Starting phenix.real_space_refine
on Mon Oct 13 05:53:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uqv_42478/10_2025/8uqv_42478_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uqv_42478/10_2025/8uqv_42478.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uqv_42478/10_2025/8uqv_42478_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uqv_42478/10_2025/8uqv_42478_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uqv_42478/10_2025/8uqv_42478.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uqv_42478/10_2025/8uqv_42478.map"
  }
  resolution = 3.6
  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=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 16140 atoms to isotropic.
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      4      9.91       5
     S      64      5.16       5
     C   11488      2.51       5
     N    3072      2.21       5
     O    3396      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18024
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 4460
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 547, 4460
          Classifications: {'peptide': 547}
          Link IDs: {'PTRANS': 40, 'TRANS': 506}
    Chain: "B"
      Number of atoms: 4460
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 547, 4460
          Classifications: {'peptide': 547}
          Link IDs: {'PTRANS': 40, 'TRANS': 506}
    Chain: "C"
      Number of atoms: 4460
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 547, 4460
          Classifications: {'peptide': 547}
          Link IDs: {'PTRANS': 40, 'TRANS': 506}
    Chain: "D"
      Number of atoms: 4460
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 547, 4460
          Classifications: {'peptide': 547}
          Link IDs: {'PTRANS': 40, 'TRANS': 506}
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 26
          Unusual residues: {' CA': 1, 'GLC': 1, 'XVC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 26
          Unusual residues: {' CA': 1, 'GLC': 1, 'XVC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 26
          Unusual residues: {' CA': 1, 'GLC': 1, 'XVC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 26
          Unusual residues: {' CA': 1, 'GLC': 1, 'XVC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 23
          Classifications: {'water': 23}
          Link IDs: {None: 22}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 14
          Classifications: {'water': 14}
          Link IDs: {None: 13}
    Chain: "C"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 22
          Classifications: {'water': 22}
          Link IDs: {None: 21}
    Chain: "D"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 21
          Classifications: {'water': 21}
          Link IDs: {None: 20}
  Time building chain proxies: 4.56, per 1000 atoms: 0.25
  Number of scatterers: 18024
  At special positions: 0
  Unit cell: (88.14, 141.25, 135.6, 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      4     19.99
     S      64     16.00
     O    3396      8.00
     N    3072      7.00
     C   11488      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.54
  Conformation dependent library (CDL) restraints added in 760.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4064

