Starting phenix.real_space_refine
on Fri Feb 14 16:52:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ram_4780/02_2025/6ram_4780.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ram_4780/02_2025/6ram_4780.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ram_4780/02_2025/6ram_4780.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ram_4780/02_2025/6ram_4780.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ram_4780/02_2025/6ram_4780.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ram_4780/02_2025/6ram_4780.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.047
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      2      5.21       5
     S      25      5.16       5
     C    6569      2.51       5
     N    1797      2.21       5
     O    1788      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10186
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 588, 4710
          Classifications: {'peptide': 588}
          Link IDs: {'PTRANS': 24, 'TRANS': 563}
    Chain: "B"
      Number of atoms: 4519
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4519
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 18, 'TRANS': 553}
    Chain: "C"
      Number of atoms: 897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 897
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 6, 'TRANS': 114}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.40, per 1000 atoms: 0.63
  Number of scatterers: 10186
  At special positions: 0
  Unit cell: (102.315, 87.237, 154.011, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      25     16.00
     P       5     15.00
     Mg      2     11.99
     O    1788      8.00
     N    1797      7.00
     C    6569      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  50 " - pdb=" SG  CYS C 108 " distance=2.06

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.28
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2344

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 8 sheets defined
      64.3% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 20
      removed outlier: 3.966A  pdb=" N   ILE A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A  19 " --> pdb=" O   PHE A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 28
      Proline residue:  A  24  - end of helix
      removed outlier: 4.927A  pdb=" N   LEU A  27 " --> pdb=" O   PRO A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 45
      removed outlier: 3.654A  pdb=" N   VAL A  38 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 56
    Processing helix  chain 'A' and resid 64 through 70
    Processing helix  chain 'A' and resid 72 through 120
      removed outlier: 3.705A  pdb=" N   ILE A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU A  97 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 138
      removed outlier: 3.526A  pdb=" N   LEU A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ARG A 136 " --> pdb=" O   ARG A 132 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL A 137 " --> pdb=" O   LEU A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 155
      removed outlier: 3.529A  pdb=" N   THR A 149 " --> pdb=" O   ASN A 145 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   LEU A 152 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   VAL A 153 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLY A 154 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 171
      removed outlier: 3.905A  pdb=" N   THR A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   VAL A 163 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 182
      removed outlier: 3.871A  pdb=" N   VAL A 179 " --> pdb=" O   LYS A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 196
      removed outlier: 3.529A  pdb=" N   LEU A 187 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   THR A 192 " --> pdb=" O   LEU A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 221
      removed outlier: 4.457A  pdb=" N   GLU A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 228
    Processing helix  chain 'A' and resid 233 through 285
      removed outlier: 3.577A  pdb=" N   GLU A 237 " --> pdb=" O   ARG A 233 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU A 242 " --> pdb=" O   LYS A 238 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TRP A 256 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU A 259 " --> pdb=" O   ARG A 255 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE A 260 " --> pdb=" O   TRP A 256 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   PHE A 261 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      Proline residue:  A 262  - end of helix
      removed outlier: 3.619A  pdb=" N   ASP A 269 " --> pdb=" O   GLY A 265 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   GLY A 281 " --> pdb=" O   TYR A 277 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ARG A 285 " --> pdb=" O   GLY A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 304
    Processing helix  chain 'A' and resid 304 through 313
    Processing helix  chain 'A' and resid 313 through 332
      removed outlier: 3.822A  pdb=" N   ARG A 326 " --> pdb=" O   ALA A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 408
      removed outlier: 3.704A  pdb=" N   VAL A 402 " --> pdb=" O   GLY A 398 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL A 403 " --> pdb=" O   LYS A 399 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU A 405 " --> pdb=" O   SER A 401 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ILE A 406 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA A 407 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 427
      No H-bonds generated for 'chain 'A' and resid 425 through 427'
    Processing helix  chain 'A' and resid 428 through 435
    Processing helix  chain 'A' and resid 450 through 455
      removed outlier: 3.673A  pdb=" N   ARG A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 473
      removed outlier: 3.874A  pdb=" N   VAL A 466 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 480
    Processing helix  chain 'A' and resid 484 through 487
      removed outlier: 3.656A  pdb=" N   GLN A 487 " --> pdb=" O   LYS A 484 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 484 through 487'
    Processing helix  chain 'A' and resid 491 through 495
      removed outlier: 3.690A  pdb=" N   GLY A 494 " --> pdb=" O   GLY A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 512
      removed outlier: 3.744A  pdb=" N   LEU A 507 " --> pdb=" O   GLN A 503 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL A 508 " --> pdb=" O   LEU A 504 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA A 510 " --> pdb=" O   ALA A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 544
      removed outlier: 3.928A  pdb=" N   ALA A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 561
      removed outlier: 3.914A  pdb=" N   ILE A 559 " --> pdb=" O   ARG A 555 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   HIS A 561 " --> pdb=" O   SER A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 586
    Processing helix  chain 'A' and resid 587 through 598
      removed outlier: 3.758A  pdb=" N   ALA A 591 " --> pdb=" O   GLY A 587 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLN A 596 " --> pdb=" O   LEU A 592 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 14
    Processing helix  chain 'B' and resid 15 through 17
      No H-bonds generated for 'chain 'B' and resid 15 through 17'
    Processing helix  chain 'B' and resid 20 through 37
      removed outlier: 3.684A  pdb=" N   TRP B  26 " --> pdb=" O   TRP B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 52
      removed outlier: 3.651A  pdb=" N   PHE B  44 " --> pdb=" O   LEU B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 103
