Starting phenix.real_space_refine
on Wed Feb 12 15:24:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6dzw_8941/02_2025/6dzw_8941.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6dzw_8941/02_2025/6dzw_8941.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6dzw_8941/02_2025/6dzw_8941.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6dzw_8941/02_2025/6dzw_8941.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6dzw_8941/02_2025/6dzw_8941.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6dzw_8941/02_2025/6dzw_8941.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    5109      2.51       5
     N    1250      2.21       5
     O    1429      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7829
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4279
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4279
          Classifications: {'peptide': 537}
          Link IDs: {'PTRANS': 22, 'TRANS': 514}
    Chain: "V"
      Number of atoms: 1743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1743
          Classifications: {'peptide': 223}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 7, 'TRANS': 212}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 912
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 912
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "L"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 829
          Classifications: {'peptide': 110}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {'8PR': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.17, per 1000 atoms: 0.66
  Number of scatterers: 7829
  At special positions: 0
  Unit cell: (86.652, 107.532, 123.192, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     F       1      9.00
     O    1429      8.00
     N    1250      7.00
     C    5109      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS V  37 " - pdb=" SG  CYS V 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS V 172 " - pdb=" SG  CYS V 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  43 " - pdb=" SG  CYS L 112 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A 704 " - " ASN A 217 "
      " NAG B   1 " - " ASN A 208 "
  Time building additional restraints: 2.18
  Conformation dependent library (CDL) restraints added in 995.2 milliseconds
  

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1804

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 13 sheets defined
      43.6% alpha, 16.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 97
      removed outlier: 4.450A  pdb=" N   PHE A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   LEU A  89 " --> pdb=" O   LYS A  85 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL A  92 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ILE A  93 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 102
      removed outlier: 3.657A  pdb=" N   ASN A 101 " --> pdb=" O   ASP A  98 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   VAL A 102 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 98 through 102'
    Processing helix  chain 'A' and resid 103 through 112
      removed outlier: 3.542A  pdb=" N   TYR A 107 " --> pdb=" O   TRP A 103 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   ILE A 108 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 116
    Processing helix  chain 'A' and resid 117 through 128
      removed outlier: 3.676A  pdb=" N   TYR A 121 " --> pdb=" O   PHE A 117 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   THR A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ILE A 123 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ALA A 125 " --> pdb=" O   TYR A 121 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ILE A 126 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 144
      removed outlier: 3.869A  pdb=" N   LEU A 132 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   LEU A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLY A 140 " --> pdb=" O   GLU A 136 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TYR A 142 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 157
      No H-bonds generated for 'chain 'A' and resid 155 through 157'
    Processing helix  chain 'A' and resid 158 through 190
      removed outlier: 4.454A  pdb=" N   GLY A 162 " --> pdb=" O   PHE A 158 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   CYS A 166 " --> pdb=" O   GLY A 162 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   ILE A 167 " --> pdb=" O   TYR A 163 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER A 174 " --> pdb=" O   PHE A 170 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   TYR A 175 " --> pdb=" O   TYR A 171 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ASN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   MET A 180 " --> pdb=" O   TYR A 176 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE A 188 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 234
