Starting phenix.real_space_refine
on Wed Sep 17 21:48:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5sy1_8315/09_2025/5sy1_8315.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5sy1_8315/09_2025/5sy1_8315.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5sy1_8315/09_2025/5sy1_8315.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5sy1_8315/09_2025/5sy1_8315.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5sy1_8315/09_2025/5sy1_8315.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5sy1_8315/09_2025/5sy1_8315.map"
  }
  resolution = 3.9
  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=   0.005
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
     Ca      8      9.91       5
     S      70      5.16       5
     C    7472      2.51       5
     N    1886      2.21       5
     O    2026      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  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: 11462
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "C"
      Number of atoms: 1154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1154
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 2, 'TRANS': 144}
    Chain: "A"
      Number of atoms: 4545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 582, 4545
          Classifications: {'peptide': 582}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 24, 'TRANS': 557}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 113
          Unresolved non-hydrogen angles: 143
          Unresolved non-hydrogen dihedrals: 99
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 5, 'ASP:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 80
    Chain: "B"
      Number of atoms: 4545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 582, 4545
          Classifications: {'peptide': 582}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 24, 'TRANS': 557}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 113
          Unresolved non-hydrogen angles: 143
          Unresolved non-hydrogen dihedrals: 99
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 5, 'ASP:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 80
    Chain: "D"
      Number of atoms: 1154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1154
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 2, 'TRANS': 144}
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' CA': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' CA': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 2.62, per 1000 atoms: 0.23
  Number of scatterers: 11462
  At special positions: 0
  Unit cell: (131.775, 81.575, 134.285, 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)
     Ca      8     19.99
     S      70     16.00
     O    2026      8.00
     N    1886      7.00
     C    7472      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 442.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2748