  Finding SS restraints...
    Secondary structure from input PDB file:
      74 helices and 16 sheets defined
      28.8% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 82
    Processing helix  chain 'A' and resid 110 through 114
      removed outlier: 3.585A  pdb=" N   GLY A 114 " --> pdb=" O   PRO A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 128
      removed outlier: 3.814A  pdb=" N   PHE A 119 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   VAL A 120 " --> pdb=" O   VAL A 116 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ALA A 121 " --> pdb=" O   ASP A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 154
      removed outlier: 3.934A  pdb=" N   SER A 152 " --> pdb=" O   TRP A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 162
      removed outlier: 4.363A  pdb=" N   ASP A 162 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 219
    Processing helix  chain 'A' and resid 223 through 228
      removed outlier: 4.179A  pdb=" N   LEU A 228 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 231
      No H-bonds generated for 'chain 'A' and resid 229 through 231'
    Processing helix  chain 'A' and resid 256 through 272
      removed outlier: 3.787A  pdb=" N   PHE A 260 " --> pdb=" O   GLU A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 321
      removed outlier: 4.572A  pdb=" N   PHE A 315 " --> pdb=" O   MET A 311 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   MET A 316 " --> pdb=" O   PRO A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 333
      removed outlier: 4.607A  pdb=" N   ILE A 329 " --> pdb=" O   PRO A 325 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   THR A 333 " --> pdb=" O   ILE A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 370
      removed outlier: 3.699A  pdb=" N   MET A 365 " --> pdb=" O   GLU A 361 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ALA A 367 " --> pdb=" O   ASP A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 389
      removed outlier: 3.727A  pdb=" N   LEU A 389 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 406
    Processing helix  chain 'A' and resid 441 through 446
    Processing helix  chain 'A' and resid 480 through 491
    Processing helix  chain 'A' and resid 544 through 549
      removed outlier: 4.341A  pdb=" N   GLN A 547 " --> pdb=" O   ASP A 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 71
      removed outlier: 3.792A  pdb=" N   LEU B  71 " --> pdb=" O   LEU B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 81
      removed outlier: 3.861A  pdb=" N   LEU B  78 " --> pdb=" O   ARG B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 114
      removed outlier: 3.710A  pdb=" N   GLY B 114 " --> pdb=" O   PRO B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 128
      removed outlier: 3.787A  pdb=" N   ARG B 128 " --> pdb=" O   ASP B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 152
    Processing helix  chain 'B' and resid 215 through 228
      removed outlier: 3.510A  pdb=" N   ALA B 219 " --> pdb=" O   ALA B 215 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   ILE B 221 " --> pdb=" O   GLN B 217 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ASP B 222 " --> pdb=" O   GLU B 218 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ILE B 224 " --> pdb=" O   MET B 220 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ARG B 225 " --> pdb=" O   ILE B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 231
      No H-bonds generated for 'chain 'B' and resid 229 through 231'
    Processing helix  chain 'B' and resid 239 through 243
    Processing helix  chain 'B' and resid 256 through 271
      removed outlier: 3.662A  pdb=" N   PHE B 260 " --> pdb=" O   GLU B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 321
      removed outlier: 4.080A  pdb=" N   PHE B 315 " --> pdb=" O   MET B 311 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   MET B 316 " --> pdb=" O   PRO B 312 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL B 318 " --> pdb=" O   ILE B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 332
      removed outlier: 4.237A  pdb=" N   ILE B 329 " --> pdb=" O   PRO B 325 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ILE B 330 " --> pdb=" O   ILE B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 363
      removed outlier: 3.518A  pdb=" N   ASP B 363 " --> pdb=" O   GLU B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 389
    Processing helix  chain 'B' and resid 392 through 406
      removed outlier: 3.848A  pdb=" N   GLU B 397 " --> pdb=" O   ARG B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 417
      No H-bonds generated for 'chain 'B' and resid 415 through 417'
    Processing helix  chain 'B' and resid 427 through 433
      removed outlier: 3.816A  pdb=" N   ASP B 430 " --> pdb=" O   GLY B 427 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLY B 431 " --> pdb=" O   ASP B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 446
    Processing helix  chain 'B' and resid 480 through 493
      removed outlier: 3.809A  pdb=" N   ARG B 486 " --> pdb=" O   LEU B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 549
      removed outlier: 4.359A  pdb=" N   GLN B 547 " --> pdb=" O   ASP B 544 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 71
    Processing helix  chain 'C' and resid 74 through 81
      removed outlier: 3.742A  pdb=" N   LEU C  78 " --> pdb=" O   ARG C  74 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLN C  79 " --> pdb=" O   LEU C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 127
      removed outlier: 3.823A  pdb=" N   VAL C 120 " --> pdb=" O   VAL C 116 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ALA C 121 " --> pdb=" O   ASP C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 153
    Processing helix  chain 'C' and resid 216 through 221
      removed outlier: 3.663A  pdb=" N   MET C 220 " --> pdb=" O   VAL C 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 223 through 228
      removed outlier: 3.830A  pdb=" N   TRP C 227 " --> pdb=" O   VAL C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 229 through 231
      No H-bonds generated for 'chain 'C' and resid 229 through 231'
    Processing helix  chain 'C' and resid 256 through 271
    Processing helix  chain 'C' and resid 284 through 289
      removed outlier: 3.903A  pdb=" N   VAL C 289 " --> pdb=" O   PRO C 285 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 290 through 292
      No H-bonds generated for 'chain 'C' and resid 290 through 292'
    Processing helix  chain 'C' and resid 294 through 298
    Processing helix  chain 'C' and resid 310 through 321
      removed outlier: 4.368A  pdb=" N   PHE C 315 " --> pdb=" O   MET C 311 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   MET C 316 " --> pdb=" O   PRO C 312 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 327 through 331
    Processing helix  chain 'C' and resid 354 through 358
      removed outlier: 4.465A  pdb=" N   VAL C 357 " --> pdb=" O   LEU C 354 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   THR C 358 " --> pdb=" O   GLU C 355 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 354 through 358'
    Processing helix  chain 'C' and resid 359 through 364
      removed outlier: 3.933A  pdb=" N   ARG C 362 " --> pdb=" O   ASP C 359 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ASP C 363 " --> pdb=" O   GLU C 360 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 384 through 389
      removed outlier: 3.548A  pdb=" N   LEU C 389 " --> pdb=" O   LEU C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 392 through 404
      removed outlier: 3.593A  pdb=" N   LEU C 404 " --> pdb=" O   THR C 400 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 442 through 446
    Processing helix  chain 'C' and resid 480 through 495
      removed outlier: 3.635A  pdb=" N   ARG C 494 " --> pdb=" O   ALA C 490 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   HIS C 495 " --> pdb=" O   VAL C 491 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 544 through 549
      removed outlier: 4.437A  pdb=" N   GLN C 547 " --> pdb=" O   ASP C 544 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   THR C 549 " --> pdb=" O   GLN C 546 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 73
      removed outlier: 3.961A  pdb=" N   ASP D  73 " --> pdb=" O   ARG D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 76 through 82
    Processing helix  chain 'D' and resid 110 through 114
      removed outlier: 3.558A  pdb=" N   GLY D 114 " --> pdb=" O   PRO D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 127
    Processing helix  chain 'D' and resid 146 through 154
      removed outlier: 4.067A  pdb=" N   ARG D 154 " --> pdb=" O   GLN D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 215 through 231
      removed outlier: 3.972A  pdb=" N   ILE D 221 " --> pdb=" O   GLN D 217 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   ILE D 224 " --> pdb=" O   MET D 220 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   GLY D 231 " --> pdb=" O   TRP D 227 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 239 through 243
    Processing helix  chain 'D' and resid 254 through 271
      removed outlier: 4.021A  pdb=" N   HIS D 258 " --> pdb=" O   LEU D 254 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA D 259 " --> pdb=" O   PRO D 255 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLU D 271 " --> pdb=" O   VAL D 267 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 290
    Processing helix  chain 'D' and resid 294 through 298
    Processing helix  chain 'D' and resid 310 through 320
      removed outlier: 4.333A  pdb=" N   PHE D 315 " --> pdb=" O   MET D 311 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   MET D 316 " --> pdb=" O   PRO D 312 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 323 through 333
      removed outlier: 3.981A  pdb=" N   ILE D 329 " --> pdb=" O   PRO D 325 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 361 through 369
      removed outlier: 3.841A  pdb=" N   ALA D 367 " --> pdb=" O   ASP D 363 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 384 through 390
    Processing helix  chain 'D' and resid 392 through 406
    Processing helix  chain 'D' and resid 441 through 446
    Processing helix  chain 'D' and resid 480 through 493
    Processing helix  chain 'D' and resid 545 through 549
      removed outlier: 3.953A  pdb=" N   THR D 549 " --> pdb=" O   GLN D 546 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 135
      removed outlier: 5.986A  pdb=" N   TYR A  50 " --> pdb=" O   TRP A  87 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   PHE A  49 " --> pdb=" O   LEU A 412 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   ILE A 344 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
      removed outlier: 8.912A  pdb=" N   TYR A 413 " --> pdb=" O   ILE A 344 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 138
      removed outlier: 7.295A  pdb=" N   LEU A 137 " --> pdb=" O   ALA A 238 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 513 through 516
      removed outlier: 3.619A  pdb=" N   VAL A 531 " --> pdb=" O   TYR A 580 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   TYR A 580 " --> pdb=" O   VAL A 531 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 539 through 543
    Processing sheet with id=AA5, first strand: chain 'B' and resid 235 through 238
      removed outlier: 6.419A  pdb=" N   ILE B  86 " --> pdb=" O   ILE B 134 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   ASP B 136 " --> pdb=" O   ILE B  86 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   LEU B  88 " --> pdb=" O   ASP B 136 " (cutoff:3.500A)
      removed outlier: 8.641A  pdb=" N   VAL B 138 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   TYR B  50 " --> pdb=" O   TRP B  87 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   PHE B  49 " --> pdb=" O   LEU B 412 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   ILE B 344 " --> pdb=" O   VAL B 411 " (cutoff:3.500A)
      removed outlier: 8.639A  pdb=" N   TYR B 413 " --> pdb=" O   ILE B 344 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 166 through 167
    Processing sheet with id=AA7, first strand: chain 'B' and resid 513 through 516
      removed outlier: 3.858A  pdb=" N   CYS B 530 " --> pdb=" O   TYR B 516 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 539 through 542
    Processing sheet with id=AA9, first strand: chain 'C' and resid 132 through 135
      removed outlier: 6.002A  pdb=" N   TYR C  50 " --> pdb=" O   TRP C  87 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   PHE C  49 " --> pdb=" O   LEU C 412 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 167
    Processing sheet with id=AB2, first strand: chain 'C' and resid 514 through 516
    Processing sheet with id=AB3, first strand: chain 'C' and resid 539 through 542
    Processing sheet with id=AB4, first strand: chain 'D' and resid 235 through 238
      removed outlier: 8.600A  pdb=" N   ARG D 236 " --> pdb=" O   ILE D 133 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   THR D 135 " --> pdb=" O   ARG D 236 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   ALA D 238 " --> pdb=" O   THR D 135 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   LEU D 137 " --> pdb=" O   ALA D 238 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 188 through 189
    Processing sheet with id=AB6, first strand: chain 'D' and resid 504 through 505
      removed outlier: 3.670A  pdb=" N   GLN D 504 " --> pdb=" O   VAL D 517 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 539 through 543

    359 hydrogen bonds defined for protein.
    915 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.61