      removed outlier: 3.565A  pdb=" N   VAL B  66 " --> pdb=" O   ALA B  62 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   TYR B  77 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU B  82 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   VAL B  85 " --> pdb=" O   ARG B  81 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU B  99 " --> pdb=" O   ARG B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 113
      removed outlier: 4.225A  pdb=" N   TYR B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   HIS B 111 " --> pdb=" O   ARG B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 133
      removed outlier: 3.552A  pdb=" N   LEU B 118 " --> pdb=" O   ARG B 114 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ASN B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 156
      removed outlier: 3.811A  pdb=" N   SER B 144 " --> pdb=" O   GLY B 140 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE B 145 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE B 151 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   TYR B 155 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ALA B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 166
      removed outlier: 3.983A  pdb=" N   ALA B 162 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 207
      removed outlier: 4.188A  pdb=" N   GLY B 171 " --> pdb=" O   LEU B 167 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA B 175 " --> pdb=" O   GLY B 171 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LEU B 182 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLU B 189 " --> pdb=" O   ARG B 185 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA B 190 " --> pdb=" O   ARG B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 214
    Processing helix  chain 'B' and resid 217 through 270
      removed outlier: 3.881A  pdb=" N   LEU B 227 " --> pdb=" O   TRP B 223 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU B 233 " --> pdb=" O   ARG B 229 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   VAL B 241 " --> pdb=" O   ALA B 237 " (cutoff:3.500A)
      Proline residue:  B 244  - end of helix
      removed outlier: 3.704A  pdb=" N   ALA B 247 " --> pdb=" O   GLY B 243 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   MET B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL B 268 " --> pdb=" O   GLY B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 317
      removed outlier: 4.209A  pdb=" N   LEU B 285 " --> pdb=" O   PHE B 281 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU B 288 " --> pdb=" O   TYR B 284 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   TRP B 290 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
      Proline residue:  B 291  - end of helix
      removed outlier: 4.378A  pdb=" N   GLY B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   TRP B 297 " --> pdb=" O   LEU B 293 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   LEU B 315 " --> pdb=" O   ARG B 311 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASP B 317 " --> pdb=" O   PHE B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 335
      removed outlier: 3.797A  pdb=" N   LEU B 335 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 383
      removed outlier: 3.602A  pdb=" N   LEU B 380 " --> pdb=" O   GLY B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 405
      removed outlier: 3.568A  pdb=" N   ARG B 404 " --> pdb=" O   GLU B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 411
    Processing helix  chain 'B' and resid 427 through 433
    Processing helix  chain 'B' and resid 440 through 451
      removed outlier: 3.882A  pdb=" N   GLU B 445 " --> pdb=" O   ARG B 441 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ARG B 449 " --> pdb=" O   GLU B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 460
    Processing helix  chain 'B' and resid 462 through 466
      removed outlier: 3.731A  pdb=" N   GLU B 465 " --> pdb=" O   LYS B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 491
      removed outlier: 4.276A  pdb=" N   LYS B 491 " --> pdb=" O   ARG B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 520
    Processing helix  chain 'B' and resid 532 through 538
      removed outlier: 3.788A  pdb=" N   LEU B 536 " --> pdb=" O   ARG B 532 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   HIS B 538 " --> pdb=" O   ALA B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 558 through 562
      removed outlier: 3.511A  pdb=" N   GLN B 561 " --> pdb=" O   SER B 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 564 through 575
      removed outlier: 3.751A  pdb=" N   LEU B 572 " --> pdb=" O   GLU B 568 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.924A  pdb=" N   THR C  91 " --> pdb=" O   PRO C  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 379
      removed outlier: 6.144A  pdb=" N   LYS A 377 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   LEU A 360 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL A 353 " --> pdb=" O   VAL A 383 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 376 through 379
      removed outlier: 6.144A  pdb=" N   LYS A 377 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   LEU A 360 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   CYS A 416 " --> pdb=" O   ARG A 356 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   VAL A 358 " --> pdb=" O   ARG A 414 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   ARG A 414 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 436 through 439
      removed outlier: 6.308A  pdb=" N   LEU A 519 " --> pdb=" O   LEU A 550 " (cutoff:3.500A)
      removed outlier: 8.236A  pdb=" N   LEU A 566 " --> pdb=" O   LYS A 388 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   ALA A 390 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   PHE A 568 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY A 577 " --> pdb=" O   ILE A 565 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   GLU A 575 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ARG A 569 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   LEU A 573 " --> pdb=" O   ARG A 569 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 449
      removed outlier: 3.532A  pdb=" N   GLY A 448 " --> pdb=" O   LEU A 490 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 351 through 361
      removed outlier: 6.434A  pdb=" N   LEU B 353 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 7.583A  pdb=" N   LYS B 347 " --> pdb=" O   LEU B 353 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ARG B 355 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   GLY B 345 " --> pdb=" O   ARG B 355 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   LEU B 357 " --> pdb=" O   GLY B 343 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY B 343 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   VAL B 344 " --> pdb=" O   GLU B 392 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   GLU B 392 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 414 through 417
      removed outlier: 6.496A  pdb=" N   GLY B 415 " --> pdb=" O   ILE B 497 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   ASP B 499 " --> pdb=" O   GLY B 415 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ALA B 417 " --> pdb=" O   ASP B 499 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   TRP B 541 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU B 552 " --> pdb=" O   VAL B 544 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ASP B 546 " --> pdb=" O   ILE B 550 " (cutoff:3.500A)
      removed outlier: 5.172A  pdb=" N   ILE B 550 " --> pdb=" O   ASP B 546 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ALA C 101 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 7
      removed outlier: 3.659A  pdb=" N   THR C  78 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.529A  pdb=" N   ALA C  92 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
      removed outlier: 5.701A  pdb=" N   ARG C  38 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   GLY C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)

    577 hydrogen bonds defined for protein.