  Finding SS restraints...
    Secondary structure from input PDB file:
      82 helices and 2 sheets defined
      73.0% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'C' and resid 6 through 19
      removed outlier: 3.502A  pdb=" N   ILE C  10 " --> pdb=" O   THR C   6 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   PHE C  13 " --> pdb=" O   GLN C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 40
      removed outlier: 3.612A  pdb=" N   THR C  35 " --> pdb=" O   LYS C  31 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   VAL C  36 " --> pdb=" O   GLU C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 57
      removed outlier: 3.751A  pdb=" N   ASN C  54 " --> pdb=" O   GLN C  50 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLU C  55 " --> pdb=" O   ASP C  51 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   VAL C  56 " --> pdb=" O   MET C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 77
      removed outlier: 3.963A  pdb=" N   MET C  72 " --> pdb=" O   GLU C  68 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   MET C  73 " --> pdb=" O   PHE C  69 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LYS C  76 " --> pdb=" O   MET C  72 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   MET C  77 " --> pdb=" O   MET C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 94
      removed outlier: 3.588A  pdb=" N   ILE C  86 " --> pdb=" O   SER C  82 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ARG C  91 " --> pdb=" O   ARG C  87 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   VAL C  92 " --> pdb=" O   GLU C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 113
      removed outlier: 4.001A  pdb=" N   VAL C 109 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 127
      removed outlier: 3.705A  pdb=" N   ILE C 126 " --> pdb=" O   VAL C 122 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ARG C 127 " --> pdb=" O   ASP C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 148
    Processing helix  chain 'A' and resid 31 through 59
      removed outlier: 4.582A  pdb=" N   LEU A  39 " --> pdb=" O   ALA A  35 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ILE A  42 " --> pdb=" O   GLY A  38 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA A  45 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   VAL A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   MET A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU A  53 " --> pdb=" O   LEU A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 107
      removed outlier: 3.849A  pdb=" N   VAL A  91 " --> pdb=" O   LYS A  87 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   CYS A  99 " --> pdb=" O   GLY A  95 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LEU A 101 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU A 106 " --> pdb=" O   VAL A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 129
      removed outlier: 4.528A  pdb=" N   LEU A 126 " --> pdb=" O   TRP A 123 " (cutoff:3.500A)
      removed outlier: 5.270A  pdb=" N   ALA A 127 " --> pdb=" O   MET A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 135
    Processing helix  chain 'A' and resid 135 through 141
      removed outlier: 3.982A  pdb=" N   LEU A 139 " --> pdb=" O   TYR A 135 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   CYS A 141 " --> pdb=" O   PRO A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 144
      No H-bonds generated for 'chain 'A' and resid 142 through 144'
    Processing helix  chain 'A' and resid 146 through 170
      removed outlier: 3.701A  pdb=" N   TYR A 150 " --> pdb=" O   ASN A 146 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL A 151 " --> pdb=" O   LYS A 147 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU A 155 " --> pdb=" O   VAL A 151 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU A 156 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ASP A 170 " --> pdb=" O   TRP A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 186
    Processing helix  chain 'A' and resid 186 through 198
      removed outlier: 3.637A  pdb=" N   LEU A 193 " --> pdb=" O   GLN A 189 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU A 196 " --> pdb=" O   CYS A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 206
    Processing helix  chain 'A' and resid 207 through 210
    Processing helix  chain 'A' and resid 222 through 235
      removed outlier: 3.749A  pdb=" N   ARG A 226 " --> pdb=" O   SER A 222 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL A 229 " --> pdb=" O   TYR A 225 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE A 232 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 262
      removed outlier: 3.782A  pdb=" N   ALA A 257 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   VAL A 258 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 298
      removed outlier: 3.657A  pdb=" N   SER A 278 " --> pdb=" O   LYS A 274 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   VAL A 279 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   VAL A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE A 294 " --> pdb=" O   ALA A 290 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU A 298 " --> pdb=" O   ILE A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 307
      removed outlier: 3.706A  pdb=" N   ILE A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   VAL A 304 " --> pdb=" O   THR A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 319
      removed outlier: 3.702A  pdb=" N   LEU A 315 " --> pdb=" O   ASN A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 377
      removed outlier: 4.564A  pdb=" N   CYS A 340 " --> pdb=" O   TYR A 336 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   GLU A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A 354 " --> pdb=" O   THR A 350 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   MET A 361 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL A 365 " --> pdb=" O   MET A 361 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   HIS A 367 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ARG A 368 " --> pdb=" O   MET A 364 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY A 377 " --> pdb=" O   GLY A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 386
      removed outlier: 3.618A  pdb=" N   HIS A 386 " --> pdb=" O   VAL A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 400
      removed outlier: 3.813A  pdb=" N   LEU A 396 " --> pdb=" O   SER A 392 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   VAL A 397 " --> pdb=" O   ARG A 393 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   CYS A 398 " --> pdb=" O   PRO A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 430
      removed outlier: 3.513A  pdb=" N   LEU A 410 " --> pdb=" O   GLN A 406 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   CYS A 411 " --> pdb=" O   ALA A 407 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ILE A 423 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU A 426 " --> pdb=" O   PHE A 422 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   PHE A 427 " --> pdb=" O   ILE A 423 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ALA A 428 " --> pdb=" O   CYS A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 438
    Processing helix  chain 'A' and resid 447 through 451
    Processing helix  chain 'A' and resid 453 through 472
      removed outlier: 3.944A  pdb=" N   THR A 457 " --> pdb=" O   PRO A 453 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LEU A 458 " --> pdb=" O   PHE A 454 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL A 459 " --> pdb=" O   TRP A 455 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER A 469 " --> pdb=" O   GLN A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 480
      No H-bonds generated for 'chain 'A' and resid 478 through 480'
    Processing helix  chain 'A' and resid 487 through 496
      removed outlier: 3.725A  pdb=" N   LEU A 491 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR A 494 " --> pdb=" O   PHE A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 522
      removed outlier: 3.828A  pdb=" N   MET A 502 " --> pdb=" O   LEU A 498 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   VAL A 506 " --> pdb=" O   MET A 502 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR A 515 " --> pdb=" O   ARG A 511 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE A 518 " --> pdb=" O   ILE A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 525
      No H-bonds generated for 'chain 'A' and resid 523 through 525'
    Processing helix  chain 'A' and resid 532 through 538
      removed outlier: 3.796A  pdb=" N   GLU A 536 " --> pdb=" O   ARG A 533 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   ALA A 537 " --> pdb=" O   ASN A 534 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   PHE A 538 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 554
      removed outlier: 3.542A  pdb=" N   ILE A 551 " --> pdb=" O   HIS A 547 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 569
      removed outlier: 3.957A  pdb=" N   GLY A 565 " --> pdb=" O   LYS A 561 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU A 566 " --> pdb=" O   ALA A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 619
      removed outlier: 3.530A  pdb=" N   TRP A 610 " --> pdb=" O   ALA A 606 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASN A 618 " --> pdb=" O   TYR A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 622
      No H-bonds generated for 'chain 'A' and resid 620 through 622'
    Processing helix  chain 'A' and resid 623 through 628
    Processing helix  chain 'B' and resid 31 through 59
      removed outlier: 4.583A  pdb=" N   LEU B  39 " --> pdb=" O   ALA B  35 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ILE B  42 " --> pdb=" O   GLY B  38 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA B  45 " --> pdb=" O   HIS B  41 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   VAL B  50 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   MET B  52 " --> pdb=" O   SER B  48 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 107
      removed outlier: 3.848A  pdb=" N   VAL B  91 " --> pdb=" O   LYS B  87 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   CYS B  99 " --> pdb=" O   GLY B  95 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU B 101 " --> pdb=" O   LEU B  97 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   LEU B 106 " --> pdb=" O   VAL B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 129
      removed outlier: 4.528A  pdb=" N   LEU B 126 " --> pdb=" O   TRP B 123 " (cutoff:3.500A)
      removed outlier: 5.270A  pdb=" N   ALA B 127 " --> pdb=" O   MET B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 135
    Processing helix  chain 'B' and resid 135 through 141
      removed outlier: 3.981A  pdb=" N   LEU B 139 " --> pdb=" O   TYR B 135 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   CYS B 141 " --> pdb=" O   PRO B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 144
      No H-bonds generated for 'chain 'B' and resid 142 through 144'
    Processing helix  chain 'B' and resid 146 through 170
      removed outlier: 3.701A  pdb=" N   TYR B 150 " --> pdb=" O   ASN B 146 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL B 151 " --> pdb=" O   LYS B 147 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU B 155 " --> pdb=" O   VAL B 151 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ASP B 170 " --> pdb=" O   TRP B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 186
    Processing helix  chain 'B' and resid 186 through 198
      removed outlier: 3.638A  pdb=" N   LEU B 193 " --> pdb=" O   GLN B 189 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU B 196 " --> pdb=" O   CYS B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 206
    Processing helix  chain 'B' and resid 207 through 210
    Processing helix  chain 'B' and resid 222 through 235
      removed outlier: 3.750A  pdb=" N   ARG B 226 " --> pdb=" O   SER B 222 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL B 229 " --> pdb=" O   TYR B 225 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE B 232 " --> pdb=" O   TYR B 228 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS B 235 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 262
      removed outlier: 3.782A  pdb=" N   ALA B 257 " --> pdb=" O   ARG B 253 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   VAL B 258 " --> pdb=" O   LEU B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 298
      removed outlier: 3.658A  pdb=" N   SER B 278 " --> pdb=" O   LYS B 274 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   VAL B 279 " --> pdb=" O   LEU B 275 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   VAL B 280 " --> pdb=" O   ALA B 276 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE B 294 " --> pdb=" O   ALA B 290 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL B 297 " --> pdb=" O   LEU B 293 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU B 298 " --> pdb=" O   ILE B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 307
      removed outlier: 3.706A  pdb=" N   ILE B 303 " --> pdb=" O   PRO B 299 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   VAL B 304 " --> pdb=" O   THR B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 319
      removed outlier: 3.702A  pdb=" N   LEU B 315 " --> pdb=" O   ASN B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 377
      removed outlier: 4.563A  pdb=" N   CYS B 340 " --> pdb=" O   TYR B 336 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLU B 342 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU B 354 " --> pdb=" O   THR B 350 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   MET B 361 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL B 365 " --> pdb=" O   MET B 361 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   HIS B 367 " --> pdb=" O   SER B 363 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ARG B 368 " --> pdb=" O   MET B 364 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY B 377 " --> pdb=" O   GLY B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 386
      removed outlier: 3.616A  pdb=" N   HIS B 386 " --> pdb=" O   VAL B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 400
      removed outlier: 3.814A  pdb=" N   LEU B 396 " --> pdb=" O   SER B 392 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   VAL B 397 " --> pdb=" O   ARG B 393 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   CYS B 398 " --> pdb=" O   PRO B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 430
      removed outlier: 3.513A  pdb=" N   LEU B 410 " --> pdb=" O   GLN B 406 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   CYS B 411 " --> pdb=" O   ALA B 407 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LEU B 412 " --> pdb=" O   ALA B 408 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ILE B 423 " --> pdb=" O   LEU B 419 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU B 426 " --> pdb=" O   PHE B 422 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   PHE B 427 " --> pdb=" O   ILE B 423 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ALA B 428 " --> pdb=" O   CYS B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 438
    Processing helix  chain 'B' and resid 447 through 451
    Processing helix  chain 'B' and resid 453 through 472
      removed outlier: 3.945A  pdb=" N   THR B 457 " --> pdb=" O   PRO B 453 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LEU B 458 " --> pdb=" O   PHE B 454 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL B 459 " --> pdb=" O   TRP B 455 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER B 469 " --> pdb=" O   GLN B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 478 through 480
      No H-bonds generated for 'chain 'B' and resid 478 through 480'
    Processing helix  chain 'B' and resid 487 through 496
      removed outlier: 3.724A  pdb=" N   LEU B 491 " --> pdb=" O   GLY B 487 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   TYR B 494 " --> pdb=" O   PHE B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 522
      removed outlier: 3.828A  pdb=" N   MET B 502 " --> pdb=" O   LEU B 498 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   VAL B 506 " --> pdb=" O   MET B 502 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   THR B 515 " --> pdb=" O   ARG B 511 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE B 518 " --> pdb=" O   ILE B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 525
      No H-bonds generated for 'chain 'B' and resid 523 through 525'
    Processing helix  chain 'B' and resid 532 through 538
      removed outlier: 3.796A  pdb=" N   GLU B 536 " --> pdb=" O   ARG B 533 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   ALA B 537 " --> pdb=" O   ASN B 534 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   PHE B 538 " --> pdb=" O   VAL B 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 554
      removed outlier: 3.542A  pdb=" N   ILE B 551 " --> pdb=" O   HIS B 547 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL B 553 " --> pdb=" O   LEU B 549 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 569
      removed outlier: 3.957A  pdb=" N   GLY B 565 " --> pdb=" O   LYS B 561 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU B 566 " --> pdb=" O   ALA B 562 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 619
      removed outlier: 3.530A  pdb=" N   TRP B 610 " --> pdb=" O   ALA B 606 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASN B 618 " --> pdb=" O   TYR B 614 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 620 through 622
      No H-bonds generated for 'chain 'B' and resid 620 through 622'
    Processing helix  chain 'B' and resid 623 through 628
    Processing helix  chain 'D' and resid 6 through 19
      removed outlier: 3.503A  pdb=" N   ILE D  10 " --> pdb=" O   THR D   6 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   PHE D  13 " --> pdb=" O   GLN D   9 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 40
      removed outlier: 3.612A  pdb=" N   THR D  35 " --> pdb=" O   LYS D  31 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   VAL D  36 " --> pdb=" O   GLU D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 57
      removed outlier: 3.752A  pdb=" N   ASN D  54 " --> pdb=" O   GLN D  50 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU D  55 " --> pdb=" O   ASP D  51 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   VAL D  56 " --> pdb=" O   MET D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 65 through 77
      removed outlier: 3.964A  pdb=" N   MET D  72 " --> pdb=" O   GLU D  68 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   MET D  73 " --> pdb=" O   PHE D  69 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LYS D  76 " --> pdb=" O   MET D  72 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   MET D  77 " --> pdb=" O   MET D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 94
      removed outlier: 3.589A  pdb=" N   ILE D  86 " --> pdb=" O   SER D  82 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ARG D  91 " --> pdb=" O   ARG D  87 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   VAL D  92 " --> pdb=" O   GLU D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 113
      removed outlier: 4.000A  pdb=" N   VAL D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 127
      removed outlier: 3.704A  pdb=" N   ILE D 126 " --> pdb=" O   VAL D 122 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ARG D 127 " --> pdb=" O   ASP D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 148
    Processing sheet with id=AA1, first strand: chain 'A' and resid 474 through 476
    Processing sheet with id=AA2, first strand: chain 'B' and resid 474 through 476