    Processing helix  chain 'A' and resid 238 through 242
    Processing helix  chain 'A' and resid 252 through 271
      removed outlier: 3.856A  pdb=" N   CYS A 258 " --> pdb=" O   GLN A 254 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ILE A 259 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   MET A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   VAL A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE A 266 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   SER A 269 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ILE A 270 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   TRP A 271 " --> pdb=" O   TYR A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 285
      removed outlier: 4.042A  pdb=" N   LYS A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   VAL A 281 " --> pdb=" O   SER A 277 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   TRP A 282 " --> pdb=" O   GLY A 278 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   THR A 284 " --> pdb=" O   VAL A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 301
      removed outlier: 3.792A  pdb=" N   SER A 293 " --> pdb=" O   TYR A 289 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG A 298 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   THR A 301 " --> pdb=" O   VAL A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 314
      removed outlier: 3.538A  pdb=" N   VAL A 309 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   PHE A 311 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 338
      removed outlier: 3.793A  pdb=" N   ILE A 327 " --> pdb=" O   THR A 323 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE A 333 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE A 334 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 350
      removed outlier: 3.732A  pdb=" N   ALA A 348 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   TYR A 350 " --> pdb=" O   ALA A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 375
      removed outlier: 3.632A  pdb=" N   VAL A 363 " --> pdb=" O   GLN A 359 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   THR A 364 " --> pdb=" O   ASP A 360 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   SER A 365 " --> pdb=" O   ALA A 361 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   CYS A 369 " --> pdb=" O   SER A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 390
      removed outlier: 3.503A  pdb=" N   THR A 381 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   VAL A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   TYR A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 398
    Processing helix  chain 'A' and resid 403 through 408
      removed outlier: 4.542A  pdb=" N   PHE A 407 " --> pdb=" O   PRO A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 416
      removed outlier: 3.851A  pdb=" N   GLU A 412 " --> pdb=" O   ILE A 408 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ALA A 413 " --> pdb=" O   THR A 409 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE A 414 " --> pdb=" O   TYR A 410 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   ALA A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ASN A 416 " --> pdb=" O   GLU A 412 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 408 through 416'
    Processing helix  chain 'A' and resid 419 through 454
      removed outlier: 3.809A  pdb=" N   PHE A 423 " --> pdb=" O   ALA A 419 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ILE A 425 " --> pdb=" O   THR A 421 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A 426 " --> pdb=" O   PHE A 422 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ILE A 432 " --> pdb=" O   PHE A 428 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLY A 435 " --> pdb=" O   LEU A 431 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   SER A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA A 441 " --> pdb=" O   ASP A 437 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU A 443 " --> pdb=" O   THR A 439 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLU A 444 " --> pdb=" O   PHE A 440 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   VAL A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ALA A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   VAL A 450 " --> pdb=" O   VAL A 446 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LEU A 451 " --> pdb=" O   ILE A 447 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ASP A 452 " --> pdb=" O   THR A 448 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   GLU A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   PHE A 454 " --> pdb=" O   VAL A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 466
      removed outlier: 3.941A  pdb=" N   VAL A 466 " --> pdb=" O   ARG A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 477