    1692 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.52

  Time building geometry restraints manager: 2.66 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1611
        1.31 -     1.44: 3256
        1.44 -     1.57: 5474
        1.57 -     1.70: 13
        1.70 -     1.83: 45
  Bond restraints: 10399
  Sorted by residual:
  bond pdb=" C4  ATP B 601 "
       pdb=" C5  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.388  1.459 -0.071 1.00e-02 1.00e+04 5.01e+01
  bond pdb=" C5  ATP B 601 "
       pdb=" N7  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.387  1.327  0.060 1.00e-02 1.00e+04 3.54e+01
  bond pdb=" C4  ATP B 601 "
       pdb=" N9  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.374  1.321  0.053 1.00e-02 1.00e+04 2.84e+01
  bond pdb=" CA  GLY B 368 "
       pdb=" C   GLY B 368 "
    ideal  model  delta    sigma   weight residual
    1.519  1.484  0.035 7.00e-03 2.04e+04 2.44e+01
  bond pdb=" C5  ATP B 601 "
       pdb=" C6  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.409  1.457 -0.048 1.00e-02 1.00e+04 2.34e+01
  ... (remaining 10394 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.78: 13684
        4.78 -     9.55: 406
        9.55 -    14.33: 16
       14.33 -    19.11: 0
       19.11 -    23.88: 2
  Bond angle restraints: 14108
  Sorted by residual:
  angle pdb=" PB  ATP B 601 "
        pdb=" O3B ATP B 601 "
        pdb=" PG  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     139.87  115.99   23.88 1.00e+00 1.00e+00 5.70e+02
  angle pdb=" PA  ATP B 601 "
        pdb=" O3A ATP B 601 "
        pdb=" PB  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     136.83  114.66   22.17 1.00e+00 1.00e+00 4.92e+02
  angle pdb=" N   VAL B 241 "
        pdb=" CA  VAL B 241 "
        pdb=" C   VAL B 241 "
      ideal   model   delta    sigma   weight residual
     111.62  101.60   10.02 7.90e-01 1.60e+00 1.61e+02
  angle pdb=" N   SER B 558 "
        pdb=" CA  SER B 558 "
        pdb=" C   SER B 558 "
      ideal   model   delta    sigma   weight residual
     111.36  100.23   11.13 1.09e+00 8.42e-01 1.04e+02
  angle pdb=" N   ILE B 473 "
        pdb=" CA  ILE B 473 "
        pdb=" C   ILE B 473 "
      ideal   model   delta    sigma   weight residual
     113.53  103.64    9.89 9.80e-01 1.04e+00 1.02e+02
  ... (remaining 14103 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.89: 5905
       18.89 -    37.78: 204
       37.78 -    56.66: 50
       56.66 -    75.55: 24
       75.55 -    94.44: 6
  Dihedral angle restraints: 6189
    sinusoidal: 2527
      harmonic: 3662
  Sorted by residual:
  dihedral pdb=" N   ASP B 349 "
           pdb=" C   ASP B 349 "
           pdb=" CA  ASP B 349 "
           pdb=" CB  ASP B 349 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.65  -12.85     0      2.50e+00 1.60e-01 2.64e+01
  dihedral pdb=" O1B ADP A 701 "
           pdb=" O3A ADP A 701 "
           pdb=" PB  ADP A 701 "
           pdb=" PA  ADP A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -154.44   94.44     1      2.00e+01 2.50e-03 2.59e+01
  dihedral pdb=" N   GLU B 438 "
           pdb=" C   GLU B 438 "
           pdb=" CA  GLU B 438 "
           pdb=" CB  GLU B 438 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  110.37   12.43     0      2.50e+00 1.60e-01 2.47e+01
  ... (remaining 6186 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 1078
       0.103 -    0.205: 399
       0.205 -    0.308: 93
       0.308 -    0.410: 25
       0.410 -    0.513: 12
  Chirality restraints: 1607
  Sorted by residual:
  chirality pdb=" CA  ASN B 123 "
            pdb=" N   ASN B 123 "
            pdb=" C   ASN B 123 "
            pdb=" CB  ASN B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.58e+00
  chirality pdb=" CA  GLU A 533 "
            pdb=" N   GLU A 533 "
            pdb=" C   GLU A 533 "
            pdb=" CB  GLU A 533 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.83e+00
  chirality pdb=" CA  GLN A 441 "
            pdb=" N   GLN A 441 "
            pdb=" C   GLN A 441 "
            pdb=" CB  GLN A 441 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.61e+00
  ... (remaining 1604 not shown)

  Planarity restraints: 1784
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 223 "    0.051 2.00e-02 2.50e+03   2.56e-02 1.64e+01
        pdb=" CG  TRP B 223 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 223 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 223 "   -0.020 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 223 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 223 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 223 "   -0.034 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 223 "    0.028 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 223 "   -0.014 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 223 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  52 "    0.053 2.00e-02 2.50e+03   2.50e-02 1.57e+01
        pdb=" CG  TRP A  52 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  52 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  52 "   -0.023 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  52 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  52 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  52 "   -0.025 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  52 "    0.031 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  52 "   -0.011 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  52 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 216 "   -0.019 2.00e-02 2.50e+03   3.94e-02 1.56e+01
        pdb=" C   LEU B 216 "    0.068 2.00e-02 2.50e+03
        pdb=" O   LEU B 216 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   GLU B 217 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 1781 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 459
        2.71 -     3.26: 10007
        3.26 -     3.80: 15369
        3.80 -     4.35: 20680
        4.35 -     4.90: 33370
  Nonbonded interactions: 79885
  Sorted by model distance:
  nonbonded pdb=" O2B ADP A 701 "
            pdb="MG    MG A 702 "
     model   vdw
     2.162 2.170
  nonbonded pdb=" OG1 THR A 400 "
            pdb="MG    MG A 702 "
     model   vdw
     2.173 2.170
  nonbonded pdb=" OE1 GLN A 441 "
