2)
  link_NAG-ASN         : angle       4.75581 (    6)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 173
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.8436 (tttt) cc_final: 0.7771 (tptt)
REVERT: A  299 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7087 (mt-10)
REVERT: A  358 MET cc_start: 0.8612 (tpp) cc_final: 0.8271 (ttp)
REVERT: B  358 MET cc_start: 0.8157 (mmm) cc_final: 0.7563 (mtp)
REVERT: B  365 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8307 (mm)
REVERT: B  390 SER cc_start: 0.8998 (t) cc_final: 0.8184 (p)
REVERT: B  420 ILE cc_start: 0.8486 (tt) cc_final: 0.8241 (tp)
  outliers start: 35
  outliers final: 24
  residues processed: 195
  average time/residue: 0.0730
  time to fit residues: 21.1574
Evaluate side-chains
  186 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  339 GLU
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  460 TRP
Chi-restraints excluded: chain B residue  670 PHE
Chi-restraints excluded: chain B residue  695 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0980
   chunk 4 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   chunk 16 optimal weight:   20.0000
   chunk 80 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
A 310 HIS
B 216 GLN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.180069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.139591 restraints weight = 12778.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.143694 restraints weight = 7172.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.145886 restraints weight = 5102.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.147733 restraints weight = 4238.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.148212 restraints weight = 3760.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8675  Z= 0.135
  Angle     :  0.649  10.662  11816  Z= 0.322
  Chirality :  0.043   0.189   1410
  Planarity :  0.005   0.071   1458
  Dihedral  : 11.499  91.820   1380
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.99 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 26.48 %
    Favored  : 68.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.25), residues: 1136
  helix:  1.91 (0.17), residues: 911
  sheet:  None (None), residues: 0
  loop : -1.31 (0.41), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 213 
 TYR   0.016   0.001   TYR B 104 
 PHE   0.022   0.001   PHE B 221 
 TRP   0.015   0.001   TRP A 460 
 HIS   0.003   0.001   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8673)
  covalent geometry    : angle       0.64115 (11810)
  hydrogen bonds       : bond        0.04166 (  655)
  hydrogen bonds       : angle       3.98797 ( 1959)
  link_NAG-ASN         : bond        0.00673 (    2)
  link_NAG-ASN         : angle       4.37989 (    6)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 179
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  185 PHE cc_start: 0.7756 (m-80) cc_final: 0.7540 (m-80)
REVERT: A  194 LYS cc_start: 0.8442 (tttt) cc_final: 0.7735 (tptt)
REVERT: A  299 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7071 (mt-10)
REVERT: A  377 TYR cc_start: 0.7079 (m-80) cc_final: 0.6781 (m-80)
REVERT: A  691 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7730 (tm-30)
REVERT: B  130 ARG cc_start: 0.6879 (mtp180) cc_final: 0.6166 (ttm110)
REVERT: B  296 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7157 (mm-30)
REVERT: B  390 SER cc_start: 0.9010 (t) cc_final: 0.8220 (p)
REVERT: B  420 ILE cc_start: 0.8465 (tt) cc_final: 0.8210 (tp)
REVERT: B  450 LEU cc_start: 0.8203 (tp) cc_final: 0.7952 (tp)
  outliers start: 38
  outliers final: 27
  residues processed: 207
  average time/residue: 0.0814
  time to fit residues: 24.3053
Evaluate side-chains
  185 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  286 LYS
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  339 GLU
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  460 TRP
Chi-restraints excluded: chain B residue  670 PHE
Chi-restraints excluded: chain B residue  695 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 113 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   chunk 104 optimal weight:    0.3980
   chunk 95 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 77 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 310 HIS
B 181 ASN
B 417 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.176352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.134870 restraints weight = 12231.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.139122 restraints weight = 6756.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.141827 restraints weight = 4696.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.143206 restraints weight = 3787.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.144401 restraints weight = 3350.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8675  Z= 0.163
  Angle     :  0.680   9.702  11816  Z= 0.337
  Chirality :  0.045   0.180   1410
  Planarity :  0.005   0.072   1458
  Dihedral  : 11.372  91.987   1380
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.08 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 27.76 %