      removed outlier: 3.618A  pdb=" N   ILE A 471 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   THR A 472 " --> pdb=" O   ALA A 468 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   CYS A 473 " --> pdb=" O   VAL A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 480
      No H-bonds generated for 'chain 'A' and resid 478 through 480'
    Processing helix  chain 'A' and resid 484 through 495
      removed outlier: 3.795A  pdb=" N   VAL A 488 " --> pdb=" O   GLY A 484 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS A 490 " --> pdb=" O   ALA A 486 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A 491 " --> pdb=" O   TYR A 487 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLU A 494 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 514
      removed outlier: 3.780A  pdb=" N   ALA A 500 " --> pdb=" O   ALA A 496 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL A 501 " --> pdb=" O   THR A 497 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   LEU A 502 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE A 507 " --> pdb=" O   THR A 503 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLU A 508 " --> pdb=" O   VAL A 504 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA A 511 " --> pdb=" O   ILE A 507 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL A 512 " --> pdb=" O   GLU A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 530
      removed outlier: 3.721A  pdb=" N   CYS A 522 " --> pdb=" O   ILE A 518 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   ARG A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASP A 524 " --> pdb=" O   GLN A 520 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL A 525 " --> pdb=" O   PHE A 521 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLU A 527 " --> pdb=" O   ARG A 523 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   MET A 528 " --> pdb=" O   ASP A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 541
      removed outlier: 3.635A  pdb=" N   ARG A 538 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE A 539 " --> pdb=" O   TRP A 535 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TRP A 541 " --> pdb=" O   TRP A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 557
      removed outlier: 4.171A  pdb=" N   LEU A 549 " --> pdb=" O   SER A 545 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU A 550 " --> pdb=" O   PRO A 546 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   PHE A 551 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   ILE A 552 " --> pdb=" O   PHE A 548 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER A 555 " --> pdb=" O   PHE A 551 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A 557 " --> pdb=" O   ILE A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 587
      removed outlier: 4.748A  pdb=" N   SER A 585 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   PHE A 586 " --> pdb=" O   GLY A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 600
      removed outlier: 3.562A  pdb=" N   THR A 591 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG A 596 " --> pdb=" O   TYR A 592 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LEU A 597 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ILE A 598 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ILE A 599 " --> pdb=" O   TYR A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 610
    Processing helix  chain 'V' and resid 77 through 80
      removed outlier: 3.617A  pdb=" N   LYS V  80 " --> pdb=" O   GLN V  77 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'V' and resid 77 through 80'
    Processing helix  chain 'V' and resid 102 through 105
    Processing helix  chain 'H' and resid 47 through 51
      removed outlier: 3.646A  pdb=" N   TYR H  50 " --> pdb=" O   ARG H  47 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER H  51 " --> pdb=" O   PHE H  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 47 through 51'
    Processing helix  chain 'L' and resid 74 through 76
      No H-bonds generated for 'chain 'L' and resid 74 through 76'
    Processing helix  chain 'L' and resid 103 through 107
      removed outlier: 3.623A  pdb=" N   ASP L 106 " --> pdb=" O   GLU L 103 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   THR L 107 " --> pdb=" O   GLU L 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 103 through 107'
    Processing sheet with id=AA1, first strand: chain 'V' and resid 18 through 19
      removed outlier: 3.795A  pdb=" N   GLN V  18 " --> pdb=" O   SER V  40 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   SER V  40 " --> pdb=" O   GLN V  18 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE V  35 " --> pdb=" O   MET V  96 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   MET V  96 " --> pdb=" O   ILE V  35 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   CYS V  37 " --> pdb=" O   ALA V  94 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ALA V  94 " --> pdb=" O   CYS V  37 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   GLU V  97 " --> pdb=" O   THR V  84 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   THR V  84 " --> pdb=" O   GLU V  97 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'V' and resid 73 through 75