    575 hydrogen bonds defined for protein.
    1677 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: 1.73

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3558
        1.34 -     1.46: 2688
        1.46 -     1.58: 5350
        1.58 -     1.70: 0
        1.70 -     1.82: 112
  Bond restraints: 11708
  Sorted by residual:
  bond pdb=" C   TRP B 452 "
       pdb=" N   PRO B 453 "
    ideal  model  delta    sigma   weight residual
    1.337  1.366 -0.029 1.24e-02 6.50e+03 5.55e+00
  bond pdb=" C   TRP A 452 "
       pdb=" N   PRO A 453 "
    ideal  model  delta    sigma   weight residual
    1.337  1.366 -0.029 1.24e-02 6.50e+03 5.44e+00
  bond pdb=" C   THR B 264 "
       pdb=" N   PRO B 265 "
    ideal  model  delta    sigma   weight residual
    1.332  1.362 -0.030 1.34e-02 5.57e+03 4.90e+00
  bond pdb=" C   THR A 264 "
       pdb=" N   PRO A 265 "
    ideal  model  delta    sigma   weight residual
    1.332  1.361 -0.029 1.34e-02 5.57e+03 4.63e+00
  bond pdb=" CB  THR A 403 "
       pdb=" CG2 THR A 403 "
    ideal  model  delta    sigma   weight residual
    1.521  1.455  0.066 3.30e-02 9.18e+02 4.00e+00
  ... (remaining 11703 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 14955
        1.94 -     3.89: 796
        3.89 -     5.83: 107
        5.83 -     7.78: 34
        7.78 -     9.72: 18
  Bond angle restraints: 15910
  Sorted by residual:
  angle pdb=" N   HIS A 109 "
        pdb=" CA  HIS A 109 "
        pdb=" C   HIS A 109 "
      ideal   model   delta    sigma   weight residual
     109.81  119.53   -9.72 2.21e+00 2.05e-01 1.93e+01
  angle pdb=" N   HIS B 109 "
        pdb=" CA  HIS B 109 "
        pdb=" C   HIS B 109 "
      ideal   model   delta    sigma   weight residual
     109.81  119.52   -9.71 2.21e+00 2.05e-01 1.93e+01
  angle pdb=" N   THR B 264 "
        pdb=" CA  THR B 264 "
        pdb=" C   THR B 264 "
      ideal   model   delta    sigma   weight residual
     109.81  119.36   -9.55 2.21e+00 2.05e-01 1.87e+01
  angle pdb=" N   THR A 264 "
        pdb=" CA  THR A 264 "
        pdb=" C   THR A 264 "
      ideal   model   delta    sigma   weight residual
     109.81  119.30   -9.49 2.21e+00 2.05e-01 1.84e+01
  angle pdb=" C   ASN B 119 "
        pdb=" N   LYS B 120 "
        pdb=" CA  LYS B 120 "
      ideal   model   delta    sigma   weight residual
     121.54  129.54   -8.00 1.91e+00 2.74e-01 1.76e+01
  ... (remaining 15905 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.36: 6593
       14.36 -    28.73: 362
       28.73 -    43.09: 75
       43.09 -    57.45: 16
       57.45 -    71.82: 2
  Dihedral angle restraints: 7048
    sinusoidal: 2796
      harmonic: 4252
  Sorted by residual:
  dihedral pdb=" CA  HIS B 109 "
           pdb=" C   HIS B 109 "
           pdb=" N   PRO B 110 "
           pdb=" CA  PRO B 110 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -125.21  -54.79     0      5.00e+00 4.00e-02 1.20e+02
  dihedral pdb=" CA  HIS A 109 "
           pdb=" C   HIS A 109 "
           pdb=" N   PRO A 110 "
           pdb=" CA  PRO A 110 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -125.25  -54.75     0      5.00e+00 4.00e-02 1.20e+02
  dihedral pdb=" CA  THR B 264 "
           pdb=" C   THR B 264 "
           pdb=" N   PRO B 265 "
           pdb=" CA  PRO B 265 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.07  -41.93     0      5.00e+00 4.00e-02 7.03e+01
  ... (remaining 7045 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1352
       0.056 -    0.112: 443
       0.112 -    0.168: 63
       0.168 -    0.223: 8
       0.223 -    0.279: 6
  Chirality restraints: 1872
  Sorted by residual:
  chirality pdb=" C13 CLR A 701 "
            pdb=" C12 CLR A 701 "
            pdb=" C14 CLR A 701 "
            pdb=" C17 CLR A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.65   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" C13 CLR B 701 "
            pdb=" C12 CLR B 701 "
            pdb=" C14 CLR B 701 "
            pdb=" C17 CLR B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.65   -0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  CYS B 171 "
            pdb=" N   CYS B 171 "
            pdb=" C   CYS B 171 "
            pdb=" CB  CYS B 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 1869 not shown)

  Planarity restraints: 1976
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 237 "    0.052 5.00e-02 4.00e+02   7.74e-02 9.59e+00
        pdb=" N   PRO A 238 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A 238 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 238 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 237 "   -0.052 5.00e-02 4.00e+02   7.72e-02 9.54e+00
        pdb=" N   PRO B 238 "    0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO B 238 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 238 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 532 "   -0.013 2.00e-02 2.50e+03   2.56e-02 6.57e+00
        pdb=" CG  ASN A 532 "    0.044 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 532 "   -0.017 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 532 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1973 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.20: 10
        2.20 -     2.87: 4203
        2.87 -     3.55: 15687
        3.55 -     4.22: 25701
        4.22 -     4.90: 41675
  Nonbonded interactions: 87276
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C  57 "
            pdb=" OD1 ASP C  59 "
     model   vdw
     1.524 3.040
  nonbonded pdb=" OD1 ASP D  57 "
            pdb=" OD1 ASP D  59 "
     model   vdw
     1.525 3.040
  nonbonded pdb=" OD2 ASP D  21 "
            pdb=" OD1 ASP D  25 "
     model   vdw
     1.782 3.040
  nonbonded pdb=" OD2 ASP C  21 "
            pdb=" OD1 ASP C  25 "
     model   vdw
     1.782 3.040
  nonbonded pdb=" OD2 ASP C  23 "
            pdb=" OE2 GLU C  32 "
     model   vdw
     1.845 3.040
  ... (remaining 87271 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.940
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6219
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      :  0.008   0.074  11708  Z= 0.354
  Angle     :  1.022   9.721  15910  Z= 0.540
  Chirality :  0.055   0.279   1872
  Planarity :  0.008   0.077   1976
  Dihedral  : 10.045  71.817   4300
  Min Nonbonded Distance : 1.524