            pdb="MG    MG A 702 "
     model   vdw
     2.233 2.170
  nonbonded pdb=" O2B ATP B 601 "
            pdb="MG    MG B 602 "
     model   vdw
     2.273 2.170
  nonbonded pdb=" O1G ATP B 601 "
            pdb="MG    MG B 602 "
     model   vdw
     2.316 2.170
  ... (remaining 79880 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.710
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
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      :  0.016   0.071  10399  Z= 1.071
  Angle     :  1.964  23.885  14108  Z= 1.407
  Chirality :  0.119   0.513   1607
  Planarity :  0.012   0.082   1784
  Dihedral  : 11.725  94.441   3839
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.82 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.96 %
    Favored  : 96.95 %
  Cbeta Deviations :  0.60 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (0.20), residues: 1275
  helix: -1.94 (0.16), residues: 745
  sheet: -0.77 (0.42), residues: 132
  loop : -1.78 (0.27), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.008   TRP A  52 
 HIS   0.006   0.001   HIS B 400 
 PHE   0.044   0.007   PHE B 313 
 TYR   0.049   0.006   TYR A 277 
 ARG   0.005   0.000   ARG B 229 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 328
  time to evaluate  : 1.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ILE cc_start: 0.9395 (mm) cc_final: 0.9150 (mm)
REVERT: A  160 PHE cc_start: 0.7924 (m-80) cc_final: 0.7686 (m-80)
REVERT: A  303 LEU cc_start: 0.9286 (tp) cc_final: 0.9051 (tp)
REVERT: A  309 ASP cc_start: 0.8722 (t0) cc_final: 0.8380 (t70)
REVERT: A  321 MET cc_start: 0.8433 (tpt) cc_final: 0.8184 (tpt)
REVERT: A  359 TRP cc_start: 0.7904 (m100) cc_final: 0.6882 (m100)
REVERT: A  372 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7913 (tptm)
REVERT: A  376 LEU cc_start: 0.8173 (mp) cc_final: 0.7903 (mm)
REVERT: A  391 LEU cc_start: 0.9224 (mp) cc_final: 0.8647 (tt)
REVERT: A  503 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8162 (tp40)
REVERT: A  538 GLU cc_start: 0.8616 (tt0) cc_final: 0.8318 (tp30)
REVERT: A  554 HIS cc_start: 0.6726 (m90) cc_final: 0.5875 (m-70)
REVERT: B   21 ARG cc_start: 0.8232 (ttp-110) cc_final: 0.7516 (ptm160)
REVERT: B  125 ASP cc_start: 0.6470 (m-30) cc_final: 0.6157 (m-30)
REVERT: B  191 GLN cc_start: 0.8573 (tp40) cc_final: 0.8209 (tm-30)
REVERT: B  282 ASN cc_start: 0.9411 (t0) cc_final: 0.8906 (t0)
REVERT: B  299 MET cc_start: 0.8777 (mmm) cc_final: 0.8475 (mmp)
REVERT: B  359 LEU cc_start: 0.8936 (tp) cc_final: 0.8703 (tt)
REVERT: B  365 MET cc_start: 0.7839 (ttp) cc_final: 0.7447 (tmm)
REVERT: B  505 VAL cc_start: 0.9116 (t) cc_final: 0.8908 (p)
REVERT: C   80 HIS cc_start: 0.7781 (m-70) cc_final: 0.6543 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 328
  average time/residue: 0.3040
  time to fit residues: 128.3061
Evaluate side-chains
  198 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 197
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  372 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 107 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 115 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 128 ASN
** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 101 HIS
B 120 ASN
B 123 ASN
C  13 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.099179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.079820 restraints weight = 25689.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.082634 restraints weight = 13670.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.084579 restraints weight = 8862.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10399  Z= 0.238
  Angle     :  0.710  10.056  14108  Z= 0.362
  Chirality :  0.042   0.182   1607
  Planarity :  0.005   0.056   1784
  Dihedral  :  6.613  63.066   1485
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 11.44 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.22), residues: 1275
  helix: -0.39 (0.18), residues: 768
  sheet: -0.39 (0.43), residues: 130
  loop : -1.40 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 290 
 HIS   0.006   0.002   HIS B 454 
 PHE   0.023   0.002   PHE A  88 
 TYR   0.017   0.002   TYR A 589 
 ARG   0.011   0.001   ARG A 569 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 225
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LEU cc_start: 0.9243 (mt) cc_final: 0.8791 (tt)
REVERT: A   40 THR cc_start: 0.9200 (m) cc_final: 0.8881 (p)
REVERT: A   94 GLU cc_start: 0.7997 (tp30) cc_final: 0.7631 (tp30)
REVERT: A  118 MET cc_start: 0.9058 (mmp) cc_final: 0.8498 (mmp)
REVERT: A  305 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8128 (tp40)
REVERT: A  309 ASP cc_start: 0.8305 (t0) cc_final: 0.7981 (t0)
REVERT: A  359 TRP cc_start: 0.7998 (m100) cc_final: 0.7404 (m100)
REVERT: A  365 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8366 (ttmt)
REVERT: A  376 LEU cc_start: 0.8301 (mp) cc_final: 0.8052 (mm)
REVERT: A  444 PHE cc_start: 0.7244 (t80) cc_final: 0.6083 (t80)
REVERT: A  569 ARG cc_start: 0.7547 (mtt90) cc_final: 0.7274 (mtt90)
REVERT: B   21 ARG cc_start: 0.8109 (ttp-110) cc_final: 0.7802 (ptt90)
REVERT: B   38 PHE cc_start: 0.8714 (t80) cc_final: 0.8500 (t80)
REVERT: B  132 MET cc_start: 0.8948 (tmm) cc_final: 0.8687 (tmm)
REVERT: B  255 PHE cc_start: 0.8728 (t80) cc_final: 0.8308 (t80)
REVERT: B  281 PHE cc_start: 0.9051 (t80) cc_final: 0.8404 (t80)
REVERT: B  282 ASN cc_start: 0.8981 (t0) cc_final: 0.8766 (t0)
REVERT: B  299 MET cc_start: 0.8774 (mmm) cc_final: 0.8474 (mmp)
REVERT: B  301 LEU cc_start: 0.8586 (tt) cc_final: 0.8324 (tp)
REVERT: B  316 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8429 (mt)
REVERT: B  505 VAL cc_start: 0.9067 (t) cc_final: 0.8854 (p)
REVERT: C   20 LEU cc_start: 0.8773 (tp) cc_final: 0.8355 (tp)
REVERT: C   46 GLU cc_start: 0.7811 (pm20) cc_final: 0.7586 (pm20)
REVERT: C   51 ILE cc_start: 0.8889 (tp) cc_final: 0.8645 (tp)
REVERT: C   65 LYS cc_start: 0.9031 (pttp) cc_final: 0.8686 (pttm)
REVERT: C   84 ASN cc_start: 0.8640 (m-40) cc_final: 0.8001 (p0)
REVERT: C   86 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8254 (mt)
  outliers start: 36
  outliers final: 14
  residues processed: 245
  average time/residue: 0.2529
  time to fit residues: 84.3371