      removed outlier: 3.521A  pdb=" N   ILE V  63 " --> pdb=" O   TRP V  51 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   TRP V  51 " --> pdb=" O   ILE V  63 " (cutoff:3.500A)
      removed outlier: 5.478A  pdb=" N   ASN V  65 " --> pdb=" O   MET V  49 " (cutoff:3.500A)
      removed outlier: 7.434A  pdb=" N   MET V  49 " --> pdb=" O   ASN V  65 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ALA V 107 " --> pdb=" O   LEU V 130 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'V' and resid 153 through 155
      removed outlier: 3.518A  pdb=" N   VAL V 168 " --> pdb=" O   ILE V 224 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ILE V 224 " --> pdb=" O   VAL V 168 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   PHE V 220 " --> pdb=" O   CYS V 172 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASP V 219 " --> pdb=" O   SER V 216 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   SER V 216 " --> pdb=" O   ASP V 219 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   THR V 221 " --> pdb=" O   SER V 214 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   SER V 214 " --> pdb=" O   THR V 221 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   THR V 223 " --> pdb=" O   THR V 212 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   THR V 212 " --> pdb=" O   THR V 223 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'V' and resid 159 through 160
      removed outlier: 7.380A  pdb=" N   LYS V 252 " --> pdb=" O   MET V 160 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   TYR V 236 " --> pdb=" O   TYR V 185 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR V 185 " --> pdb=" O   TYR V 236 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'V' and resid 197 through 198
    Processing sheet with id=AA6, first strand: chain 'H' and resid 22 through 25
      removed outlier: 3.866A  pdb=" N   GLN H  22 " --> pdb=" O   SER H  44 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   SER H  44 " --> pdb=" O   GLN H  22 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLN H  24 " --> pdb=" O   LYS H  42 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE H  39 " --> pdb=" O   MET H 100 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   CYS H  41 " --> pdb=" O   VAL H  98 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   THR H  97 " --> pdb=" O   ASP H  92 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ASP H  92 " --> pdb=" O   THR H  97 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 30
      removed outlier: 3.897A  pdb=" N   GLU H  29 " --> pdb=" O   SER H 135 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   THR H 137 " --> pdb=" O   GLU H  29 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   TYR H 113 " --> pdb=" O   THR H 134 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE H 114 " --> pdb=" O   VAL H  56 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL H  56 " --> pdb=" O   PHE H 114 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   MET H  53 " --> pdb=" O   ARG H  69 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   ARG H  69 " --> pdb=" O   MET H  53 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   TRP H  55 " --> pdb=" O   ILE H  67 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ARG H  69 " --> pdb=" O   LYS H  78 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LYS H  78 " --> pdb=" O   ARG H  69 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 29 through 30
      removed outlier: 3.897A  pdb=" N   GLU H  29 " --> pdb=" O   SER H 135 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   THR H 137 " --> pdb=" O   GLU H  29 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   TYR H 113 " --> pdb=" O   THR H 134 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   CYS H 115 " --> pdb=" O   TRP H 130 " (cutoff:3.500A)
      removed outlier: 4.949A  pdb=" N   TRP H 130 " --> pdb=" O   CYS H 115 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   ARG H 117 " --> pdb=" O   ASP H 128 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 24 through 27
      removed outlier: 4.224A  pdb=" N   SER L  27 " --> pdb=" O   SER L  42 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   SER L  42 " --> pdb=" O   SER L  27 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 32
      removed outlier: 3.735A  pdb=" N   THR L 126 " --> pdb=" O   TYR L 110 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   TYR L 110 " --> pdb=" O   THR L 126 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   PHE L 111 " --> pdb=" O   PHE L  60 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   PHE L  60 " --> pdb=" O   PHE L 111 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLN L 113 " --> pdb=" O   ASN L  58 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 30 through 32