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.12 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.63 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    Twisted General : 0.29 %

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: -5.23 (0.16), residues: 1446
  helix: -3.96 (0.08), residues: 936
  sheet: -2.76 (1.03), residues: 20
  loop : -1.90 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 486 
 TYR   0.014   0.003   TYR B  94 
 PHE   0.038   0.004   PHE A  40 
 TRP   0.018   0.002   TRP A 399 
 HIS   0.007   0.002   HIS B 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00791 (11708)
  covalent geometry    : angle       1.02182 (15910)
  hydrogen bonds       : bond        0.31774 (  575)
  hydrogen bonds       : angle       9.72055 ( 1677)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 396
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    3 ASP cc_start: 0.7028 (m-30) cc_final: 0.6428 (t70)
REVERT: C    4 GLN cc_start: 0.8855 (tt0) cc_final: 0.8605 (tt0)
REVERT: C    8 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8197 (pm20)
REVERT: C   15 GLU cc_start: 0.8639 (tp30) cc_final: 0.8371 (tp30)
REVERT: C   38 ARG cc_start: 0.8518 (ttm110) cc_final: 0.8168 (ptp-110)
REVERT: C   52 MET cc_start: 0.8763 (mtp) cc_final: 0.8066 (ttp)
REVERT: C   73 MET cc_start: 0.8033 (mmm) cc_final: 0.7756 (mmp)
REVERT: C   77 MET cc_start: 0.7526 (mpt) cc_final: 0.6730 (mpp)
REVERT: C   85 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7907 (tm-30)
REVERT: C   93 PHE cc_start: 0.7242 (m-80) cc_final: 0.6484 (m-80)
REVERT: C  101 ILE cc_start: 0.6517 (mt) cc_final: 0.6267 (mp)
REVERT: C  124 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7943 (tp30)
REVERT: C  125 MET cc_start: 0.7466 (mtt) cc_final: 0.6561 (mmm)
REVERT: A   52 MET cc_start: 0.7390 (mtp) cc_final: 0.6923 (ttt)
REVERT: A  104 MET cc_start: 0.8396 (ttp) cc_final: 0.8059 (tmm)
REVERT: A  109 HIS cc_start: 0.7137 (p90) cc_final: 0.6588 (t70)
REVERT: A  150 TYR cc_start: 0.8249 (m-80) cc_final: 0.8022 (m-80)
REVERT: A  187 LEU cc_start: 0.8634 (mt) cc_final: 0.8409 (mt)
REVERT: A  215 ASN cc_start: 0.6243 (p0) cc_final: 0.5617 (m-40)
REVERT: A  220 LEU cc_start: 0.8833 (tp) cc_final: 0.8534 (mt)
REVERT: A  249 LYS cc_start: 0.6213 (tttt) cc_final: 0.6004 (mtmt)
REVERT: A  268 VAL cc_start: 0.8414 (t) cc_final: 0.7780 (p)
REVERT: A  286 LEU cc_start: 0.6102 (tp) cc_final: 0.5902 (tp)
REVERT: A  532 ASN cc_start: 0.8530 (t0) cc_final: 0.8102 (t0)
REVERT: A  550 LYS cc_start: 0.7850 (ttmm) cc_final: 0.7459 (mmtp)
REVERT: A  602 ASN cc_start: 0.7139 (t0) cc_final: 0.6652 (t0)
REVERT: A  604 LYS cc_start: 0.8333 (tptt) cc_final: 0.8083 (mtpp)
REVERT: B   53 LEU cc_start: 0.7843 (mt) cc_final: 0.7418 (tt)
REVERT: B  109 HIS cc_start: 0.7039 (p90) cc_final: 0.6189 (t70)
REVERT: B  125 ILE cc_start: 0.7715 (mt) cc_final: 0.7458 (pt)
REVERT: B  130 TYR cc_start: 0.7500 (t80) cc_final: 0.7263 (t80)
REVERT: B  181 TYR cc_start: 0.8668 (t80) cc_final: 0.8468 (t80)
REVERT: B  186 SER cc_start: 0.7362 (m) cc_final: 0.7123 (p)
REVERT: B  220 LEU cc_start: 0.8656 (tp) cc_final: 0.8371 (mt)
REVERT: B  235 LYS cc_start: 0.7346 (tttt) cc_final: 0.6555 (tmtt)
REVERT: B  268 VAL cc_start: 0.8198 (t) cc_final: 0.7456 (p)
REVERT: B  326 ASP cc_start: 0.6283 (t0) cc_final: 0.5855 (t0)
REVERT: D    4 GLN cc_start: 0.9047 (tt0) cc_final: 0.8237 (tm-30)
REVERT: D    8 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8182 (pm20)
REVERT: D   15 GLU cc_start: 0.8882 (tp30) cc_final: 0.8680 (tp30)
REVERT: D   17 PHE cc_start: 0.8742 (t80) cc_final: 0.8515 (t80)
REVERT: D   38 ARG cc_start: 0.8606 (ttm110) cc_final: 0.8385 (ptp-110)
REVERT: D   69 PHE cc_start: 0.6796 (t80) cc_final: 0.6557 (t80)
REVERT: D   85 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7774 (tm-30)
REVERT: D   93 PHE cc_start: 0.7375 (m-80) cc_final: 0.6851 (m-80)
REVERT: D   95 LYS cc_start: 0.7247 (mttt) cc_final: 0.6959 (mtmt)
REVERT: D  101 ILE cc_start: 0.7001 (mt) cc_final: 0.6519 (mp)
REVERT: D  124 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7740 (tp30)
REVERT: D  125 MET cc_start: 0.7875 (mtt) cc_final: 0.7095 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 397
  average time/residue: 0.1234
  time to fit residues: 66.8544
Evaluate side-chains
  225 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0570
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    8.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
C 108 HIS
A 465 GLN
A 466 HIS
A 500 ASN
B 209 GLN
B 465 GLN
B 519 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.136516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.098676 restraints weight = 23250.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.101213 restraints weight = 13964.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.102813 restraints weight = 10362.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.103527 restraints weight = 8772.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.103527 restraints weight = 8096.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11708  Z= 0.152
  Angle     :  0.714   8.253  15910  Z= 0.373
  Chirality :  0.043   0.203   1872
  Planarity :  0.007   0.084   1976
  Dihedral  :  6.455  47.359   1692
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 10.42 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    Twisted General : 0.14 %