    Favored  : 67.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.26), residues: 1136
  helix:  1.94 (0.17), residues: 914
  sheet:  None (None), residues: 0
  loop : -1.26 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 213 
 TYR   0.016   0.001   TYR B 104 
 PHE   0.023   0.002   PHE B 221 
 TRP   0.015   0.001   TRP A 460 
 HIS   0.004   0.001   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 8673)
  covalent geometry    : angle       0.67371 (11810)
  hydrogen bonds       : bond        0.04399 (  655)
  hydrogen bonds       : angle       4.07483 ( 1959)
  link_NAG-ASN         : bond        0.00594 (    2)
  link_NAG-ASN         : angle       4.17377 (    6)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 167
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 PHE cc_start: 0.7871 (m-80) cc_final: 0.7610 (m-80)
REVERT: A  194 LYS cc_start: 0.8454 (tttt) cc_final: 0.7758 (tptt)
REVERT: A  299 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7218 (mt-10)
REVERT: A  377 TYR cc_start: 0.7394 (m-80) cc_final: 0.7104 (m-80)
REVERT: A  432 TRP cc_start: 0.7797 (t-100) cc_final: 0.7580 (t-100)
REVERT: A  691 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7609 (tm-30)
REVERT: B  130 ARG cc_start: 0.6899 (mtp180) cc_final: 0.6057 (ttm110)
REVERT: B  365 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8260 (mm)
REVERT: B  420 ILE cc_start: 0.8479 (tt) cc_final: 0.8219 (tp)
REVERT: B  450 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7901 (tp)
  outliers start: 38
  outliers final: 27
  residues processed: 192
  average time/residue: 0.0826
  time to fit residues: 22.9282
Evaluate side-chains
  187 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 157
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  339 GLU
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  460 TRP
Chi-restraints excluded: chain B residue  670 PHE
Chi-restraints excluded: chain B residue  695 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 107 optimal weight:    9.9990
   chunk 74 optimal weight:    1.9990
   chunk 93 optimal weight:    0.4980
   chunk 31 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 47 optimal weight:   30.0000
   chunk 12 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 380 GLN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 703 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.177535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.136479 restraints weight = 12021.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.140731 restraints weight = 6680.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.143379 restraints weight = 4675.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.144940 restraints weight = 3760.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.146024 restraints weight = 3331.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8675  Z= 0.144
  Angle     :  0.664   9.836  11816  Z= 0.327
  Chirality :  0.044   0.189   1410
  Planarity :  0.004   0.073   1458
  Dihedral  : 10.999  91.159   1380
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.26 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 28.66 %
    Favored  : 66.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.26), residues: 1136
  helix:  2.04 (0.17), residues: 913
  sheet:  None (None), residues: 0
  loop : -1.26 (0.42), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 213 
 TYR   0.012   0.001   TYR B 104 
 PHE   0.021   0.001   PHE B 221 
 TRP   0.016   0.001   TRP A 460 
 HIS   0.003   0.001   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8673)
  covalent geometry    : angle       0.65730 (11810)
  hydrogen bonds       : bond        0.04169 (  655)
  hydrogen bonds       : angle       3.97240 ( 1959)
  link_NAG-ASN         : bond        0.00566 (    2)
  link_NAG-ASN         : angle       4.11951 (    6)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 169
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A  185 PHE cc_start: 0.7739 (m-80) cc_final: 0.7516 (m-80)
REVERT: A  194 LYS cc_start: 0.8475 (tttt) cc_final: 0.7784 (tptt)
REVERT: A  235 ARG cc_start: 0.7591 (mtp85) cc_final: 0.7293 (mtp85)
REVERT: A  299 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7151 (mt-10)
REVERT: A  377 TYR cc_start: 0.7363 (m-80) cc_final: 0.7075 (m-80)
REVERT: A  432 TRP cc_start: 0.7882 (t-100) cc_final: 0.7668 (t-100)
REVERT: A  691 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7489 (tm-30)
REVERT: B   41 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7691 (ttp80)
REVERT: B  130 ARG cc_start: 0.6883 (mtp180) cc_final: 0.6031 (ttm110)
REVERT: B  361 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8451 (t)
REVERT: B  365 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8229 (mm)
REVERT: B  420 ILE cc_start: 0.8393 (tt) cc_final: 0.8123 (tp)
REVERT: B  450 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7884 (tp)
  outliers start: 40
  outliers final: 27
  residues processed: 195
  average time/residue: 0.0893
  time to fit residues: 24.4212
Evaluate side-chains
  190 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 158