Evaluate side-chains
  185 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  305 GLN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue  108 CYS
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 83 optimal weight:    0.3980
   chunk 2 optimal weight:    0.5980
   chunk 58 optimal weight:    4.9990
   chunk 38 optimal weight:    0.1980
   chunk 1 optimal weight:    0.8980
   chunk 98 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 287 GLN
C  80 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.097923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.078997 restraints weight = 25707.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.081746 restraints weight = 13627.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.083639 restraints weight = 8874.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.4434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10399  Z= 0.186
  Angle     :  0.661   8.253  14108  Z= 0.324
  Chirality :  0.041   0.214   1607
  Planarity :  0.004   0.038   1784
  Dihedral  :  5.805  53.009   1481
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.59 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.23), residues: 1275
  helix:  0.30 (0.18), residues: 773
  sheet: -0.40 (0.43), residues: 126
  loop : -1.20 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 290 
 HIS   0.008   0.001   HIS C  80 
 PHE   0.022   0.001   PHE A 444 
 TYR   0.023   0.001   TYR B  92 
 ARG   0.008   0.001   ARG C  45 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 191
  time to evaluate  : 1.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9196 (m) cc_final: 0.8923 (p)
REVERT: A   72 LEU cc_start: 0.7837 (mm) cc_final: 0.7533 (mm)
REVERT: A   94 GLU cc_start: 0.8101 (tp30) cc_final: 0.7843 (tp30)
REVERT: A  140 ASP cc_start: 0.6836 (m-30) cc_final: 0.6248 (m-30)
REVERT: A  145 ASN cc_start: 0.8635 (m-40) cc_final: 0.8082 (m110)
REVERT: A  152 LEU cc_start: 0.8365 (mt) cc_final: 0.7678 (mt)
REVERT: A  359 TRP cc_start: 0.8144 (m100) cc_final: 0.7272 (m100)
REVERT: A  376 LEU cc_start: 0.8305 (mp) cc_final: 0.8006 (mm)
REVERT: A  417 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8739 (p)
REVERT: B   21 ARG cc_start: 0.8053 (ttp-110) cc_final: 0.7641 (ptt90)
REVERT: B  132 MET cc_start: 0.8984 (tmm) cc_final: 0.8727 (tmm)
REVERT: B  255 PHE cc_start: 0.8695 (t80) cc_final: 0.8260 (t80)
REVERT: B  281 PHE cc_start: 0.8983 (t80) cc_final: 0.8711 (t80)
REVERT: B  282 ASN cc_start: 0.9036 (t0) cc_final: 0.8741 (t0)
REVERT: B  365 MET cc_start: 0.8433 (tmm) cc_final: 0.8175 (tmm)
REVERT: B  505 VAL cc_start: 0.8915 (t) cc_final: 0.8683 (p)
REVERT: C   13 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7578 (tp-100)
REVERT: C   20 LEU cc_start: 0.8834 (tp) cc_final: 0.8537 (tp)
REVERT: C   45 ARG cc_start: 0.8277 (mtm110) cc_final: 0.7940 (mtm110)
REVERT: C   52 SER cc_start: 0.8559 (t) cc_final: 0.8319 (p)
REVERT: C   65 LYS cc_start: 0.9042 (pttp) cc_final: 0.8685 (pttm)
  outliers start: 25
  outliers final: 14
  residues processed: 210
  average time/residue: 0.2614
  time to fit residues: 74.7374
Evaluate side-chains
  177 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 161
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 HIS
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain C residue   13 GLN
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 101 optimal weight:    0.0270
   chunk 35 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 120 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.7038

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.097260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.078257 restraints weight = 25773.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.081070 restraints weight = 13657.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.082977 restraints weight = 8884.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.4855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10399  Z= 0.192
  Angle     :  0.628   7.817  14108  Z= 0.306
  Chirality :  0.040   0.156   1607
  Planarity :  0.004   0.043   1784
  Dihedral  :  5.491  57.048   1481
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.40 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.23), residues: 1275
  helix:  0.70 (0.19), residues: 776
  sheet: -0.20 (0.45), residues: 125
  loop : -1.24 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 446 
 HIS   0.005   0.001   HIS C  80 
 PHE   0.034   0.001   PHE A  15 
 TYR   0.026   0.001   TYR C 113 
 ARG   0.006   0.000   ARG C  72 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 180
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9237 (m) cc_final: 0.8961 (p)
REVERT: A   72 LEU cc_start: 0.7838 (mm) cc_final: 0.7550 (mm)
REVERT: A   94 GLU cc_start: 0.8112 (tp30) cc_final: 0.7826 (tp30)
REVERT: A  140 ASP cc_start: 0.6735 (m-30) cc_final: 0.6220 (m-30)
REVERT: A  145 ASN cc_start: 0.8646 (m-40) cc_final: 0.8022 (m110)
REVERT: A  331 LEU cc_start: 0.8519 (tt) cc_final: 0.8212 (tt)
REVERT: A  359 TRP cc_start: 0.8085 (m100) cc_final: 0.7292 (m100)
REVERT: A  365 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8361 (ttmt)
REVERT: A  376 LEU cc_start: 0.8346 (mp) cc_final: 0.7907 (mt)
REVERT: A  391 LEU cc_start: 0.8997 (mp) cc_final: 0.8696 (mt)
REVERT: A  417 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8708 (p)
REVERT: B  112 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8127 (mttp)
REVERT: B  132 MET cc_start: 0.9089 (tmm) cc_final: 0.8746 (tmm)
REVERT: B  154 MET cc_start: 0.8600 (mmm) cc_final: 0.7888 (mmm)
REVERT: B  319 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8400 (mmmt)
REVERT: B  365 MET cc_start: 0.8411 (tmm) cc_final: 0.8202 (tmm)
REVERT: B  505 VAL cc_start: 0.8888 (t) cc_final: 0.8658 (p)
REVERT: C   13 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7139 (tp40)
REVERT: C   20 LEU cc_start: 0.8924 (tp) cc_final: 0.8526 (tp)
REVERT: C   45 ARG cc_start: 0.8418 (mtm110) cc_final: 0.8014 (mtm110)
REVERT: C   76 LYS cc_start: 0.8978 (tppt) cc_final: 0.8713 (tptp)
REVERT: C  107 ARG cc_start: 0.7601 (mmm160) cc_final: 0.7310 (tpt-90)
  outliers start: 37
  outliers final: 20
  residues processed: 202
  average time/residue: 0.2429
  time to fit residues: 67.1175