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: -2.97 (0.19), residues: 1446
  helix: -1.79 (0.13), residues: 996
  sheet: -1.51 (1.26), residues: 20
  loop : -1.95 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  69 
 TYR   0.025   0.001   TYR B 178 
 PHE   0.023   0.001   PHE C  17 
 TRP   0.015   0.001   TRP B 158 
 HIS   0.004   0.001   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (11708)
  covalent geometry    : angle       0.71422 (15910)
  hydrogen bonds       : bond        0.06437 (  575)
  hydrogen bonds       : angle       5.05167 ( 1677)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 287
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 GLN cc_start: 0.8534 (tt0) cc_final: 0.8124 (tm-30)
REVERT: C   38 ARG cc_start: 0.8253 (ttm110) cc_final: 0.8030 (ttm110)
REVERT: C   91 ARG cc_start: 0.7777 (mtt90) cc_final: 0.7377 (mmt90)
REVERT: C   93 PHE cc_start: 0.7539 (m-80) cc_final: 0.6883 (m-80)
REVERT: C  125 MET cc_start: 0.7533 (mtt) cc_final: 0.7314 (mmm)
REVERT: A   52 MET cc_start: 0.7185 (mtp) cc_final: 0.6577 (ttm)
REVERT: A  186 SER cc_start: 0.8610 (m) cc_final: 0.8091 (p)
REVERT: A  215 ASN cc_start: 0.7131 (p0) cc_final: 0.5996 (m-40)
REVERT: A  224 TYR cc_start: 0.8242 (t80) cc_final: 0.7966 (t80)
REVERT: A  268 VAL cc_start: 0.9054 (t) cc_final: 0.8799 (p)
REVERT: A  343 ILE cc_start: 0.8808 (mt) cc_final: 0.8432 (tp)
REVERT: A  354 LEU cc_start: 0.9287 (tp) cc_final: 0.9085 (tp)
REVERT: A  496 LEU cc_start: 0.8487 (mt) cc_final: 0.8211 (mt)
REVERT: A  602 ASN cc_start: 0.6678 (t0) cc_final: 0.6191 (t0)
REVERT: B   53 LEU cc_start: 0.7980 (mt) cc_final: 0.7540 (tt)
REVERT: B  186 SER cc_start: 0.8561 (m) cc_final: 0.7995 (p)
REVERT: B  235 LYS cc_start: 0.7742 (tttt) cc_final: 0.6853 (tmtt)
REVERT: B  268 VAL cc_start: 0.8654 (t) cc_final: 0.8340 (p)
REVERT: B  455 TRP cc_start: 0.8326 (m-10) cc_final: 0.8078 (m-10)
REVERT: B  552 GLU cc_start: 0.8915 (tp30) cc_final: 0.8712 (tp30)
REVERT: B  610 TRP cc_start: 0.7364 (m-10) cc_final: 0.7116 (m-10)
REVERT: D    4 GLN cc_start: 0.8753 (tt0) cc_final: 0.8312 (tm-30)
REVERT: D   38 ARG cc_start: 0.8244 (ttm110) cc_final: 0.8002 (ptp-110)
REVERT: D   91 ARG cc_start: 0.8198 (mtt90) cc_final: 0.7489 (mtt-85)
REVERT: D  106 LEU cc_start: 0.8695 (tt) cc_final: 0.8405 (pp)
REVERT: D  117 LEU cc_start: 0.6398 (mt) cc_final: 0.6135 (tp)
REVERT: D  120 GLU cc_start: 0.7763 (pm20) cc_final: 0.7548 (pm20)
REVERT: D  125 MET cc_start: 0.7369 (mtt) cc_final: 0.7094 (mmm)
REVERT: D  139 TYR cc_start: 0.7353 (t80) cc_final: 0.6881 (t80)
  outliers start: 22
  outliers final: 9
  residues processed: 301
  average time/residue: 0.0974
  time to fit residues: 42.5082
Evaluate side-chains
  211 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 202
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain B residue  141 CYS
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain D residue   53 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 96 optimal weight:    0.1980
   chunk 31 optimal weight:    8.9990
   chunk 114 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 3 optimal weight:   10.0000
   chunk 68 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 91 optimal weight:   10.0000
   chunk 127 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
C  54 ASN
C 112 ASN
B 109 HIS
B 465 GLN
D  54 ASN
** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.133937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.098101 restraints weight = 23813.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.098209 restraints weight = 15605.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.099014 restraints weight = 12509.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.099504 restraints weight = 10935.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.099491 restraints weight = 10310.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.3913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  11708  Z= 0.161
  Angle     :  0.686   7.805  15910  Z= 0.354
  Chirality :  0.043   0.203   1872
  Planarity :  0.006   0.087   1976
  Dihedral  :  5.954  45.962   1692
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 12.38 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    Twisted General : 0.14 %

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: -1.67 (0.21), residues: 1446
  helix: -0.72 (0.15), residues: 996
  sheet: -1.52 (1.24), residues: 20
  loop : -1.69 (0.32), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 376 
 TYR   0.029   0.002   TYR B 178 
 PHE   0.051   0.002   PHE B  40 
 TRP   0.014   0.001   TRP B 452 
 HIS   0.010   0.001   HIS D 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (11708)
  covalent geometry    : angle       0.68624 (15910)
  hydrogen bonds       : bond        0.05440 (  575)
  hydrogen bonds       : angle       4.63151 ( 1677)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 223
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 GLN cc_start: 0.8701 (tt0) cc_final: 0.8216 (tm-30)
REVERT: C   12 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8100 (tp30)
REVERT: C   15 GLU cc_start: 0.8046 (tt0) cc_final: 0.7703 (mt-10)
REVERT: C   72 MET cc_start: 0.8469 (mtp) cc_final: 0.8192 (mtp)
REVERT: C   81 ASP cc_start: 0.7211 (p0) cc_final: 0.6921 (p0)
REVERT: C   93 PHE cc_start: 0.7549 (m-80) cc_final: 0.6902 (m-80)
REVERT: C  125 MET cc_start: 0.7712 (mtt) cc_final: 0.7462 (mmm)
REVERT: A   52 MET cc_start: 0.7207 (mtp) cc_final: 0.6622 (ttm)
REVERT: A  200 TYR cc_start: 0.8219 (m-10) cc_final: 0.7896 (m-80)
REVERT: A  215 ASN cc_start: 0.6694 (p0) cc_final: 0.5923 (m-40)
REVERT: A  268 VAL cc_start: 0.9032 (t) cc_final: 0.8825 (p)
REVERT: B   53 LEU cc_start: 0.7792 (mt) cc_final: 0.7560 (tt)
REVERT: B  135 TYR cc_start: 0.8438 (m-80) cc_final: 0.8076 (m-80)
REVERT: B  235 LYS cc_start: 0.7748 (tttt) cc_final: 0.6688 (tmtt)
REVERT: B  268 VAL cc_start: 0.8729 (t) cc_final: 0.8405 (p)
REVERT: B  364 MET cc_start: 0.8661 (tpp) cc_final: 0.8372 (tpp)
REVERT: B  610 TRP cc_start: 0.7309 (m-10) cc_final: 0.7086 (m-10)
REVERT: D    4 GLN cc_start: 0.8784 (tt0) cc_final: 0.8295 (tm-30)
REVERT: D   72 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8125 (mtp)
REVERT: D   91 ARG cc_start: 0.8259 (mtt90) cc_final: 0.7507 (mtt-85)
REVERT: D  120 GLU cc_start: 0.7617 (pm20) cc_final: 0.7336 (pm20)
REVERT: D  125 MET cc_start: 0.7433 (mtt) cc_final: 0.7100 (mmm)
REVERT: D  139 TYR cc_start: 0.7093 (t80) cc_final: 0.6872 (t80)
  outliers start: 39
  outliers final: 27
  residues processed: 246
  average time/residue: 0.1040
  time to fit residues: 36.7665
Evaluate side-chains
  222 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 194
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   84 THR
Chi-restraints excluded: chain A residue  109 HIS
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  141 CYS
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  412 LEU
Chi-restraints excluded: chain B residue  452 TRP
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  554 SER
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue   72 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 136 optimal weight:    0.9980
   chunk 100 optimal weight:   10.0000
   chunk 55 optimal weight:   10.0000
   chunk 132 optimal weight:    8.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
C 112 ASN
A 109 HIS
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 547 HIS
B 465 GLN
B 547 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.132641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.098916 restraints weight = 23945.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.098134 restraints weight = 17477.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.098708 restraints weight = 14691.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.099204 restraints weight = 12215.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.099202 restraints weight = 11347.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.4369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11708  Z= 0.180
  Angle     :  0.694   9.014  15910  Z= 0.356
  Chirality :  0.043   0.202   1872
  Planarity :  0.006   0.086   1976
  Dihedral  :  5.828  45.864   1692
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 13.03 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.77 %
    Twisted General : 0.14 %