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain B residue   41 ARG
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  297 MET
Chi-restraints excluded: chain B residue  339 GLU
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  361 SER
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  460 TRP
Chi-restraints excluded: chain B residue  670 PHE
Chi-restraints excluded: chain B residue  695 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 70 optimal weight:    0.8980
   chunk 64 optimal weight:    0.1980
   chunk 85 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 20 optimal weight:    0.3980
   chunk 49 optimal weight:    5.9990
   chunk 59 optimal weight:    0.0070
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
A 380 GLN
** A 703 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 = 0.4126 r_free = 0.4126 target = 0.180860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.139730 restraints weight = 12218.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.144145 restraints weight = 6743.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.147012 restraints weight = 4673.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.148521 restraints weight = 3734.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.149770 restraints weight = 3294.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8675  Z= 0.128
  Angle     :  0.667  11.488  11816  Z= 0.323
  Chirality :  0.044   0.206   1410
  Planarity :  0.004   0.075   1458
  Dihedral  : 10.469  88.010   1380
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.17 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 29.69 %
    Favored  : 65.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.16 (0.26), residues: 1136
  helix:  2.07 (0.17), residues: 916
  sheet:  None (None), residues: 0
  loop : -1.37 (0.42), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 235 
 TYR   0.019   0.001   TYR A 689 
 PHE   0.021   0.001   PHE B 221 
 TRP   0.017   0.001   TRP A 460 
 HIS   0.003   0.001   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8673)
  covalent geometry    : angle       0.66016 (11810)
  hydrogen bonds       : bond        0.03914 (  655)
  hydrogen bonds       : angle       3.90835 ( 1959)
  link_NAG-ASN         : bond        0.00576 (    2)
  link_NAG-ASN         : angle       4.15636 (    6)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 181
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 LYS cc_start: 0.8507 (tttt) cc_final: 0.7727 (tptt)
REVERT: A  235 ARG cc_start: 0.7464 (mtp85) cc_final: 0.7216 (mtp85)
REVERT: A  299 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7127 (mt-10)
REVERT: A  377 TYR cc_start: 0.7350 (m-80) cc_final: 0.7068 (m-80)
REVERT: A  432 TRP cc_start: 0.7838 (t-100) cc_final: 0.7551 (t-100)
REVERT: A  691 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7461 (tm-30)
REVERT: B   89 ASN cc_start: 0.7273 (m110) cc_final: 0.7039 (m110)
REVERT: B  130 ARG cc_start: 0.6838 (mtp180) cc_final: 0.6008 (ttm110)
REVERT: B  293 LEU cc_start: 0.7842 (mt) cc_final: 0.7461 (tp)
REVERT: B  361 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8356 (t)
REVERT: B  365 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8238 (mm)
REVERT: B  390 SER cc_start: 0.9061 (t) cc_final: 0.8203 (p)
REVERT: B  420 ILE cc_start: 0.8471 (tt) cc_final: 0.8219 (tp)
REVERT: B  450 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7855 (tp)
  outliers start: 34
  outliers final: 21
  residues processed: 204
  average time/residue: 0.0843
  time to fit residues: 24.6233
Evaluate side-chains
  190 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  361 SER
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  670 PHE
Chi-restraints excluded: chain B residue  695 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 103 optimal weight:   50.0000
   chunk 108 optimal weight:   40.0000
   chunk 102 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    0.2980
   chunk 112 optimal weight:    1.9990
   chunk 24 optimal weight:    0.2980
   chunk 34 optimal weight:    0.7980
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 716 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.180155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.139538 restraints weight = 12054.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.143950 restraints weight = 6631.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.146558 restraints weight = 4578.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.148461 restraints weight = 3676.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.149187 restraints weight = 3207.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.3699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8675  Z= 0.134
  Angle     :  0.684   9.328  11816  Z= 0.334
  Chirality :  0.044   0.212   1410
  Planarity :  0.004   0.075   1458
  Dihedral  : 10.251  88.031   1380
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.99 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 30.85 %
    Favored  : 65.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.26), residues: 1136
  helix:  2.02 (0.17), residues: 915