  Time building geometry restraints manager: 1.97 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4691
        1.33 -     1.45: 3896
        1.45 -     1.57: 9797
        1.57 -     1.69: 0
        1.69 -     1.81: 112
  Bond restraints: 18496
  Sorted by residual:
  bond pdb=" N   PRO B 214 "
       pdb=" CD  PRO B 214 "
    ideal  model  delta    sigma   weight residual
    1.473  1.545 -0.072 1.40e-02 5.10e+03 2.68e+01
  bond pdb=" N2  XVC A 602 "
       pdb=" N3  XVC A 602 "
    ideal  model  delta    sigma   weight residual
    1.125  1.215 -0.090 2.00e-02 2.50e+03 2.02e+01
  bond pdb=" N2  XVC C 602 "
       pdb=" N3  XVC C 602 "
    ideal  model  delta    sigma   weight residual
    1.125  1.215 -0.090 2.00e-02 2.50e+03 2.00e+01
  bond pdb=" N2  XVC D 602 "
       pdb=" N3  XVC D 602 "
    ideal  model  delta    sigma   weight residual
    1.125  1.213 -0.088 2.00e-02 2.50e+03 1.96e+01
  bond pdb=" N2  XVC B 602 "
       pdb=" N3  XVC B 602 "
    ideal  model  delta    sigma   weight residual
    1.125  1.212 -0.087 2.00e-02 2.50e+03 1.91e+01
  ... (remaining 18491 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    12.68: 25232
       12.68 -    25.35: 0
       25.35 -    38.03: 0
       38.03 -    50.71: 0
       50.71 -    63.39: 4
  Bond angle restraints: 25236
  Sorted by residual:
  angle pdb=" C6  XVC C 602 "
        pdb=" N1  XVC C 602 "
        pdb=" N2  XVC C 602 "
      ideal   model   delta    sigma   weight residual
     116.55  179.94  -63.39 3.00e+00 1.11e-01 4.46e+02
  angle pdb=" C6  XVC D 602 "
        pdb=" N1  XVC D 602 "
        pdb=" N2  XVC D 602 "
      ideal   model   delta    sigma   weight residual
     116.55  178.65  -62.10 3.00e+00 1.11e-01 4.28e+02
  angle pdb=" C6  XVC B 602 "
        pdb=" N1  XVC B 602 "
        pdb=" N2  XVC B 602 "
      ideal   model   delta    sigma   weight residual
     116.55  178.62  -62.07 3.00e+00 1.11e-01 4.28e+02
  angle pdb=" C6  XVC A 602 "
        pdb=" N1  XVC A 602 "
        pdb=" N2  XVC A 602 "
      ideal   model   delta    sigma   weight residual
     116.55  176.23  -59.68 3.00e+00 1.11e-01 3.96e+02
  angle pdb=" N   ILE C 381 "
        pdb=" CA  ILE C 381 "
        pdb=" C   ILE C 381 "
      ideal   model   delta    sigma   weight residual
     113.20  108.93    4.27 9.60e-01 1.09e+00 1.98e+01
  ... (remaining 25231 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.74: 10203
       25.74 -    51.48: 616
       51.48 -    77.23: 59
       77.23 -   102.97: 32
      102.97 -   128.71: 14
  Dihedral angle restraints: 10924
    sinusoidal: 4576
      harmonic: 6348
  Sorted by residual:
  dihedral pdb=" CA  GLU B 361 "
           pdb=" C   GLU B 361 "
           pdb=" N   ARG B 362 "
           pdb=" CA  ARG B 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.82   24.18     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CA  TYR B 516 "
           pdb=" C   TYR B 516 "
           pdb=" N   VAL B 517 "
           pdb=" CA  VAL B 517 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.26   22.74     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  GLN A 217 "
           pdb=" C   GLN A 217 "
           pdb=" N   GLU A 218 "
           pdb=" CA  GLU A 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.47   22.53     0      5.00e+00 4.00e-02 2.03e+01
  ... (remaining 10921 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 2115
       0.054 -    0.109: 455
       0.109 -    0.163: 53
       0.163 -    0.218: 6
       0.218 -    0.272: 3
  Chirality restraints: 2632
  Sorted by residual:
  chirality pdb=" C1  GLC A 601 "
            pdb=" C2  GLC A 601 "
            pdb=" O1  GLC A 601 "
            pdb=" O5  GLC A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.04   -2.31    0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" C1  GLC B 601 "
            pdb=" C2  GLC B 601 "
            pdb=" O1  GLC B 601 "
            pdb=" O5  GLC B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.04   -2.31    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" C1  GLC C 601 "
            pdb=" C2  GLC C 601 "
            pdb=" O1  GLC C 601 "
            pdb=" O5  GLC C 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.04   -2.30    0.26 2.00e-01 2.50e+01 1.68e+00
  ... (remaining 2629 not shown)

  Planarity restraints: 3344
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 191 "   -0.055 5.00e-02 4.00e+02   8.47e-02 1.15e+01
        pdb=" N   PRO C 192 "    0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO C 192 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO C 192 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 254 "   -0.035 5.00e-02 4.00e+02   5.37e-02 4.61e+00
        pdb=" N   PRO B 255 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B 255 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 255 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 166 "   -0.010 2.00e-02 2.50e+03   1.22e-02 3.70e+00
        pdb=" CG  TRP A 166 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 166 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 166 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 166 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 166 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 166 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 166 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 166 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 166 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 3341 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 86
        2.35 -     2.98: 11266
        2.98 -     3.62: 24500
        3.62 -     4.26: 39199
        4.26 -     4.90: 67646
  Nonbonded interactions: 142697
  Sorted by model distance:
  nonbonded pdb=" O   PRO D 192 "
            pdb=" NH1 ARG D 195 "
     model   vdw
     1.708 3.120
  nonbonded pdb=" OE2 GLU A 280 "
            pdb=" O3  XVC A 602 "
     model   vdw
     1.874 3.040
  nonbonded pdb=" OD1 ASN B 253 "
            pdb=" OH  TYR B 291 "
     model   vdw
     1.887 3.040
  nonbonded pdb=" O   ASN A 140 "
            pdb=" OD1 ASN A 140 "
     model   vdw
     1.932 3.040
  nonbonded pdb=" CD  GLU A 280 "
            pdb=" O3  XVC A 602 "
     model   vdw
     1.941 3.270
  ... (remaining 142692 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             3.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     17.040
  Find NCS groups from input model:        0.480
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5755
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.090  18500  Z= 0.204
  Angle     :  0.996  63.386  25236  Z= 0.413
  Chirality :  0.045   0.272   2632
  Planarity :  0.005   0.085   3344
  Dihedral  : 16.965 128.710   6860
  Min Nonbonded Distance : 1.708

Molprobity Statistics.
  All-atom Clashscore : 46.49
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 17.52 %
    Favored  : 82.43 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.21 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.66 (0.17), residues: 2180
  helix: -1.41 (0.23), residues: 492
  sheet: -2.74 (0.31), residues: 288
  loop : -2.91 (0.16), residues: 1400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 236 
 TYR   0.030   0.002   TYR A 101 
 PHE   0.016   0.001   PHE C 503 
 TRP   0.030   0.002   TRP A 166 
 HIS   0.012   0.001   HIS D 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (18496)
  covalent geometry    : angle       0.99569 (25236)
  hydrogen bonds       : bond        0.19574 (  359)
  hydrogen bonds       : angle       7.19982 (  915)
  Misc. bond           : bond        0.02782 (    4)