Evaluate side-chains
  173 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 HIS
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  305 GLN
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 116 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 105 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
B 123 ASN
B 280 GLN
B 282 ASN
B 419 GLN
B 538 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.095000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.075949 restraints weight = 25633.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.078683 restraints weight = 13636.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.080564 restraints weight = 8928.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.5191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10399  Z= 0.231
  Angle     :  0.639   8.036  14108  Z= 0.312
  Chirality :  0.040   0.159   1607
  Planarity :  0.004   0.061   1784
  Dihedral  :  5.383  57.379   1481
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.30 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.23), residues: 1275
  helix:  0.91 (0.19), residues: 774
  sheet: -0.10 (0.46), residues: 125
  loop : -1.18 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  36 
 HIS   0.004   0.001   HIS B 454 
 PHE   0.018   0.001   PHE A 317 
 TYR   0.018   0.001   TYR B  92 
 ARG   0.005   0.000   ARG C  72 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 165
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9250 (m) cc_final: 0.8986 (p)
REVERT: A   94 GLU cc_start: 0.8184 (tp30) cc_final: 0.7881 (tp30)
REVERT: A  140 ASP cc_start: 0.6890 (m-30) cc_final: 0.6402 (m-30)
REVERT: A  145 ASN cc_start: 0.8704 (m-40) cc_final: 0.7949 (m110)
REVERT: A  308 GLN cc_start: 0.7667 (mt0) cc_final: 0.7397 (pt0)
REVERT: A  326 ARG cc_start: 0.8730 (mmm-85) cc_final: 0.8497 (mmm-85)
REVERT: A  391 LEU cc_start: 0.9025 (mp) cc_final: 0.8734 (mt)
REVERT: A  417 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8715 (p)
REVERT: A  441 GLN cc_start: 0.8063 (tt0) cc_final: 0.7659 (tp-100)
REVERT: B  132 MET cc_start: 0.9124 (tmm) cc_final: 0.8427 (tmm)
REVERT: B  154 MET cc_start: 0.8664 (mmm) cc_final: 0.8001 (mmm)
REVERT: B  188 ARG cc_start: 0.9071 (mmm-85) cc_final: 0.8740 (tpp80)
REVERT: B  282 ASN cc_start: 0.9131 (t0) cc_final: 0.8641 (t0)
REVERT: B  319 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8649 (mmtt)
REVERT: B  365 MET cc_start: 0.8301 (tmm) cc_final: 0.8087 (tmm)
REVERT: B  505 VAL cc_start: 0.8889 (t) cc_final: 0.8659 (p)
REVERT: C   65 LYS cc_start: 0.9015 (pttp) cc_final: 0.8724 (pttm)
REVERT: C   76 LYS cc_start: 0.8988 (tppt) cc_final: 0.8747 (tptp)
REVERT: C   83 MET cc_start: 0.9055 (mpp) cc_final: 0.8767 (mpp)
REVERT: C  107 ARG cc_start: 0.7510 (mmm160) cc_final: 0.7162 (tpt-90)
  outliers start: 32
  outliers final: 20
  residues processed: 184
  average time/residue: 0.2567
  time to fit residues: 64.2026
Evaluate side-chains
  174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 85 optimal weight:    3.9990
   chunk 14 optimal weight:    9.9990
   chunk 41 optimal weight:    0.7980
   chunk 81 optimal weight:    0.4980
   chunk 30 optimal weight:    5.9990
   overall best weight:    0.8384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.095665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.076555 restraints weight = 25820.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.079335 restraints weight = 13626.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.081240 restraints weight = 8869.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.5351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10399  Z= 0.200
  Angle     :  0.634   8.111  14108  Z= 0.308
  Chirality :  0.040   0.151   1607
  Planarity :  0.004   0.040   1784
  Dihedral  :  5.256  61.247   1481
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 18.11 %
    Favored  : 78.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.23), residues: 1275
  helix:  1.07 (0.19), residues: 781
  sheet:  0.18 (0.45), residues: 132
  loop : -1.15 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  36 
 HIS   0.004   0.001   HIS B 454 
 PHE   0.011   0.001   PHE A  88 
 TYR   0.018   0.001   TYR B  92 
 ARG   0.004   0.000   ARG C  72 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 168
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9264 (m) cc_final: 0.8994 (p)
REVERT: A  140 ASP cc_start: 0.7048 (m-30) cc_final: 0.6560 (m-30)
REVERT: A  145 ASN cc_start: 0.8655 (m-40) cc_final: 0.8066 (m-40)
REVERT: A  326 ARG cc_start: 0.8706 (mmm-85) cc_final: 0.8453 (mmm-85)
REVERT: A  391 LEU cc_start: 0.9014 (mp) cc_final: 0.8702 (mt)
REVERT: A  417 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8664 (p)
REVERT: A  441 GLN cc_start: 0.7988 (tt0) cc_final: 0.7696 (tp-100)
REVERT: B  112 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8119 (mttp)
REVERT: B  130 ARG cc_start: 0.8346 (tmm-80) cc_final: 0.7964 (tmm-80)
REVERT: B  132 MET cc_start: 0.9146 (tmm) cc_final: 0.8498 (tmm)
REVERT: B  154 MET cc_start: 0.8645 (mmm) cc_final: 0.8022 (mmm)
REVERT: B  188 ARG cc_start: 0.9089 (mmm-85) cc_final: 0.8788 (tpp80)
REVERT: B  282 ASN cc_start: 0.9071 (t0) cc_final: 0.8867 (t0)
REVERT: B  365 MET cc_start: 0.8285 (tmm) cc_final: 0.8049 (tmm)
REVERT: B  505 VAL cc_start: 0.8940 (t) cc_final: 0.8702 (p)
REVERT: C   20 LEU cc_start: 0.8941 (tp) cc_final: 0.8581 (tp)
REVERT: C   83 MET cc_start: 0.9099 (mpp) cc_final: 0.8836 (mpp)
REVERT: C  107 ARG cc_start: 0.7456 (mmm160) cc_final: 0.7134 (tpt-90)
  outliers start: 35
  outliers final: 24
  residues processed: 189
  average time/residue: 0.2333
  time to fit residues: 61.0601
Evaluate side-chains
  176 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 151
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  457 ILE
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 93 optimal weight:    0.0070
   chunk 78 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0770
   chunk 126 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 122 optimal weight:    0.3980
   chunk 95 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
A 308 GLN