      removed outlier: 3.735A  pdb=" N   THR L 126 " --> pdb=" O   TYR L 110 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   TYR L 110 " --> pdb=" O   THR L 126 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLN L 114 " --> pdb=" O   THR L 121 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   THR L 121 " --> pdb=" O   GLN L 114 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 72 through 73
    Processing sheet with id=AB4, first strand: chain 'L' and resid 86 through 91
      removed outlier: 3.670A  pdb=" N   SER L  89 " --> pdb=" O   SER L  96 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   SER L  91 " --> pdb=" O   TYR L  94 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   TYR L  94 " --> pdb=" O   SER L  91 " (cutoff:3.500A)

    224 hydrogen bonds defined for protein.
    630 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.21

  Time building geometry restraints manager: 2.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2288
        1.34 -     1.46: 1607
        1.46 -     1.57: 4098
        1.57 -     1.69: 1
        1.69 -     1.81: 59
  Bond restraints: 8053
  Sorted by residual:
  bond pdb=" CAT 8PR A 701 "
       pdb=" CAX 8PR A 701 "
    ideal  model  delta    sigma   weight residual
    1.509  1.577 -0.068 2.00e-02 2.50e+03 1.15e+01
  bond pdb=" CAV 8PR A 701 "
       pdb=" OAQ 8PR A 701 "
    ideal  model  delta    sigma   weight residual
    1.354  1.415 -0.061 2.00e-02 2.50e+03 9.43e+00
  bond pdb=" CAI 8PR A 701 "
       pdb=" NAN 8PR A 701 "
    ideal  model  delta    sigma   weight residual
    1.452  1.508 -0.056 2.00e-02 2.50e+03 7.86e+00
  bond pdb=" CAU 8PR A 701 "
       pdb=" OAP 8PR A 701 "
    ideal  model  delta    sigma   weight residual
    1.362  1.416 -0.054 2.00e-02 2.50e+03 7.16e+00
  bond pdb=" CAK 8PR A 701 "
       pdb=" NAN 8PR A 701 "
    ideal  model  delta    sigma   weight residual
    1.451  1.502 -0.051 2.00e-02 2.50e+03 6.39e+00
  ... (remaining 8048 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 10750
        2.56 -     5.11: 149
        5.11 -     7.67: 41
        7.67 -    10.23: 12
       10.23 -    12.78: 2
  Bond angle restraints: 10954
  Sorted by residual:
  angle pdb=" C   GLU L  47 "
        pdb=" N   SER L  48 "
        pdb=" CA  SER L  48 "
      ideal   model   delta    sigma   weight residual
     121.70  134.48  -12.78 1.80e+00 3.09e-01 5.04e+01
  angle pdb=" N   GLY A 249 "
        pdb=" CA  GLY A 249 "
        pdb=" C   GLY A 249 "
      ideal   model   delta    sigma   weight residual
     111.02  122.35  -11.33 1.86e+00 2.89e-01 3.71e+01
  angle pdb=" N   ILE A 251 "
        pdb=" CA  ILE A 251 "
        pdb=" C   ILE A 251 "
      ideal   model   delta    sigma   weight residual
     109.30  115.39   -6.09 1.25e+00 6.40e-01 2.37e+01
  angle pdb=" C   GLY A 129 "
        pdb=" N   ILE A 130 "
        pdb=" CA  ILE A 130 "
      ideal   model   delta    sigma   weight residual
     120.33  124.05   -3.72 8.00e-01 1.56e+00 2.16e+01
  angle pdb=" C   GLY H  81 "
        pdb=" N   LYS H  82 "
        pdb=" CA  LYS H  82 "
      ideal   model   delta    sigma   weight residual
     122.08  128.69   -6.61 1.47e+00 4.63e-01 2.02e+01
  ... (remaining 10949 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.27: 4481
       27.27 -    54.54: 178
       54.54 -    81.80: 11
       81.80 -   109.07: 3
      109.07 -   136.34: 1
  Dihedral angle restraints: 4674
    sinusoidal: 1829
      harmonic: 2845
  Sorted by residual:
  dihedral pdb=" CA  GLU L  47 "
           pdb=" C   GLU L  47 "
           pdb=" N   SER L  48 "
           pdb=" CA  SER L  48 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   32.90  -32.90     0      5.00e+00 4.00e-02 4.33e+01
  dihedral pdb=" CAX 8PR A 701 "
           pdb=" CAM 8PR A 701 "
           pdb=" CAW 8PR A 701 "
           pdb=" OAO 8PR A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     182.60   46.26  136.34     1      3.00e+01 1.11e-03 1.84e+01
  dihedral pdb=" CA  GLY A 249 "
           pdb=" C   GLY A 249 "
           pdb=" N   GLY A 250 "
           pdb=" CA  GLY A 250 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.04  -20.96     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 4671 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.472: 1207
       0.472 -    0.943: 1
       0.943 -    1.415: 0
       1.415 -    1.886: 0
       1.886 -    2.358: 1
  Chirality restraints: 1209
  Sorted by residual:
  chirality pdb=" C1  NAG A 704 "
            pdb=" ND2 ASN A 217 "
            pdb=" C2  NAG A 704 "
            pdb=" O5  NAG A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.04   -2.36 2.00e-01 2.50e+01 1.39e+02