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

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

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  497 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 496
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.7269 (t) cc_final: 0.7002 (t)
REVERT: A  389 LEU cc_start: 0.5554 (mt) cc_final: 0.5324 (mt)
REVERT: A  556 LEU cc_start: 0.6091 (mt) cc_final: 0.5091 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 496
  average time/residue: 0.1623
  time to fit residues: 117.9691
Evaluate side-chains
  299 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 299
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 194 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0040
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0570
   chunk 200 optimal weight:    1.9990
   chunk 212 optimal weight:    0.0670
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.3248

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 HIS
** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 391 ASN
B 510 ASN
** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
C 253 ASN
C 395 GLN
C 443 ASN
** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 146 HIS
D 187 ASN
D 282 ASN
D 283 GLN
** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 395 GLN
D 470 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.162283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.150847 restraints weight = 22884.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.153716 restraints weight = 13483.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.155624 restraints weight = 8887.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.156915 restraints weight = 6344.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.157847 restraints weight = 4801.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6229
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  18500  Z= 0.158
  Angle     :  0.764   9.610  25236  Z= 0.382
  Chirality :  0.049   0.200   2632
  Planarity :  0.006   0.091   3344
  Dihedral  :  9.514  96.682   2628
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.33 %
    Favored  : 88.58 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 11.87 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.38 (0.18), residues: 2180
  helix: -1.43 (0.22), residues: 504
  sheet: -2.80 (0.27), residues: 376
  loop : -2.48 (0.17), residues: 1300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 132 
 TYR   0.034   0.002   TYR D 173 
 PHE   0.025   0.002   PHE A 345 
 TRP   0.026   0.002   TRP D 199 
 HIS   0.009   0.001   HIS B 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (18496)
  covalent geometry    : angle       0.76384 (25236)
  hydrogen bonds       : bond        0.04183 (  359)
  hydrogen bonds       : angle       5.25685 (  915)
  Misc. bond           : bond        0.00084 (    4)

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

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

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  388 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 336
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 MET cc_start: 0.6115 (tpp) cc_final: 0.5536 (tpp)
REVERT: A  356 MET cc_start: 0.4493 (ppp) cc_final: 0.3864 (ppp)
REVERT: A  556 LEU cc_start: 0.6709 (mt) cc_final: 0.6259 (mt)
REVERT: B  316 MET cc_start: 0.5329 (ptm) cc_final: 0.5074 (ptp)
REVERT: C  184 GLU cc_start: 0.7719 (tp30) cc_final: 0.7499 (tp30)
REVERT: C  243 LEU cc_start: 0.6858 (mp) cc_final: 0.6599 (mp)
REVERT: D  187 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7593 (t0)
REVERT: D  374 ARG cc_start: 0.6295 (tpp-160) cc_final: 0.3550 (tpp-160)
  outliers start: 52
  outliers final: 26
  residues processed: 370
  average time/residue: 0.1362
  time to fit residues: 77.9344
Evaluate side-chains
  303 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 276
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  520 VAL
Chi-restraints excluded: chain B residue  527 THR
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  534 LEU
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  178 ILE
Chi-restraints excluded: chain C residue  443 ASN
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  530 CYS
Chi-restraints excluded: chain C residue  537 PHE
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  133 ILE
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  187 ASN
Chi-restraints excluded: chain D residue  344 ILE
Chi-restraints excluded: chain D residue  359 ASP
Chi-restraints excluded: chain D residue  432 VAL
Chi-restraints excluded: chain D residue  477 THR
Chi-restraints excluded: chain D residue  523 ASP
Chi-restraints excluded: chain D residue  549 THR
Chi-restraints excluded: chain D residue  554 VAL
Chi-restraints excluded: chain D residue  560 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 174 optimal weight:    2.9990
   chunk 176 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 130 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 208 optimal weight:    0.3980
   chunk 171 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 127 HIS
A 140 ASN
A 253 ASN
B 200 HIS
B 349 HIS
** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 577 HIS
C 127 HIS
C 146 HIS
** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 141 HIS
D 146 HIS
D 258 HIS
** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 349 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.163248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.151364 restraints weight = 23356.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.154172 restraints weight = 14144.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.156117 restraints weight = 9547.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.157471 restraints weight = 6901.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.158410 restraints weight = 5246.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.6826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  18500  Z= 0.231
  Angle     :  0.842  12.165  25236  Z= 0.430
  Chirality :  0.052   0.444   2632
  Planarity :  0.007   0.100   3344
  Dihedral  :  7.588 116.238   2628
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 13.26 %
    Favored  : 86.70 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 15.19 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.05 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -3.70 (0.17), residues: 2180
  helix: -1.81 (0.21), residues: 524
  sheet: -2.64 (0.26), residues: 408
  loop : -2.75 (0.17), residues: 1248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.001   ARG A 429 
 TYR   0.033   0.002   TYR A 198 
 PHE   0.027   0.002   PHE B 190 
 TRP   0.044   0.003   TRP D 199 
 HIS   0.008   0.002   HIS D 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 (18496)
  covalent geometry    : angle       0.84202 (25236)
  hydrogen bonds       : bond        0.04788 (  359)
  hydrogen bonds       : angle       5.33901 (  915)
  Misc. bond           : bond        0.00392 (    4)

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

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

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  413 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 335
  time to evaluate  : 0.694 
Fit side-chains
REVERT: A   74 ARG cc_start: 0.7191 (mmm-85) cc_final: 0.6970 (mmt180)
REVERT: A  195 ARG cc_start: 0.6659 (mtm-85) cc_final: 0.6192 (mmt180)
REVERT: A  414 TYR cc_start: 0.8473 (p90) cc_final: 0.8189 (p90)
REVERT: A  464 TYR cc_start: 0.8297 (m-10) cc_final: 0.7650 (m-80)
REVERT: B   83 ILE cc_start: 0.7690 (mm) cc_final: 0.7378 (mm)
REVERT: B  163 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.6582 (t80)
REVERT: B  316 MET cc_start: 0.7073 (ptm) cc_final: 0.5711 (ptp)
REVERT: B  413 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6531 (t80)
REVERT: C  396 ILE cc_start: 0.8768 (mm) cc_final: 0.8421 (mt)
REVERT: D  106 PHE cc_start: 0.7159 (m-10) cc_final: 0.6913 (m-10)
REVERT: D  282 ASN cc_start: 0.8013 (t0) cc_final: 0.7709 (t0)
REVERT: D  304 MET cc_start: 0.7855 (mtt) cc_final: 0.7499 (mtt)
REVERT: D  365 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.5785 (ttt)
REVERT: D  374 ARG cc_start: 0.7301 (tpp-160) cc_final: 0.6960 (tpp-160)
REVERT: D  381 ILE cc_start: 0.6530 (OUTLIER) cc_final: 0.6267 (mt)
REVERT: D  393 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6681 (tmm-80)
REVERT: D  429 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7381 (mtm180)
  outliers start: 78
  outliers final: 36
  residues processed: 391
  average time/residue: 0.1360
  time to fit residues: 82.5061
Evaluate side-chains
  292 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 251
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain B residue  190 PHE
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  303 HIS
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain B residue  413 TYR
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain B residue  516 TYR
Chi-restraints excluded: chain B residue  520 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  178 ILE
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain C residue  568 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  133 ILE
Chi-restraints excluded: chain D residue  187 ASN
Chi-restraints excluded: chain D residue  243 LEU
Chi-restraints excluded: chain D residue  359 ASP
Chi-restraints excluded: chain D residue  365 MET
Chi-restraints excluded: chain D residue  366 TYR
Chi-restraints excluded: chain D residue  381 ILE
Chi-restraints excluded: chain D residue  393 ARG
Chi-restraints excluded: chain D residue  423 VAL
Chi-restraints excluded: chain D residue  477 THR
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  523 ASP
Chi-restraints excluded: chain D residue  544 ASP
Chi-restraints excluded: chain D residue  549 THR
Chi-restraints excluded: chain D residue  554 VAL
Chi-restraints excluded: chain D residue  560 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 209 optimal weight:    0.3980
   chunk 23 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 213 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 198 optimal weight:    0.0980
   chunk 201 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 532 ASN
A 539 GLN
** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 395 GLN
** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 443 ASN
** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 258 HIS
** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 349 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.162946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.150227 restraints weight = 23470.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.153382 restraints weight = 13652.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.155479 restraints weight = 9023.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.156942 restraints weight = 6476.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.157999 restraints weight = 4903.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.7707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  18500  Z= 0.167
  Angle     :  0.716  13.042  25236  Z= 0.360
  Chirality :  0.047   0.160   2632
  Planarity :  0.006   0.065   3344
  Dihedral  :  6.609 118.067   2628
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 10.92 %
    Favored  : 89.04 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 17.46 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.36 (0.17), residues: 2180
  helix: -1.48 (0.22), residues: 512
  sheet: -2.73 (0.26), residues: 408
  loop : -2.43 (0.17), residues: 1260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 362 
 TYR   0.022   0.002   TYR D 173 
 PHE   0.017   0.002   PHE C 203 
 TRP   0.043   0.002   TRP D 199 
 HIS   0.007   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (18496)
  covalent geometry    : angle       0.71646 (25236)
  hydrogen bonds       : bond        0.03659 (  359)
  hydrogen bonds       : angle       4.91687 (  915)
  Misc. bond           : bond        0.00060 (    4)