** C  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.096358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.077137 restraints weight = 25921.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.079963 restraints weight = 13679.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.081904 restraints weight = 8909.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.5537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10399  Z= 0.181
  Angle     :  0.639  10.109  14108  Z= 0.307
  Chirality :  0.039   0.150   1607
  Planarity :  0.004   0.044   1784
  Dihedral  :  5.155  63.307   1481
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.07 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.23), residues: 1275
  helix:  1.18 (0.19), residues: 786
  sheet:  0.19 (0.45), residues: 134
  loop : -1.13 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 290 
 HIS   0.003   0.001   HIS B 454 
 PHE   0.021   0.001   PHE A  15 
 TYR   0.019   0.001   TYR C 113 
 ARG   0.005   0.000   ARG A 493 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 163
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9302 (m) cc_final: 0.9042 (p)
REVERT: A   94 GLU cc_start: 0.7808 (tp30) cc_final: 0.7589 (tp30)
REVERT: A  140 ASP cc_start: 0.7043 (m-30) cc_final: 0.6546 (m-30)
REVERT: A  391 LEU cc_start: 0.9010 (mp) cc_final: 0.8712 (mt)
REVERT: A  441 GLN cc_start: 0.7980 (tt0) cc_final: 0.7684 (tp-100)
REVERT: B   92 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7813 (t80)
REVERT: B  112 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8213 (mttp)
REVERT: B  130 ARG cc_start: 0.8387 (tmm-80) cc_final: 0.8036 (tmm-80)
REVERT: B  132 MET cc_start: 0.9165 (tmm) cc_final: 0.8530 (tmm)
REVERT: B  154 MET cc_start: 0.8639 (mmm) cc_final: 0.8035 (mmm)
REVERT: B  188 ARG cc_start: 0.9095 (mmm-85) cc_final: 0.8735 (tpp80)
REVERT: B  281 PHE cc_start: 0.8764 (t80) cc_final: 0.7501 (t80)
REVERT: B  365 MET cc_start: 0.8259 (tmm) cc_final: 0.8014 (tmm)
REVERT: B  505 VAL cc_start: 0.8902 (t) cc_final: 0.8652 (p)
REVERT: C   13 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7304 (tp40)
REVERT: C   20 LEU cc_start: 0.8950 (tp) cc_final: 0.8649 (tp)
REVERT: C   65 LYS cc_start: 0.8986 (pttp) cc_final: 0.8582 (ptpt)
REVERT: C   83 MET cc_start: 0.9086 (mpp) cc_final: 0.8842 (mpp)
  outliers start: 34
  outliers final: 22
  residues processed: 183
  average time/residue: 0.2393
  time to fit residues: 60.8954
Evaluate side-chains
  176 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  308 GLN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  597 PHE
Chi-restraints excluded: chain B residue   92 TYR
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  457 ILE
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 13 optimal weight:    0.3980
   chunk 19 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 60 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 106 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.096699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.077601 restraints weight = 25946.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.080375 restraints weight = 13722.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.082290 restraints weight = 8934.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.5658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10399  Z= 0.184
  Angle     :  0.656  10.072  14108  Z= 0.312
  Chirality :  0.040   0.148   1607
  Planarity :  0.004   0.039   1784
  Dihedral  :  5.112  63.636   1481
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 20.40 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.23), residues: 1275
  helix:  1.25 (0.19), residues: 786
  sheet:  0.27 (0.45), residues: 134
  loop : -1.05 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 262 
 HIS   0.003   0.001   HIS B 454 
 PHE   0.018   0.001   PHE B  38 
 TYR   0.016   0.001   TYR B  92 
 ARG   0.005   0.000   ARG C  45 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 159
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9354 (m) cc_final: 0.9078 (p)
REVERT: A  140 ASP cc_start: 0.7091 (m-30) cc_final: 0.6645 (m-30)
REVERT: A  391 LEU cc_start: 0.9031 (mp) cc_final: 0.8740 (mt)
REVERT: A  441 GLN cc_start: 0.7966 (tt0) cc_final: 0.7714 (tp-100)
REVERT: A  508 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.7996 (p)
REVERT: B  112 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8201 (mttp)
REVERT: B  130 ARG cc_start: 0.8471 (tmm-80) cc_final: 0.8034 (tmm-80)
REVERT: B  132 MET cc_start: 0.9172 (tmm) cc_final: 0.8555 (tmm)
REVERT: B  154 MET cc_start: 0.8632 (mmm) cc_final: 0.7997 (mmm)
REVERT: B  188 ARG cc_start: 0.9083 (mmm-85) cc_final: 0.8766 (tpp80)
REVERT: B  281 PHE cc_start: 0.8695 (t80) cc_final: 0.7466 (t80)
REVERT: B  290 TRP cc_start: 0.8283 (t60) cc_final: 0.8027 (t60)
REVERT: B  365 MET cc_start: 0.8225 (tmm) cc_final: 0.7987 (tmm)
REVERT: B  505 VAL cc_start: 0.8887 (t) cc_final: 0.8623 (p)
REVERT: C   20 LEU cc_start: 0.8958 (tp) cc_final: 0.8370 (tp)
REVERT: C   65 LYS cc_start: 0.8969 (pttp) cc_final: 0.8589 (ptpt)
REVERT: C   83 MET cc_start: 0.9089 (mpp) cc_final: 0.8842 (mpp)
  outliers start: 25
  outliers final: 18
  residues processed: 177
  average time/residue: 0.2473
  time to fit residues: 60.1064
Evaluate side-chains
  173 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 154
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  457 ILE
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 93 optimal weight:    0.2980
   chunk 25 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 125 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 109 optimal weight:    1.9990
   chunk 126 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** C  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.096422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.077280 restraints weight = 26202.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.080063 restraints weight = 13950.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.081951 restraints weight = 9095.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.5765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10399  Z= 0.194
  Angle     :  0.656  10.773  14108  Z= 0.314
  Chirality :  0.040   0.149   1607
  Planarity :  0.004   0.046   1784
  Dihedral  :  5.081  63.535   1481