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: -1.11 (0.22), residues: 1446
  helix: -0.24 (0.16), residues: 996
  sheet: -1.55 (1.22), residues: 20
  loop : -1.63 (0.32), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 255 
 TYR   0.029   0.002   TYR B 178 
 PHE   0.024   0.002   PHE D  17 
 TRP   0.013   0.001   TRP B 452 
 HIS   0.009   0.001   HIS C 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (11708)
  covalent geometry    : angle       0.69443 (15910)
  hydrogen bonds       : bond        0.05136 (  575)
  hydrogen bonds       : angle       4.63843 ( 1677)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 206
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 GLN cc_start: 0.8691 (tt0) cc_final: 0.8154 (tm-30)
REVERT: C   12 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7954 (tp30)
REVERT: C   72 MET cc_start: 0.8438 (mtp) cc_final: 0.8224 (mtp)
REVERT: C   93 PHE cc_start: 0.7445 (m-80) cc_final: 0.6850 (m-80)
REVERT: C  125 MET cc_start: 0.7671 (mtt) cc_final: 0.7278 (mmm)
REVERT: A   52 MET cc_start: 0.7243 (mtp) cc_final: 0.6683 (ttm)
REVERT: A  215 ASN cc_start: 0.6683 (p0) cc_final: 0.5879 (m-40)
REVERT: A  268 VAL cc_start: 0.9034 (t) cc_final: 0.8815 (p)
REVERT: A  343 ILE cc_start: 0.8843 (mt) cc_final: 0.8357 (tp)
REVERT: B  109 HIS cc_start: 0.6826 (OUTLIER) cc_final: 0.6331 (t-90)
REVERT: B  135 TYR cc_start: 0.8397 (m-80) cc_final: 0.8031 (m-80)
REVERT: B  268 VAL cc_start: 0.8776 (t) cc_final: 0.8448 (p)
REVERT: B  361 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7629 (ttp)
REVERT: B  568 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8729 (mm)
REVERT: D    4 GLN cc_start: 0.8676 (tt0) cc_final: 0.8266 (tm-30)
REVERT: D   72 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8381 (mtp)
REVERT: D   77 MET cc_start: 0.8796 (mpp) cc_final: 0.8531 (mpp)
REVERT: D   91 ARG cc_start: 0.8231 (mtt90) cc_final: 0.7502 (mtt-85)
REVERT: D  120 GLU cc_start: 0.7622 (pm20) cc_final: 0.7351 (pm20)
  outliers start: 51
  outliers final: 37
  residues processed: 234
  average time/residue: 0.0920
  time to fit residues: 32.0670
Evaluate side-chains
  225 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 184
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   84 THR
Chi-restraints excluded: chain A residue  109 HIS
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  109 HIS
Chi-restraints excluded: chain B residue  141 CYS
Chi-restraints excluded: chain B residue  197 SER
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  412 LEU
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  433 ILE
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  452 TRP
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  509 ILE
Chi-restraints excluded: chain B residue  554 SER
Chi-restraints excluded: chain B residue  566 LEU
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   72 MET
Chi-restraints excluded: chain D residue  109 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 110 optimal weight:    0.1980
   chunk 36 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0570
   chunk 24 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 10 optimal weight:   30.0000
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
C 136 GLN
** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 465 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.135321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.099700 restraints weight = 23632.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.100592 restraints weight = 14891.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.100945 restraints weight = 11240.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.101474 restraints weight = 10609.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.101430 restraints weight = 10143.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.4709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11708  Z= 0.126
  Angle     :  0.640   7.670  15910  Z= 0.325
  Chirality :  0.041   0.205   1872
  Planarity :  0.005   0.084   1976
  Dihedral  :  5.492  43.292   1692
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.15 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    Twisted General : 0.14 %

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: -0.57 (0.22), residues: 1446
  helix:  0.16 (0.16), residues: 998
  sheet: -1.48 (1.18), residues: 20
  loop : -1.42 (0.33), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 255 
 TYR   0.024   0.001   TYR B 178 
 PHE   0.020   0.001   PHE A 427 
 TRP   0.010   0.001   TRP B 158 
 HIS   0.014   0.001   HIS A 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (11708)
  covalent geometry    : angle       0.63999 (15910)
  hydrogen bonds       : bond        0.04405 (  575)
  hydrogen bonds       : angle       4.29983 ( 1677)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 216
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 GLN cc_start: 0.8730 (tt0) cc_final: 0.8177 (tm-30)
REVERT: C   12 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7847 (tp30)
REVERT: C  125 MET cc_start: 0.7728 (mtt) cc_final: 0.7290 (mmm)
REVERT: A   52 MET cc_start: 0.7388 (mtp) cc_final: 0.7161 (ttp)
REVERT: A  168 LYS cc_start: 0.7490 (mmmm) cc_final: 0.7145 (mmmm)
REVERT: A  215 ASN cc_start: 0.6489 (p0) cc_final: 0.5670 (m-40)
REVERT: A  220 LEU cc_start: 0.8270 (tt) cc_final: 0.8017 (mp)
REVERT: A  259 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8095 (pttm)
REVERT: A  268 VAL cc_start: 0.8940 (t) cc_final: 0.8700 (p)
REVERT: A  316 LEU cc_start: 0.6421 (mt) cc_final: 0.6025 (mt)
REVERT: A  509 ILE cc_start: 0.9211 (pt) cc_final: 0.8963 (mm)
REVERT: B  109 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6722 (t-90)
REVERT: B  135 TYR cc_start: 0.8321 (m-80) cc_final: 0.7967 (m-80)
REVERT: B  268 VAL cc_start: 0.8631 (t) cc_final: 0.8366 (p)
REVERT: B  316 LEU cc_start: 0.6574 (mt) cc_final: 0.6174 (tp)
REVERT: B  361 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7547 (ttp)
REVERT: B  568 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8730 (mm)
REVERT: D    4 GLN cc_start: 0.8674 (tt0) cc_final: 0.8367 (tm-30)
REVERT: D   91 ARG cc_start: 0.8244 (mtt90) cc_final: 0.7455 (mtt-85)
REVERT: D  120 GLU cc_start: 0.7645 (pm20) cc_final: 0.7411 (pm20)
REVERT: D  125 MET cc_start: 0.7586 (mtt) cc_final: 0.7196 (mmm)
  outliers start: 28
  outliers final: 11
  residues processed: 230
  average time/residue: 0.0945
  time to fit residues: 32.0680
Evaluate side-chains
  205 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 190
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain B residue  109 HIS
Chi-restraints excluded: chain B residue  141 CYS
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  452 TRP
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain D residue   64 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 79 optimal weight:    7.9990
   chunk 52 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 142 optimal weight:    0.0980
   chunk 50 optimal weight:    9.9990
   chunk 131 optimal weight:    0.9990
   chunk 89 optimal weight:    7.9990
   chunk 112 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 115 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
C 108 HIS
** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 602 ASN
B 465 GLN
D   9 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.134644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.099155 restraints weight = 23443.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.100196 restraints weight = 14206.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.100509 restraints weight = 10660.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.100972 restraints weight = 10305.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.100973 restraints weight = 9586.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.4915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11708  Z= 0.126
  Angle     :  0.644   8.681  15910  Z= 0.325
  Chirality :  0.041   0.208   1872
  Planarity :  0.005   0.086   1976
  Dihedral  :  5.371  43.348   1692
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.72 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.14 %