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

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

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 284
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.7394 (mmm-85) cc_final: 0.6978 (mmt180)
REVERT: A  195 ARG cc_start: 0.7282 (mtm-85) cc_final: 0.6621 (mmt180)
REVERT: A  414 TYR cc_start: 0.8568 (p90) cc_final: 0.8350 (p90)
REVERT: A  464 TYR cc_start: 0.8500 (m-10) cc_final: 0.8170 (m-80)
REVERT: B  102 ASP cc_start: 0.8154 (p0) cc_final: 0.7859 (p0)
REVERT: B  168 ASP cc_start: 0.7988 (t0) cc_final: 0.7785 (t0)
REVERT: B  422 ASP cc_start: 0.8339 (p0) cc_final: 0.8086 (p0)
REVERT: B  472 GLU cc_start: 0.7533 (tp30) cc_final: 0.7006 (tt0)
REVERT: C  375 MET cc_start: 0.6436 (mtm) cc_final: 0.5991 (mtt)
REVERT: C  396 ILE cc_start: 0.8924 (mm) cc_final: 0.8706 (mt)
REVERT: D  365 MET cc_start: 0.6615 (ttp) cc_final: 0.6204 (ttt)
REVERT: D  374 ARG cc_start: 0.7278 (tpp-160) cc_final: 0.7049 (tpp-160)
REVERT: D  381 ILE cc_start: 0.6555 (mt) cc_final: 0.6208 (mt)
REVERT: D  583 GLN cc_start: 0.7449 (tm-30) cc_final: 0.7067 (tm-30)
  outliers start: 78
  outliers final: 40
  residues processed: 337
  average time/residue: 0.1297
  time to fit residues: 69.4750
Evaluate side-chains
  294 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 254
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  546 GLN
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  463 VAL
Chi-restraints excluded: chain B residue  556 LEU
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  205 HIS
Chi-restraints excluded: chain C residue  296 ASN
Chi-restraints excluded: chain C residue  426 LEU
Chi-restraints excluded: chain C residue  477 THR
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  357 VAL
Chi-restraints excluded: chain D residue  359 ASP
Chi-restraints excluded: chain D residue  405 SER
Chi-restraints excluded: chain D residue  434 ILE
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  477 THR
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  500 VAL
Chi-restraints excluded: chain D residue  523 ASP
Chi-restraints excluded: chain D residue  537 PHE
Chi-restraints excluded: chain D residue  554 VAL
Chi-restraints excluded: chain D residue  560 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 107 optimal weight:    0.5980
   chunk 126 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 192 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 72 optimal weight:    0.4980
   chunk 141 optimal weight:    0.9980
   chunk 87 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 195 optimal weight:    0.1980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 127 HIS
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 443 ASN
** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 ASN
C 146 HIS
** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 187 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.157753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.144346 restraints weight = 23658.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.147607 restraints weight = 13463.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.149805 restraints weight = 8741.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.151329 restraints weight = 6177.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.152377 restraints weight = 4653.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.8132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  18500  Z= 0.133
  Angle     :  0.672  14.216  25236  Z= 0.339
  Chirality :  0.046   0.198   2632
  Planarity :  0.005   0.061   3344
  Dihedral  :  6.330 116.695   2628
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 10.78 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 18.30 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.96 (0.18), residues: 2180
  helix: -1.24 (0.23), residues: 504
  sheet: -2.39 (0.29), residues: 352
  loop : -2.21 (0.17), residues: 1324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 225 
 TYR   0.019   0.001   TYR D 173 
 PHE   0.019   0.001   PHE B 190 
 TRP   0.027   0.001   TRP D 199 
 HIS   0.007   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (18496)
  covalent geometry    : angle       0.67236 (25236)
  hydrogen bonds       : bond        0.03339 (  359)
  hydrogen bonds       : angle       4.73845 (  915)
  Misc. bond           : bond        0.00035 (    4)