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 20.50 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.23), residues: 1275
  helix:  1.31 (0.19), residues: 784
  sheet:  0.24 (0.44), residues: 134
  loop : -1.07 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 446 
 HIS   0.003   0.001   HIS B 454 
 PHE   0.026   0.001   PHE A  70 
 TYR   0.020   0.001   TYR B  92 
 ARG   0.008   0.000   ARG C  72 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 158
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9366 (m) cc_final: 0.9097 (p)
REVERT: A  140 ASP cc_start: 0.7104 (m-30) cc_final: 0.6691 (m-30)
REVERT: A  391 LEU cc_start: 0.9025 (mp) cc_final: 0.8749 (mt)
REVERT: A  441 GLN cc_start: 0.7942 (tt0) cc_final: 0.7703 (tp-100)
REVERT: A  508 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8059 (p)
REVERT: B  112 LYS cc_start: 0.8853 (mmmt) cc_final: 0.8252 (mttp)
REVERT: B  130 ARG cc_start: 0.8385 (tmm-80) cc_final: 0.7995 (tmm-80)
REVERT: B  132 MET cc_start: 0.9184 (tmm) cc_final: 0.8535 (tmm)
REVERT: B  154 MET cc_start: 0.8637 (mmm) cc_final: 0.8209 (mmm)
REVERT: B  188 ARG cc_start: 0.9069 (mmm-85) cc_final: 0.8788 (tpp80)
REVERT: B  290 TRP cc_start: 0.8314 (t60) cc_final: 0.7995 (t60)
REVERT: B  365 MET cc_start: 0.8206 (tmm) cc_final: 0.7954 (tmm)
REVERT: B  505 VAL cc_start: 0.8882 (t) cc_final: 0.8607 (p)
REVERT: C   65 LYS cc_start: 0.8967 (pttp) cc_final: 0.8618 (ptpt)
REVERT: C   83 MET cc_start: 0.9068 (mpp) cc_final: 0.8837 (mpp)
REVERT: C   89 GLU cc_start: 0.7775 (pp20) cc_final: 0.7476 (pp20)
REVERT: C  107 ARG cc_start: 0.7868 (tpt-90) cc_final: 0.7587 (tpt-90)
  outliers start: 26
  outliers final: 22
  residues processed: 173
  average time/residue: 0.2458
  time to fit residues: 59.4917
Evaluate side-chains
  174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 151
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  457 ILE
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain C residue   84 ASN
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 114 optimal weight:    3.9990
   chunk 123 optimal weight:    0.8980
   chunk 111 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 121 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0470
   chunk 70 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.9280

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

Flipped N/Q/H residues before XYZ refinement:
B 282 ASN
** C  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.096074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.076859 restraints weight = 26210.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.079602 restraints weight = 14018.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.081469 restraints weight = 9171.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.5835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10399  Z= 0.206
  Angle     :  0.669  11.271  14108  Z= 0.320
  Chirality :  0.040   0.152   1607
  Planarity :  0.004   0.052   1784
  Dihedral  :  5.058  63.507   1481
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 20.88 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.23), residues: 1275
  helix:  1.33 (0.19), residues: 785
  sheet:  0.31 (0.45), residues: 128
  loop : -1.12 (0.29), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  36 
 HIS   0.004   0.001   HIS B 454 
 PHE   0.023   0.001   PHE B  38 
 TYR   0.019   0.001   TYR B  92 
 ARG   0.013   0.001   ARG C  38 

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 156
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9364 (m) cc_final: 0.9095 (p)
REVERT: A  140 ASP cc_start: 0.7092 (m-30) cc_final: 0.6697 (m-30)
REVERT: A  391 LEU cc_start: 0.9035 (mp) cc_final: 0.8763 (mt)
REVERT: A  441 GLN cc_start: 0.7925 (tt0) cc_final: 0.7706 (tp-100)
REVERT: B  112 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8327 (mttp)
REVERT: B  130 ARG cc_start: 0.8521 (tmm-80) cc_final: 0.8010 (tmm-80)
REVERT: B  132 MET cc_start: 0.9166 (tmm) cc_final: 0.8510 (tmm)
REVERT: B  154 MET cc_start: 0.8651 (mmm) cc_final: 0.8214 (mmm)
REVERT: B  188 ARG cc_start: 0.9073 (mmm-85) cc_final: 0.8857 (tpp80)
REVERT: B  290 TRP cc_start: 0.8434 (t60) cc_final: 0.8132 (t60)
REVERT: B  365 MET cc_start: 0.8195 (tmm) cc_final: 0.7939 (tmm)
REVERT: B  505 VAL cc_start: 0.8888 (t) cc_final: 0.8618 (p)
REVERT: C   83 MET cc_start: 0.9061 (mpp) cc_final: 0.8831 (mpp)
REVERT: C   89 GLU cc_start: 0.7710 (pp20) cc_final: 0.7494 (pp20)
REVERT: C  107 ARG cc_start: 0.7682 (tpt-90) cc_final: 0.7418 (tpt-90)
  outliers start: 26
  outliers final: 25
  residues processed: 172
  average time/residue: 0.2454
  time to fit residues: 58.4990
Evaluate side-chains
  174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 149
  time to evaluate  : 1.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  457 ILE
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain C residue   84 ASN
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0870
   chunk 91 optimal weight:    0.0980
   chunk 5 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
B 123 ASN
** C  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.097672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.078526 restraints weight = 25944.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.081345 restraints weight = 13706.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.083221 restraints weight = 8888.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.5962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10399  Z= 0.169
  Angle     :  0.673  11.915  14108  Z= 0.316
  Chirality :  0.039   0.146   1607
  Planarity :  0.004   0.048   1784
  Dihedral  :  4.981  66.325   1481
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 21.16 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.23), residues: 1275
  helix:  1.39 (0.19), residues: 788
  sheet:  0.33 (0.45), residues: 128
  loop : -1.13 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  36 
 HIS   0.003   0.001   HIS B 454 
 PHE   0.025   0.001   PHE A  15 
 TYR   0.026   0.001   TYR B  92 
 ARG   0.012   0.001   ARG C  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2997.78 seconds
wall clock time: 54 minutes 29.13 seconds (3269.13 seconds total)