  sheet:  None (None), residues: 0
  loop : -1.35 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 213 
 TYR   0.014   0.001   TYR B 104 
 PHE   0.021   0.001   PHE B 221 
 TRP   0.017   0.001   TRP A 460 
 HIS   0.009   0.002   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8673)
  covalent geometry    : angle       0.67779 (11810)
  hydrogen bonds       : bond        0.03976 (  655)
  hydrogen bonds       : angle       3.95800 ( 1959)
  link_NAG-ASN         : bond        0.00513 (    2)
  link_NAG-ASN         : angle       4.21697 (    6)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 174
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  185 PHE cc_start: 0.7531 (m-80) cc_final: 0.7182 (m-80)
REVERT: A  194 LYS cc_start: 0.8368 (tttt) cc_final: 0.7712 (tptt)
REVERT: A  221 PHE cc_start: 0.8085 (p90) cc_final: 0.7880 (p90)
REVERT: A  235 ARG cc_start: 0.7460 (mtp85) cc_final: 0.7217 (mtp85)
REVERT: A  299 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7144 (mt-10)
REVERT: A  377 TYR cc_start: 0.7389 (m-80) cc_final: 0.7113 (m-80)
REVERT: A  432 TRP cc_start: 0.7842 (t-100) cc_final: 0.7572 (t-100)
REVERT: A  691 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7409 (tm-30)
REVERT: B  130 ARG cc_start: 0.6839 (mtp180) cc_final: 0.5993 (ttm110)
REVERT: B  365 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8238 (mm)
REVERT: B  390 SER cc_start: 0.9063 (t) cc_final: 0.8220 (p)
REVERT: B  420 ILE cc_start: 0.8397 (tt) cc_final: 0.8134 (tp)
REVERT: B  450 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7808 (tp)
  outliers start: 31
  outliers final: 23
  residues processed: 195
  average time/residue: 0.0813
  time to fit residues: 22.8609
Evaluate side-chains
  190 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 164
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  197 GLN
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  670 PHE
Chi-restraints excluded: chain B residue  695 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0170
   chunk 34 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 54 optimal weight:    9.9990
   chunk 93 optimal weight:    5.9990
   chunk 112 optimal weight:    0.0670
   chunk 105 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.4756

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 716 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.181247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.140533 restraints weight = 12133.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.144891 restraints weight = 6707.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.147686 restraints weight = 4658.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.149206 restraints weight = 3734.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.150119 restraints weight = 3296.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8675  Z= 0.134
  Angle     :  0.708  12.930  11816  Z= 0.341
  Chirality :  0.044   0.252   1410
  Planarity :  0.004   0.075   1458
  Dihedral  : 10.088  87.470   1380
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.90 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 30.98 %
    Favored  : 65.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.26), residues: 1136
  helix:  2.04 (0.17), residues: 914
  sheet:  None (None), residues: 0
  loop : -1.32 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 213 
 TYR   0.019   0.001   TYR A 689 
 PHE   0.023   0.001   PHE A 701 
 TRP   0.018   0.001   TRP A 460 
 HIS   0.003   0.001   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8673)
  covalent geometry    : angle       0.70155 (11810)
  hydrogen bonds       : bond        0.03920 (  655)
  hydrogen bonds       : angle       3.94494 ( 1959)
  link_NAG-ASN         : bond        0.00502 (    2)
  link_NAG-ASN         : angle       4.31052 (    6)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 170
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 PHE cc_start: 0.7479 (m-80) cc_final: 0.7124 (m-80)
REVERT: A  194 LYS cc_start: 0.8380 (tttt) cc_final: 0.7701 (tptt)
REVERT: A  221 PHE cc_start: 0.8030 (p90) cc_final: 0.7823 (p90)
REVERT: A  235 ARG cc_start: 0.7416 (mtp85) cc_final: 0.7202 (mtp85)
REVERT: A  299 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7097 (mt-10)
REVERT: A  377 TYR cc_start: 0.7336 (m-80) cc_final: 0.7072 (m-80)
REVERT: A  432 TRP cc_start: 0.7799 (t-100) cc_final: 0.7522 (t-100)
REVERT: A  691 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7415 (tm-30)
REVERT: B  130 ARG cc_start: 0.6859 (mtp180) cc_final: 0.6041 (ttm110)
REVERT: B  365 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8222 (mm)
REVERT: B  390 SER cc_start: 0.9063 (t) cc_final: 0.8219 (p)
REVERT: B  420 ILE cc_start: 0.8352 (tt) cc_final: 0.8068 (tp)
REVERT: B  450 LEU cc_start: 0.8070 (tp) cc_final: 0.7802 (tp)
  outliers start: 30
  outliers final: 25
  residues processed: 191
  average time/residue: 0.0795
  time to fit residues: 22.2312
Evaluate side-chains
  192 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 165
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  197 GLN
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  670 PHE