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

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

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 279
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.7375 (mmm-85) cc_final: 0.6999 (mmt180)
REVERT: A  195 ARG cc_start: 0.7393 (mtm-85) cc_final: 0.6714 (mmt180)
REVERT: A  262 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7701 (mttp)
REVERT: A  365 MET cc_start: 0.7866 (mtp) cc_final: 0.7284 (mtp)
REVERT: A  413 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7318 (t80)
REVERT: A  464 TYR cc_start: 0.8481 (m-10) cc_final: 0.8131 (m-80)
REVERT: B  139 MET cc_start: 0.7522 (mtm) cc_final: 0.7090 (mtp)
REVERT: B  368 GLU cc_start: 0.7061 (mm-30) cc_final: 0.5999 (mm-30)
REVERT: B  420 MET cc_start: 0.8487 (tpp) cc_final: 0.8158 (ttm)
REVERT: B  422 ASP cc_start: 0.8458 (p0) cc_final: 0.8224 (p0)
REVERT: B  472 GLU cc_start: 0.7335 (tp30) cc_final: 0.6838 (tt0)
REVERT: C  208 ASP cc_start: 0.7442 (m-30) cc_final: 0.7084 (m-30)
REVERT: C  375 MET cc_start: 0.6325 (mtm) cc_final: 0.6007 (mtt)
REVERT: C  396 ILE cc_start: 0.8966 (mm) cc_final: 0.8751 (mt)
REVERT: D  351 GLU cc_start: 0.6298 (mp0) cc_final: 0.6011 (mp0)
REVERT: D  365 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6110 (ttt)
REVERT: D  381 ILE cc_start: 0.6170 (OUTLIER) cc_final: 0.5762 (mt)
REVERT: D  383 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7514 (mtt-85)
REVERT: D  583 GLN cc_start: 0.7440 (tm-30) cc_final: 0.7004 (tm-30)
  outliers start: 83
  outliers final: 45
  residues processed: 337
  average time/residue: 0.1332
  time to fit residues: 71.3126
Evaluate side-chains
  293 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 244
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  413 TYR
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  190 PHE
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  463 VAL
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  546 GLN
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  205 HIS
Chi-restraints excluded: chain C residue  296 ASN
Chi-restraints excluded: chain C residue  346 LEU
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  357 VAL
Chi-restraints excluded: chain D residue  359 ASP
Chi-restraints excluded: chain D residue  365 MET
Chi-restraints excluded: chain D residue  381 ILE
Chi-restraints excluded: chain D residue  383 ARG
Chi-restraints excluded: chain D residue  405 SER
Chi-restraints excluded: chain D residue  423 VAL
Chi-restraints excluded: chain D residue  434 ILE
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  500 VAL
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  523 ASP
Chi-restraints excluded: chain D residue  537 PHE
Chi-restraints excluded: chain D residue  544 ASP
Chi-restraints excluded: chain D residue  554 VAL
Chi-restraints excluded: chain D residue  560 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 214 optimal weight:    0.3980
   chunk 80 optimal weight:    4.9990
   chunk 123 optimal weight:    0.1980
   chunk 215 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 114 optimal weight:    3.9990
   chunk 107 optimal weight:    0.6980
   chunk 201 optimal weight:    2.9990
   chunk 165 optimal weight:    1.9990
   chunk 135 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.155390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.142557 restraints weight = 23681.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.145637 restraints weight = 13701.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.147724 restraints weight = 8996.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.149140 restraints weight = 6430.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.150171 restraints weight = 4893.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.8622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  18500  Z= 0.139
  Angle     :  0.675  15.080  25236  Z= 0.338
  Chirality :  0.046   0.179   2632
  Planarity :  0.005   0.054   3344
  Dihedral  :  6.196 115.733   2628
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 10.60 %
    Favored  : 89.36 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 20.25 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.81 (0.18), residues: 2180
  helix: -1.10 (0.23), residues: 504
  sheet: -2.32 (0.28), residues: 352
  loop : -2.11 (0.17), residues: 1324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 536 
 TYR   0.017   0.001   TYR D 173 
 PHE   0.022   0.001   PHE A  44 
 TRP   0.039   0.002   TRP D 199 
 HIS   0.007   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (18496)
  covalent geometry    : angle       0.67510 (25236)
  hydrogen bonds       : bond        0.03309 (  359)
  hydrogen bonds       : angle       4.61458 (  915)
  Misc. bond           : bond        0.00036 (    4)

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

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

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 267
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A  195 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.6918 (mmp-170)
REVERT: A  262 LYS cc_start: 0.7924 (ttmt) cc_final: 0.7546 (mttp)
REVERT: A  356 MET cc_start: 0.4962 (ppp) cc_final: 0.3977 (ppp)
REVERT: A  414 TYR cc_start: 0.8851 (p90) cc_final: 0.8530 (p90)
REVERT: A  464 TYR cc_start: 0.8546 (m-10) cc_final: 0.8255 (m-80)
REVERT: B  102 ASP cc_start: 0.8063 (p0) cc_final: 0.7631 (p0)
REVERT: B  422 ASP cc_start: 0.8482 (p0) cc_final: 0.8235 (p0)
REVERT: B  472 GLU cc_start: 0.7319 (tp30) cc_final: 0.6862 (tt0)
REVERT: C  208 ASP cc_start: 0.7510 (m-30) cc_final: 0.7162 (m-30)
REVERT: C  375 MET cc_start: 0.6387 (mtm) cc_final: 0.5887 (mtt)
REVERT: D  365 MET cc_start: 0.6657 (ttp) cc_final: 0.6215 (ttt)
REVERT: D  583 GLN cc_start: 0.7474 (tm-30) cc_final: 0.6975 (tm-30)
  outliers start: 69
  outliers final: 43
  residues processed: 317
  average time/residue: 0.1294
  time to fit residues: 65.3782
Evaluate side-chains
  286 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 243
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  213 ASN
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  546 GLN
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  463 VAL
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  520 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  205 HIS
Chi-restraints excluded: chain C residue  346 LEU
Chi-restraints excluded: chain C residue  477 THR
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain C residue  568 VAL
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  280 GLU
Chi-restraints excluded: chain D residue  357 VAL
Chi-restraints excluded: chain D residue  359 ASP
Chi-restraints excluded: chain D residue  366 TYR
Chi-restraints excluded: chain D residue  405 SER
Chi-restraints excluded: chain D residue  423 VAL
Chi-restraints excluded: chain D residue  434 ILE
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  500 VAL
Chi-restraints excluded: chain D residue  513 VAL
Chi-restraints excluded: chain D residue  523 ASP
Chi-restraints excluded: chain D residue  544 ASP
Chi-restraints excluded: chain D residue  554 VAL
Chi-restraints excluded: chain D residue  560 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 191 optimal weight:    0.0370
   chunk 78 optimal weight:    0.0770
   chunk 198 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 154 optimal weight:    0.0980
   chunk 178 optimal weight:    2.9990
   chunk 118 optimal weight:    0.3980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.2416

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

Flipped N/Q/H residues before XYZ refinement:
** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.159477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.146424 restraints weight = 23726.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.149620 restraints weight = 13648.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.151767 restraints weight = 8896.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.153256 restraints weight = 6317.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.154303 restraints weight = 4760.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.8787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  18500  Z= 0.114
  Angle     :  0.650  14.123  25236  Z= 0.325
  Chirality :  0.044   0.223   2632
  Planarity :  0.005   0.053   3344
  Dihedral  :  5.868 113.599   2628
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  9.86 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 21.57 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.58 (0.18), residues: 2180
  helix: -0.79 (0.23), residues: 500
  sheet: -2.19 (0.28), residues: 356
  loop : -2.00 (0.17), residues: 1324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 536 
 TYR   0.013   0.001   TYR D 173 
 PHE   0.021   0.001   PHE A  44 
 TRP   0.036   0.001   TRP D 199 
 HIS   0.007   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (18496)
  covalent geometry    : angle       0.64995 (25236)
  hydrogen bonds       : bond        0.03046 (  359)
  hydrogen bonds       : angle       4.44056 (  915)
  Misc. bond           : bond        0.00028 (    4)