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: -0.27 (0.23), residues: 1446
  helix:  0.42 (0.16), residues: 1000
  sheet: -1.40 (1.16), residues: 20
  loop : -1.39 (0.33), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 255 
 TYR   0.025   0.001   TYR B 178 
 PHE   0.016   0.001   PHE A 427 
 TRP   0.011   0.001   TRP B 452 
 HIS   0.008   0.001   HIS A 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (11708)
  covalent geometry    : angle       0.64363 (15910)
  hydrogen bonds       : bond        0.04239 (  575)
  hydrogen bonds       : angle       4.25191 ( 1677)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 205
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 GLN cc_start: 0.8747 (tt0) cc_final: 0.8150 (tm-30)
REVERT: C   12 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7830 (tp30)
REVERT: C   72 MET cc_start: 0.8006 (mtp) cc_final: 0.7795 (mtp)
REVERT: C  125 MET cc_start: 0.7777 (mtt) cc_final: 0.7344 (mmm)
REVERT: A   52 MET cc_start: 0.7428 (mtp) cc_final: 0.7209 (ttp)
REVERT: A  168 LYS cc_start: 0.7452 (mmmm) cc_final: 0.7186 (mmmm)
REVERT: A  215 ASN cc_start: 0.6056 (p0) cc_final: 0.5648 (m-40)
REVERT: A  259 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8075 (pttm)
REVERT: A  268 VAL cc_start: 0.8944 (t) cc_final: 0.8699 (p)
REVERT: A  316 LEU cc_start: 0.6725 (mt) cc_final: 0.6387 (mt)
REVERT: A  343 ILE cc_start: 0.8866 (mt) cc_final: 0.8396 (tp)
REVERT: B  109 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.7058 (t-90)
REVERT: B  135 TYR cc_start: 0.8381 (m-80) cc_final: 0.7981 (m-80)
REVERT: B  268 VAL cc_start: 0.8631 (t) cc_final: 0.8329 (p)
REVERT: B  316 LEU cc_start: 0.6581 (mt) cc_final: 0.6184 (tp)
REVERT: B  410 LEU cc_start: 0.8982 (tp) cc_final: 0.8747 (tp)
REVERT: B  443 MET cc_start: 0.7380 (mtt) cc_final: 0.7110 (mtt)
REVERT: B  568 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8719 (mm)
REVERT: D    4 GLN cc_start: 0.8578 (tt0) cc_final: 0.8339 (tm-30)
REVERT: D   15 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7643 (mt-10)
REVERT: D   91 ARG cc_start: 0.8290 (mtt90) cc_final: 0.7721 (mtm-85)
REVERT: D  120 GLU cc_start: 0.7801 (pm20) cc_final: 0.7481 (pm20)
REVERT: D  136 GLN cc_start: 0.6872 (tt0) cc_final: 0.6375 (mm110)
  outliers start: 32
  outliers final: 22
  residues processed: 223
  average time/residue: 0.0912
  time to fit residues: 30.5287
Evaluate side-chains
  211 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 186
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  109 HIS
Chi-restraints excluded: chain B residue  141 CYS
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  452 TRP
Chi-restraints excluded: chain B residue  455 TRP
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  554 SER
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain D residue   53 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 88 optimal weight:    5.9990
   chunk 109 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 128 optimal weight:    6.9990
   chunk 120 optimal weight:    0.6980
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 465 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.134477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.100833 restraints weight = 23495.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.100289 restraints weight = 16583.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.101019 restraints weight = 12882.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.101313 restraints weight = 11460.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.101588 restraints weight = 10203.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.5057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11708  Z= 0.130
  Angle     :  0.631   8.492  15910  Z= 0.320
  Chirality :  0.041   0.203   1872
  Planarity :  0.005   0.081   1976
  Dihedral  :  5.295  42.841   1692
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.88 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.77 %
    Twisted General : 0.14 %

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:  0.02 (0.23), residues: 1446
  helix:  0.61 (0.16), residues: 994
  sheet: -1.24 (1.19), residues: 20
  loop : -1.17 (0.33), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 255 
 TYR   0.023   0.001   TYR B 178 
 PHE   0.020   0.001   PHE A 427 
 TRP   0.011   0.001   TRP B 452 
 HIS   0.009   0.001   HIS C 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (11708)
  covalent geometry    : angle       0.63113 (15910)
  hydrogen bonds       : bond        0.04124 (  575)
  hydrogen bonds       : angle       4.17553 ( 1677)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 203
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 GLN cc_start: 0.8651 (tt0) cc_final: 0.8242 (tm-30)
REVERT: C   12 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7813 (tp30)
REVERT: C  125 MET cc_start: 0.7704 (mtt) cc_final: 0.7347 (mmm)
REVERT: A  215 ASN cc_start: 0.6092 (p0) cc_final: 0.5599 (m-40)
REVERT: A  259 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8036 (pttm)
REVERT: A  268 VAL cc_start: 0.8954 (t) cc_final: 0.8720 (p)
REVERT: A  316 LEU cc_start: 0.6655 (mt) cc_final: 0.6323 (mt)
REVERT: B  109 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.7167 (t-90)
REVERT: B  268 VAL cc_start: 0.8596 (t) cc_final: 0.8343 (p)
REVERT: B  316 LEU cc_start: 0.6521 (mt) cc_final: 0.6126 (tp)
REVERT: B  443 MET cc_start: 0.7476 (mtt) cc_final: 0.7186 (mtt)
REVERT: B  568 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8769 (mm)
REVERT: D    4 GLN cc_start: 0.8627 (tt0) cc_final: 0.8389 (tm-30)
REVERT: D  120 GLU cc_start: 0.7769 (pm20) cc_final: 0.7456 (pm20)
REVERT: D  125 MET cc_start: 0.7481 (mtt) cc_final: 0.7132 (mmm)
REVERT: D  136 GLN cc_start: 0.6720 (tt0) cc_final: 0.6286 (mm110)
  outliers start: 29
  outliers final: 22
  residues processed: 218
  average time/residue: 0.0895
  time to fit residues: 29.3909
Evaluate side-chains
  214 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 189
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  109 HIS
Chi-restraints excluded: chain B residue  141 CYS
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  452 TRP
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  554 SER
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain D residue   53 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 59 optimal weight:    9.9990
   chunk 49 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0050
   chunk 43 optimal weight:   30.0000
   chunk 74 optimal weight:    7.9990
   chunk 127 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    3.4002

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

Flipped N/Q/H residues before XYZ refinement:
** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 465 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.130508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.096042 restraints weight = 23746.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.096728 restraints weight = 15169.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.096783 restraints weight = 11155.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.097102 restraints weight = 10712.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.097298 restraints weight = 9647.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.5142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  11708  Z= 0.210
  Angle     :  0.714   9.652  15910  Z= 0.363
  Chirality :  0.044   0.203   1872
  Planarity :  0.006   0.082   1976
  Dihedral  :  5.561  42.145   1692
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.72 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.77 %
    Twisted General : 0.14 %

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: -0.23 (0.22), residues: 1446
  helix:  0.45 (0.16), residues: 988
  sheet: -1.52 (1.08), residues: 20
  loop : -1.32 (0.32), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 255 
 TYR   0.028   0.002   TYR B 178 
 PHE   0.019   0.002   PHE B 427 
 TRP   0.014   0.002   TRP B 452 
 HIS   0.008   0.001   HIS C 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 (11708)
  covalent geometry    : angle       0.71376 (15910)
  hydrogen bonds       : bond        0.04772 (  575)
  hydrogen bonds       : angle       4.50976 ( 1677)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 189
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 GLN cc_start: 0.8559 (tt0) cc_final: 0.8171 (tm-30)
REVERT: C   12 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8006 (tp30)
REVERT: C  125 MET cc_start: 0.7765 (mtt) cc_final: 0.7406 (mmm)
REVERT: A  215 ASN cc_start: 0.6321 (p0) cc_final: 0.5654 (t0)
REVERT: A  259 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8041 (pttm)
REVERT: A  316 LEU cc_start: 0.6586 (mt) cc_final: 0.6314 (mt)
REVERT: B  109 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.7255 (t-90)
REVERT: B  220 LEU cc_start: 0.8716 (mp) cc_final: 0.8510 (tt)
REVERT: B  268 VAL cc_start: 0.8775 (t) cc_final: 0.8409 (p)
REVERT: B  316 LEU cc_start: 0.6692 (mt) cc_final: 0.6244 (tp)
REVERT: B  443 MET cc_start: 0.7657 (mtt) cc_final: 0.7360 (mtt)
REVERT: B  568 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8938 (mm)
REVERT: D    4 GLN cc_start: 0.8626 (tt0) cc_final: 0.8247 (tm-30)
REVERT: D   72 MET cc_start: 0.8161 (mtp) cc_final: 0.7894 (mtp)
REVERT: D  120 GLU cc_start: 0.7721 (pm20) cc_final: 0.7398 (pm20)
  outliers start: 35
  outliers final: 28
  residues processed: 207
  average time/residue: 0.0924
  time to fit residues: 28.7825
Evaluate side-chains
  210 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 179
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 LEU
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  109 HIS
Chi-restraints excluded: chain B residue  141 CYS
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  452 TRP
Chi-restraints excluded: chain B residue  455 TRP
Chi-restraints excluded: chain B residue  459 VAL
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain D residue   40 LEU
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   64 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 92 optimal weight:    0.7980
   chunk 115 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   chunk 134 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0470
   chunk 129 optimal weight:    0.0770
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.5636