Chi-restraints excluded: chain B residue  695 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 91 optimal weight:    0.7980
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0980
   chunk 16 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 716 HIS
B 181 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.181093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.140150 restraints weight = 12164.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.144521 restraints weight = 6768.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.147200 restraints weight = 4719.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.149022 restraints weight = 3798.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.149847 restraints weight = 3320.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8675  Z= 0.138
  Angle     :  0.711  12.187  11816  Z= 0.345
  Chirality :  0.045   0.247   1410
  Planarity :  0.004   0.075   1458
  Dihedral  :  9.977  87.905   1380
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.17 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 31.75 %
    Favored  : 64.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.26), residues: 1136
  helix:  2.03 (0.17), residues: 914
  sheet:  None (None), residues: 0
  loop : -1.30 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  41 
 TYR   0.026   0.001   TYR B 455 
 PHE   0.023   0.001   PHE B 221 
 TRP   0.020   0.001   TRP A 460 
 HIS   0.014   0.003   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8673)
  covalent geometry    : angle       0.70448 (11810)
  hydrogen bonds       : bond        0.03974 (  655)
  hydrogen bonds       : angle       3.94552 ( 1959)
  link_NAG-ASN         : bond        0.00467 (    2)
  link_NAG-ASN         : angle       4.43287 (    6)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 168
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 PHE cc_start: 0.7517 (m-80) cc_final: 0.7151 (m-80)
REVERT: A  221 PHE cc_start: 0.8027 (p90) cc_final: 0.7801 (p90)
REVERT: A  231 PHE cc_start: 0.7804 (m-10) cc_final: 0.7568 (m-10)
REVERT: A  235 ARG cc_start: 0.7451 (mtp85) cc_final: 0.7201 (mtp85)
REVERT: A  299 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7131 (mt-10)
REVERT: A  377 TYR cc_start: 0.7398 (m-80) cc_final: 0.7141 (m-80)
REVERT: A  432 TRP cc_start: 0.7849 (t-100) cc_final: 0.7576 (t-100)
REVERT: A  691 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7401 (tm-30)
REVERT: B  130 ARG cc_start: 0.6873 (mtp180) cc_final: 0.6036 (ttm110)
REVERT: B  365 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8245 (mm)
REVERT: B  390 SER cc_start: 0.9061 (t) cc_final: 0.8218 (p)
REVERT: B  420 ILE cc_start: 0.8346 (tt) cc_final: 0.8047 (tp)
REVERT: B  450 LEU cc_start: 0.8066 (tp) cc_final: 0.7802 (tp)
  outliers start: 28
  outliers final: 26
  residues processed: 186
  average time/residue: 0.0766
  time to fit residues: 20.9069
Evaluate side-chains
  190 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 162
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  197 GLN
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  181 ASN
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  458 TYR
Chi-restraints excluded: chain B residue  670 PHE
Chi-restraints excluded: chain B residue  695 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 109 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 716 HIS
B 181 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.180552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.139403 restraints weight = 12235.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.143800 restraints weight = 6801.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.146527 restraints weight = 4734.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.148269 restraints weight = 3805.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.148927 restraints weight = 3337.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.3855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8675  Z= 0.147
  Angle     :  0.736  11.767  11816  Z= 0.355
  Chirality :  0.045   0.239   1410
  Planarity :  0.005   0.075   1458
  Dihedral  :  9.927  88.138   1380
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.17 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 31.62 %
    Favored  : 64.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.26), residues: 1136
  helix:  2.03 (0.17), residues: 914
  sheet:  None (None), residues: 0
  loop : -1.29 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  41 
 TYR   0.025   0.001   TYR B 455 
 PHE   0.023   0.001   PHE B 221 
 TRP   0.020   0.001   TRP A 460 
 HIS   0.005   0.001   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8673)
  covalent geometry    : angle       0.72960 (11810)
  hydrogen bonds       : bond        0.04047 (  655)
  hydrogen bonds       : angle       3.96783 ( 1959)
  link_NAG-ASN         : bond        0.00446 (    2)
  link_NAG-ASN         : angle       4.51954 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1569.71 seconds
wall clock time: 27 minutes 51.52 seconds (1671.52 seconds total)