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

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

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 260
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A  195 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.6870 (mmp-170)
REVERT: A  262 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7500 (mttm)
REVERT: A  356 MET cc_start: 0.4691 (ppp) cc_final: 0.3615 (ppp)
REVERT: A  414 TYR cc_start: 0.8788 (p90) cc_final: 0.8473 (p90)
REVERT: A  464 TYR cc_start: 0.8361 (m-10) cc_final: 0.8054 (m-80)
REVERT: B  102 ASP cc_start: 0.7996 (p0) cc_final: 0.7682 (p0)
REVERT: B  341 GLN cc_start: 0.7300 (tp40) cc_final: 0.6960 (tp40)
REVERT: B  368 GLU cc_start: 0.6998 (mm-30) cc_final: 0.5853 (mm-30)
REVERT: B  422 ASP cc_start: 0.8426 (p0) cc_final: 0.8156 (p0)
REVERT: B  472 GLU cc_start: 0.7307 (tp30) cc_final: 0.6963 (tt0)
REVERT: C  208 ASP cc_start: 0.7478 (m-30) cc_final: 0.7239 (m-30)
REVERT: C  346 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7890 (mt)
REVERT: D  365 MET cc_start: 0.6700 (OUTLIER) cc_final: 0.6272 (ttt)
REVERT: D  583 GLN cc_start: 0.7459 (tm-30) cc_final: 0.6972 (tm-30)
  outliers start: 53
  outliers final: 37
  residues processed: 302
  average time/residue: 0.1282
  time to fit residues: 60.8789
Evaluate side-chains
  273 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 234
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  213 ASN
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  151 GLU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  516 TYR
Chi-restraints excluded: chain B residue  520 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  144 GLU
Chi-restraints excluded: chain C residue  346 LEU
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain C residue  568 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  357 VAL
Chi-restraints excluded: chain D residue  365 MET
Chi-restraints excluded: chain D residue  366 TYR
Chi-restraints excluded: chain D residue  423 VAL
Chi-restraints excluded: chain D residue  434 ILE
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  500 VAL
Chi-restraints excluded: chain D residue  523 ASP
Chi-restraints excluded: chain D residue  537 PHE
Chi-restraints excluded: chain D residue  554 VAL
Chi-restraints excluded: chain D residue  560 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 201 optimal weight:    0.7980
   chunk 171 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 149 optimal weight:    0.8980
   chunk 140 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 160 optimal weight:    0.6980
   chunk 142 optimal weight:    0.0070
   chunk 157 optimal weight:    0.6980
   chunk 117 optimal weight:    1.9990
   chunk 136 optimal weight:    1.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
** B 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 567 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.155480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.142573 restraints weight = 23802.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.145658 restraints weight = 13719.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.147753 restraints weight = 9004.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.149205 restraints weight = 6431.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.150153 restraints weight = 4873.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.9075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  18500  Z= 0.138
  Angle     :  0.677  15.348  25236  Z= 0.337
  Chirality :  0.046   0.218   2632
  Planarity :  0.005   0.051   3344
  Dihedral  :  5.860 113.706   2628
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 10.60 %
    Favored  : 89.36 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 22.20 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.57 (0.18), residues: 2180
  helix: -0.74 (0.24), residues: 476
  sheet: -2.13 (0.29), residues: 356
  loop : -2.01 (0.17), residues: 1348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 383 
 TYR   0.016   0.001   TYR D 173 
 PHE   0.025   0.001   PHE A 484 
 TRP   0.046   0.001   TRP D 199 
 HIS   0.007   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (18496)
  covalent geometry    : angle       0.67712 (25236)
  hydrogen bonds       : bond        0.03251 (  359)
  hydrogen bonds       : angle       4.48136 (  915)
  Misc. bond           : bond        0.00041 (    4)

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

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

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 263
  time to evaluate  : 0.656 
Fit side-chains
REVERT: A  195 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7068 (mmp-170)
REVERT: A  262 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7605 (mttp)
REVERT: A  381 ILE cc_start: 0.7346 (mm) cc_final: 0.7013 (mm)
REVERT: A  414 TYR cc_start: 0.8785 (p90) cc_final: 0.8534 (p90)
REVERT: B  102 ASP cc_start: 0.8042 (p0) cc_final: 0.7741 (p0)
REVERT: B  184 GLU cc_start: 0.6139 (OUTLIER) cc_final: 0.4830 (mp0)
REVERT: B  341 GLN cc_start: 0.7356 (tp40) cc_final: 0.7042 (tp40)
REVERT: B  368 GLU cc_start: 0.7050 (mm-30) cc_final: 0.5799 (mm-30)
REVERT: B  422 ASP cc_start: 0.8476 (p0) cc_final: 0.8241 (p0)
REVERT: B  472 GLU cc_start: 0.7370 (tp30) cc_final: 0.7007 (tt0)
REVERT: C  181 VAL cc_start: 0.7148 (t) cc_final: 0.6935 (m)
REVERT: D  365 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6278 (ttt)
REVERT: D  442 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.7067 (ttm-80)
REVERT: D  453 ARG cc_start: 0.8081 (mmt90) cc_final: 0.7777 (mmt90)
REVERT: D  583 GLN cc_start: 0.7568 (tm-30) cc_final: 0.7002 (tm-30)
  outliers start: 53
  outliers final: 36
  residues processed: 307
  average time/residue: 0.1334
  time to fit residues: 64.4188
Evaluate side-chains
  279 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 241
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  184 GLU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  346 LEU
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain C residue  568 VAL
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  357 VAL
Chi-restraints excluded: chain D residue  365 MET
Chi-restraints excluded: chain D residue  366 TYR
Chi-restraints excluded: chain D residue  423 VAL
Chi-restraints excluded: chain D residue  434 ILE
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  500 VAL
Chi-restraints excluded: chain D residue  523 ASP
Chi-restraints excluded: chain D residue  537 PHE
Chi-restraints excluded: chain D residue  554 VAL
Chi-restraints excluded: chain D residue  560 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 159 optimal weight:    1.9990
   chunk 194 optimal weight:    1.9990
   chunk 208 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   chunk 116 optimal weight:    2.9990
   chunk 143 optimal weight:    1.9990
   chunk 212 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 182 optimal weight:    0.9980
   chunk 154 optimal weight:    3.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 547 GLN
** B 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 567 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.151605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.138295 restraints weight = 24358.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.141478 restraints weight = 13961.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.143633 restraints weight = 9183.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.145117 restraints weight = 6578.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.146143 restraints weight = 5013.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.9597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  18500  Z= 0.194
  Angle     :  0.743  15.399  25236  Z= 0.374
  Chirality :  0.048   0.259   2632
  Planarity :  0.006   0.074   3344
  Dihedral  :  6.231 116.348   2628
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.06 %
    Favored  : 87.84 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 21.78 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.78 (0.18), residues: 2180
  helix: -0.90 (0.23), residues: 492
  sheet: -2.32 (0.28), residues: 356
  loop : -2.15 (0.17), residues: 1332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 382 
 TYR   0.028   0.002   TYR D 198 
 PHE   0.025   0.002   PHE A 484 
 TRP   0.045   0.002   TRP D 199 
 HIS   0.007   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (18496)
  covalent geometry    : angle       0.74280 (25236)
  hydrogen bonds       : bond        0.03822 (  359)
  hydrogen bonds       : angle       4.73823 (  915)
  Misc. bond           : bond        0.00082 (    4)