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

Flipped N/Q/H residues before XYZ refinement:
A 109 HIS
D  54 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.134817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.099144 restraints weight = 23231.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.099713 restraints weight = 14866.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.099975 restraints weight = 11393.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.100463 restraints weight = 10720.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.100596 restraints weight = 10165.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.5377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11708  Z= 0.122
  Angle     :  0.642   8.733  15910  Z= 0.326
  Chirality :  0.041   0.208   1872
  Planarity :  0.005   0.078   1976
  Dihedral  :  5.287  42.472   1692
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 17.43 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.14 %

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:  0.13 (0.23), residues: 1446
  helix:  0.71 (0.16), residues: 992
  sheet: -1.17 (1.23), residues: 20
  loop : -1.19 (0.32), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 255 
 TYR   0.020   0.001   TYR B 178 
 PHE   0.019   0.001   PHE A 427 
 TRP   0.010   0.001   TRP B 452 
 HIS   0.008   0.001   HIS C 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (11708)
  covalent geometry    : angle       0.64229 (15910)
  hydrogen bonds       : bond        0.04124 (  575)
  hydrogen bonds       : angle       4.21020 ( 1677)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 199
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 GLN cc_start: 0.8598 (tt0) cc_final: 0.8202 (tm-30)
REVERT: C   12 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7909 (tp30)
REVERT: C  125 MET cc_start: 0.7750 (mtt) cc_final: 0.7333 (mmm)
REVERT: A  121 GLU cc_start: 0.5332 (mm-30) cc_final: 0.4451 (mm-30)
REVERT: A  316 LEU cc_start: 0.6671 (mt) cc_final: 0.6467 (mt)
REVERT: B  109 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.7176 (t-90)
REVERT: B  268 VAL cc_start: 0.8460 (t) cc_final: 0.8250 (p)
REVERT: B  316 LEU cc_start: 0.6858 (mt) cc_final: 0.6528 (tp)
REVERT: B  443 MET cc_start: 0.7527 (mtt) cc_final: 0.7219 (mtt)
REVERT: B  568 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8956 (mm)
REVERT: D    4 GLN cc_start: 0.8577 (tt0) cc_final: 0.8306 (tm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 207
  average time/residue: 0.1045
  time to fit residues: 31.9898
Evaluate side-chains
  193 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 180
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  109 HIS
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain B residue  612 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 94 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 120 optimal weight:    2.9990
   chunk 101 optimal weight:   30.0000
   chunk 78 optimal weight:    0.0370
   chunk 141 optimal weight:    9.9990
   chunk 71 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
C 108 HIS
** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  54 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.135095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.101185 restraints weight = 23654.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.101000 restraints weight = 16496.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.101612 restraints weight = 13581.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.102015 restraints weight = 10552.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.102108 restraints weight = 9756.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.5588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11708  Z= 0.128
  Angle     :  0.696  12.273  15910  Z= 0.346
  Chirality :  0.041   0.203   1872
  Planarity :  0.005   0.078   1976
  Dihedral  :  5.156  41.722   1692
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 18.40 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.14 %

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:  0.33 (0.23), residues: 1446
  helix:  0.83 (0.16), residues: 996
  sheet: -0.98 (1.29), residues: 20
  loop : -1.03 (0.33), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 255 
 TYR   0.021   0.001   TYR B 178 
 PHE   0.043   0.001   PHE A  40 
 TRP   0.024   0.001   TRP A 452 
 HIS   0.007   0.001   HIS C 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (11708)
  covalent geometry    : angle       0.69579 (15910)
  hydrogen bonds       : bond        0.04061 (  575)
  hydrogen bonds       : angle       4.22400 ( 1677)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 198
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 GLN cc_start: 0.8522 (tt0) cc_final: 0.8140 (tm-30)
REVERT: C   12 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7898 (tp30)
REVERT: C  125 MET cc_start: 0.7665 (mtt) cc_final: 0.7340 (mmm)
REVERT: A  124 MET cc_start: 0.7827 (tmm) cc_final: 0.7436 (mtt)
REVERT: A  316 LEU cc_start: 0.6628 (mt) cc_final: 0.6403 (mt)
REVERT: B  109 HIS cc_start: 0.7576 (OUTLIER) cc_final: 0.7101 (t-90)
REVERT: B  168 LYS cc_start: 0.7931 (mmmm) cc_final: 0.7187 (mmmm)
REVERT: B  259 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8110 (pttm)
REVERT: B  268 VAL cc_start: 0.8467 (t) cc_final: 0.8224 (p)
REVERT: B  316 LEU cc_start: 0.6937 (mt) cc_final: 0.6600 (tp)
REVERT: B  414 MET cc_start: 0.9220 (mmm) cc_final: 0.9017 (mmt)
REVERT: B  443 MET cc_start: 0.7511 (mtt) cc_final: 0.7214 (mtt)
REVERT: B  568 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8958 (mm)
REVERT: D   72 MET cc_start: 0.8019 (mtp) cc_final: 0.7759 (mtp)
  outliers start: 17
  outliers final: 11
  residues processed: 208
  average time/residue: 0.0916
  time to fit residues: 29.2891
Evaluate side-chains
  200 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 186
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  455 TRP
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  109 HIS
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  259 LYS
Chi-restraints excluded: chain B residue  554 SER
Chi-restraints excluded: chain B residue  568 LEU
Chi-restraints excluded: chain B residue  612 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 126 optimal weight:    7.9990
   chunk 141 optimal weight:    8.9990
   chunk 85 optimal weight:    5.9990
   chunk 120 optimal weight:    2.9990
   chunk 86 optimal weight:    9.9990
   chunk 110 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   4 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.129918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.096288 restraints weight = 24150.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.095491 restraints weight = 15960.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.096014 restraints weight = 14619.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.096390 restraints weight = 12748.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.096395 restraints weight = 12018.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.5505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077  11708  Z= 0.274
  Angle     :  0.814  11.420  15910  Z= 0.411
  Chirality :  0.047   0.202   1872
  Planarity :  0.006   0.081   1976
  Dihedral  :  5.705  41.661   1692
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.92 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.69 %
    Twisted General : 0.14 %

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: -0.30 (0.22), residues: 1446
  helix:  0.36 (0.16), residues: 1006
  sheet: -1.54 (1.10), residues: 20
  loop : -1.29 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 255 
 TYR   0.035   0.002   TYR A 178 
 PHE   0.021   0.002   PHE D 100 
 TRP   0.026   0.002   TRP A 452 
 HIS   0.010   0.002   HIS C 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00632 (11708)
  covalent geometry    : angle       0.81446 (15910)
  hydrogen bonds       : bond        0.05187 (  575)
  hydrogen bonds       : angle       4.78734 ( 1677)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1840.36 seconds
wall clock time: 32 minutes 40.42 seconds (1960.42 seconds total)