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.31   -0.09 2.00e-02 2.50e+03 1.92e+01
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 208 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.62   -0.78 2.00e-01 2.50e+01 1.52e+01
  ... (remaining 1206 not shown)

  Planarity restraints: 1354
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 217 "   -0.179 2.00e-02 2.50e+03   1.66e-01 3.44e+02
        pdb=" CG  ASN A 217 "    0.055 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 217 "    0.067 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 217 "    0.248 2.00e-02 2.50e+03
        pdb=" C1  NAG A 704 "   -0.191 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 208 "    0.100 2.00e-02 2.50e+03   1.05e-01 1.39e+02
        pdb=" CG  ASN A 208 "   -0.038 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 208 "   -0.031 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 208 "   -0.162 2.00e-02 2.50e+03
        pdb=" C1  NAG B   1 "    0.130 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   2 "   -0.095 2.00e-02 2.50e+03   7.83e-02 7.66e+01
        pdb=" C7  NAG B   2 "    0.025 2.00e-02 2.50e+03
        pdb=" C8  NAG B   2 "   -0.071 2.00e-02 2.50e+03
        pdb=" N2  NAG B   2 "    0.125 2.00e-02 2.50e+03
        pdb=" O7  NAG B   2 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1351 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 51
        2.62 -     3.19: 6155
        3.19 -     3.76: 11748
        3.76 -     4.33: 16047
        4.33 -     4.90: 25697
  Nonbonded interactions: 59698
  Sorted by model distance:
  nonbonded pdb=" O3  NAG B   2 "
            pdb=" O7  NAG B   2 "
     model   vdw
     2.052 3.040
  nonbonded pdb=" OH  TYR A 495 "
            pdb=" O   PRO A 561 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OG  SER V  59 "
            pdb=" O   GLY V 248 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" OG1 THR V 112 "
            pdb=" O   TYR V 123 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" O   SER H  96 "
            pdb=" OG  SER H  96 "
     model   vdw
     2.340 3.040
  ... (remaining 59693 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:             0.000
  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:             0.460
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.090
  Process input model:                     22.210
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5450
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      :  0.004   0.068   8053  Z= 0.263
  Angle     :  0.870  12.783  10954  Z= 0.468
  Chirality :  0.087   2.358   1209
  Planarity :  0.006   0.078   1352
  Dihedral  : 13.751 136.338   2855
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  5.54 %
    Favored  : 94.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.21 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -4.99 (0.19), residues: 978
  helix: -4.98 (0.08), residues: 313
  sheet: -1.85 (0.34), residues: 156
  loop : -2.64 (0.21), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 151 
 HIS   0.001   0.000   HIS V 240 
 PHE   0.012   0.001   PHE A 423 
 TYR   0.008   0.001   TYR V  48 
 ARG   0.005   0.000   ARG A 596 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 293
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLU cc_start: 0.6967 (mp0) cc_final: 0.5820 (tt0)
REVERT: A  103 TRP cc_start: 0.8712 (p-90) cc_final: 0.8297 (p-90)
REVERT: A  104 ARG cc_start: 0.8278 (tpt170) cc_final: 0.7907 (tpp80)
REVERT: A  111 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8359 (mm-40)
REVERT: A  136 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8251 (tm-30)
REVERT: A  158 PHE cc_start: 0.8517 (m-80) cc_final: 0.7924 (m-80)
REVERT: A  172 ILE cc_start: 0.9383 (mt) cc_final: 0.9086 (tt)
REVERT: A  187 LEU cc_start: 0.9220 (tp) cc_final: 0.9007 (tp)
REVERT: A  229 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8326 (tm-30)
REVERT: A  230 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8047 (mm-30)
REVERT: A  253 TRP cc_start: 0.5958 (m100) cc_final: 0.5680 (p-90)
REVERT: A  260 MET cc_start: 0.3788 (ttt) cc_final: 0.3560 (ttt)
REVERT: A  317 TRP cc_start: 0.7144 (p-90) cc_final: 0.6853 (m-10)
REVERT: A  344 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7732 (tt)
REVERT: A  392 GLU cc_start: 0.5982 (mp0) cc_final: 0.5334 (mp0)
REVERT: A  407 PHE cc_start: 0.8610 (m-80) cc_final: 0.8173 (m-80)
REVERT: A  430 MET cc_start: 0.7831 (ttt) cc_final: 0.7181 (ttp)
REVERT: A  490 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8578 (mmmt)
REVERT: A  595 TYR cc_start: 0.6293 (t80) cc_final: 0.5651 (t80)
REVERT: A  596 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7633 (mtt-85)
REVERT: A  607 ARG cc_start: 0.7349 (ptm160) cc_final: 0.6689 (mtp180)
REVERT: V   20 GLN cc_start: 0.8034 (mp10) cc_final: 0.7832 (mp10)