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

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

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 237
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A   84 ASP cc_start: 0.7406 (p0) cc_final: 0.6272 (t0)
REVERT: A  195 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7310 (mmm160)
REVERT: A  262 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7744 (mttm)
REVERT: A  414 TYR cc_start: 0.8771 (p90) cc_final: 0.8515 (p90)
REVERT: B  102 ASP cc_start: 0.8143 (p0) cc_final: 0.7861 (p0)
REVERT: B  184 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.4752 (mp0)
REVERT: B  203 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6650 (t80)
REVERT: B  551 TYR cc_start: 0.6367 (OUTLIER) cc_final: 0.5233 (m-80)
REVERT: C  564 ARG cc_start: 0.8389 (tpp80) cc_final: 0.7973 (tpp80)
REVERT: D  365 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6454 (ttt)
REVERT: D  583 GLN cc_start: 0.7550 (tm-30) cc_final: 0.6932 (tm-30)
  outliers start: 63
  outliers final: 46
  residues processed: 286
  average time/residue: 0.1332
  time to fit residues: 60.3648
Evaluate side-chains
  272 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 222
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 CYS
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  213 ASN
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  420 MET
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  184 GLU
Chi-restraints excluded: chain B residue  203 PHE
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  463 VAL
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  551 TYR
Chi-restraints excluded: chain C residue   46 HIS
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  141 HIS
Chi-restraints excluded: chain C residue  426 LEU
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain C residue  568 VAL
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  280 GLU
Chi-restraints excluded: chain D residue  357 VAL
Chi-restraints excluded: chain D residue  363 ASP
Chi-restraints excluded: chain D residue  365 MET
Chi-restraints excluded: chain D residue  366 TYR
Chi-restraints excluded: chain D residue  391 ASN
Chi-restraints excluded: chain D residue  405 SER
Chi-restraints excluded: chain D residue  423 VAL
Chi-restraints excluded: chain D residue  434 ILE
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  500 VAL
Chi-restraints excluded: chain D residue  513 VAL
Chi-restraints excluded: chain D residue  523 ASP
Chi-restraints excluded: chain D residue  554 VAL
Chi-restraints excluded: chain D residue  560 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 191 optimal weight:    0.1980
   chunk 85 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0870
   chunk 171 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 98 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
** B 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.156247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.143198 restraints weight = 23940.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.146376 restraints weight = 13895.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.148539 restraints weight = 9111.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.150012 restraints weight = 6497.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.151064 restraints weight = 4935.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.9711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  18500  Z= 0.131
  Angle     :  0.698  15.571  25236  Z= 0.347
  Chirality :  0.046   0.227   2632
  Planarity :  0.005   0.074   3344
  Dihedral  :  5.948 115.412   2628
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 10.46 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 22.73 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.60 (0.18), residues: 2180
  helix: -0.70 (0.23), residues: 492
  sheet: -2.22 (0.28), residues: 356
  loop : -2.05 (0.17), residues: 1332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 383 
 TYR   0.015   0.001   TYR D 173 
 PHE   0.021   0.001   PHE A  44 
 TRP   0.046   0.002   TRP D 199 
 HIS   0.007   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (18496)
  covalent geometry    : angle       0.69843 (25236)
  hydrogen bonds       : bond        0.03262 (  359)
  hydrogen bonds       : angle       4.57467 (  915)
  Misc. bond           : bond        0.00052 (    4)

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

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

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4360 Ramachandran restraints generated.
    2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 240
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A   84 ASP cc_start: 0.7345 (p0) cc_final: 0.6135 (t0)
REVERT: A  195 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7206 (mmm160)
REVERT: A  262 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7759 (mttm)
REVERT: A  341 GLN cc_start: 0.7363 (tp40) cc_final: 0.7093 (mm-40)
REVERT: A  381 ILE cc_start: 0.7110 (mm) cc_final: 0.6864 (mm)
REVERT: A  414 TYR cc_start: 0.8769 (p90) cc_final: 0.8551 (p90)
REVERT: B  102 ASP cc_start: 0.8056 (p0) cc_final: 0.7812 (p0)
REVERT: B  184 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.4705 (mp0)
REVERT: B  351 GLU cc_start: 0.5879 (tp30) cc_final: 0.5176 (tp30)
REVERT: B  551 TYR cc_start: 0.6243 (OUTLIER) cc_final: 0.4969 (m-80)
REVERT: B  574 LEU cc_start: 0.7514 (mt) cc_final: 0.7107 (mt)
REVERT: C  346 LEU cc_start: 0.8080 (tt) cc_final: 0.7841 (mt)
REVERT: C  564 ARG cc_start: 0.8303 (tpp80) cc_final: 0.7883 (tpp80)
REVERT: D  365 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6399 (ttt)
REVERT: D  453 ARG cc_start: 0.8067 (mmt90) cc_final: 0.7855 (mmt90)
REVERT: D  583 GLN cc_start: 0.7501 (tm-30) cc_final: 0.6933 (tm-30)
  outliers start: 50
  outliers final: 42
  residues processed: 282
  average time/residue: 0.1277
  time to fit residues: 57.4542
Evaluate side-chains
  272 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 227
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  213 ASN
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  546 GLN
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain B residue   58 PHE
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  184 GLU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  463 VAL
Chi-restraints excluded: chain B residue  479 THR
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  520 VAL
Chi-restraints excluded: chain B residue  551 TYR
Chi-restraints excluded: chain C residue   46 HIS
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  141 HIS
Chi-restraints excluded: chain C residue  205 HIS
Chi-restraints excluded: chain C residue  477 THR
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  560 VAL
Chi-restraints excluded: chain C residue  568 VAL
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  357 VAL
Chi-restraints excluded: chain D residue  365 MET
Chi-restraints excluded: chain D residue  366 TYR
Chi-restraints excluded: chain D residue  423 VAL
Chi-restraints excluded: chain D residue  434 ILE
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  500 VAL
Chi-restraints excluded: chain D residue  513 VAL
Chi-restraints excluded: chain D residue  523 ASP
Chi-restraints excluded: chain D residue  554 VAL
Chi-restraints excluded: chain D residue  560 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 187 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0980
   chunk 99 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 131 optimal weight:    1.9990
   chunk 209 optimal weight:    0.0170
   chunk 63 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 158 optimal weight:    2.9990
   overall best weight:    0.5820

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

Flipped N/Q/H residues before XYZ refinement:
** B 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 567 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.155960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.142877 restraints weight = 24153.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.146043 restraints weight = 13995.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.148213 restraints weight = 9184.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.149694 restraints weight = 6556.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.150754 restraints weight = 4975.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.9836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  18500  Z= 0.136
  Angle     :  0.694  15.771  25236  Z= 0.344
  Chirality :  0.046   0.223   2632
  Planarity :  0.005   0.072   3344
  Dihedral  :  5.871 115.796   2628
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 10.78 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 22.31 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.58 (0.18), residues: 2180
  helix: -0.71 (0.23), residues: 492
  sheet: -2.18 (0.28), residues: 356
  loop : -2.04 (0.17), residues: 1332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 383 
 TYR   0.015   0.001   TYR D 173 
 PHE   0.026   0.001   PHE C 484 
 TRP   0.046   0.002   TRP D 199 
 HIS   0.006   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (18496)
  covalent geometry    : angle       0.69427 (25236)
  hydrogen bonds       : bond        0.03269 (  359)
  hydrogen bonds       : angle       4.51965 (  915)
  Misc. bond           : bond        0.00057 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2820.72 seconds
wall clock time: 49 minutes 30.86 seconds (2970.86 seconds total)