REVERT: V   49 MET cc_start: 0.8074 (tpt) cc_final: 0.7618 (tpt)
REVERT: V   63 ILE cc_start: 0.7694 (mt) cc_final: 0.7373 (mt)
REVERT: V   76 ASN cc_start: 0.8140 (t0) cc_final: 0.7574 (t0)
REVERT: V  244 PRO cc_start: 0.8263 (Cg_exo) cc_final: 0.8062 (Cg_endo)
REVERT: L  100 HIS cc_start: 0.6117 (m170) cc_final: 0.5726 (m-70)
REVERT: L  127 LYS cc_start: 0.6752 (mttt) cc_final: 0.6121 (tttm)
  outliers start: 3
  outliers final: 1
  residues processed: 293
  average time/residue: 0.2148
  time to fit residues: 82.0564
Evaluate side-chains
  215 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 213
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 73 optimal weight:    0.7980
   chunk 40 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 39 optimal weight:    0.3980
   chunk 76 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
A 223 HIS
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
A 416 ASN
** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 239 GLN
H  58 GLN
L  58 ASN
L  78 GLN
L 114 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.211539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.169677 restraints weight = 13221.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.177190 restraints weight = 8893.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.183385 restraints weight = 6425.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.4372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5599
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8053  Z= 0.225
  Angle     :  0.672  10.477  10954  Z= 0.344
  Chirality :  0.045   0.379   1209
  Planarity :  0.005   0.037   1352
  Dihedral  :  6.624 129.283   1159
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  6.02 %
    Favored  : 93.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.32 %
    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: -3.42 (0.23), residues: 978
  helix: -3.24 (0.20), residues: 322
  sheet: -1.11 (0.36), residues: 181
  loop : -1.92 (0.26), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP V 184 
 HIS   0.005   0.001   HIS V 240 
 PHE   0.026   0.002   PHE A 191 
 TYR   0.020   0.001   TYR H 120 
 ARG   0.004   0.001   ARG H  69 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 254
  time to evaluate  : 0.783 
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: A   80 GLU cc_start: 0.7170 (mp0) cc_final: 0.5816 (tt0)
REVERT: A   90 LEU cc_start: 0.9584 (tp) cc_final: 0.9347 (tp)
REVERT: A  104 ARG cc_start: 0.8396 (tpt170) cc_final: 0.7873 (tpp80)
REVERT: A  136 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8697 (tm-30)
REVERT: A  144 ARG cc_start: 0.5842 (ptm160) cc_final: 0.5588 (ptt180)
REVERT: A  158 PHE cc_start: 0.8811 (m-80) cc_final: 0.8596 (m-80)
REVERT: A  166 CYS cc_start: 0.8536 (t) cc_final: 0.7652 (t)
REVERT: A  172 ILE cc_start: 0.9334 (mt) cc_final: 0.8753 (tt)
REVERT: A  182 TRP cc_start: 0.8572 (m-10) cc_final: 0.7576 (m-10)
REVERT: A  205 ASN cc_start: 0.8826 (t0) cc_final: 0.8569 (t0)
REVERT: A  223 HIS cc_start: 0.7591 (m170) cc_final: 0.7346 (m-70)
REVERT: A  237 LEU cc_start: 0.9228 (mm) cc_final: 0.8738 (mm)
REVERT: A  238 GLN cc_start: 0.8255 (mt0) cc_final: 0.7791 (mt0)
REVERT: A  253 TRP cc_start: 0.5445 (m100) cc_final: 0.4717 (p-90)
REVERT: A  302 LEU cc_start: 0.7799 (tt) cc_final: 0.7035 (mt)
REVERT: A  312 TYR cc_start: 0.8242 (t80) cc_final: 0.7928 (t80)
REVERT: A  317 TRP cc_start: 0.7567 (p-90) cc_final: 0.6886 (m-10)
REVERT: A  332 GLN cc_start: 0.7773 (tp40) cc_final: 0.7445 (tp40)
REVERT: A  343 VAL cc_start: 0.9189 (t) cc_final: 0.8817 (t)
REVERT: A  358 TYR cc_start: 0.7780 (t80) cc_final: 0.6757 (t80)
REVERT: A  407 PHE cc_start: 0.8980 (m-80) cc_final: 0.8481 (m-10)
REVERT: A  430 MET cc_start: 0.7557 (ttt) cc_final: 0.6714 (ttp)
REVERT: A  595 TYR cc_start: 0.6756 (t80) cc_final: 0.5914 (t80)
REVERT: A  596 ARG cc_start: 0.8842 (mtm-85) cc_final: 0.8088 (mpt180)
REVERT: V   45 THR cc_start: 0.7284 (p) cc_final: 0.6315 (t)
REVERT: V   63 ILE cc_start: 0.8514 (mt) cc_final: 0.7886 (mt)
REVERT: V   76 ASN cc_start: 0.8128 (t0) cc_final: 0.7842 (p0)
REVERT: V   85 LEU cc_start: 0.6701 (mt) cc_final: 0.6403 (mt)
REVERT: H   21 VAL cc_start: 0.7587 (t) cc_final: 0.5219 (t)
REVERT: L   33 VAL cc_start: 0.7314 (t) cc_final: 0.7021 (t)
REVERT: L  100 HIS cc_start: 0.6210 (m170) cc_final: 0.5813 (m-70)
REVERT: L  102 MET cc_start: 0.5249 (ptt) cc_final: 0.4926 (ptt)
REVERT: L  110 TYR cc_start: 0.8196 (m-10) cc_final: 0.7714 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 255
  average time/residue: 0.1837
  time to fit residues: 63.8951
Evaluate side-chains
  203 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 31 optimal weight:    0.0370
   chunk 42 optimal weight:    0.0870
   chunk 57 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 47 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 26 optimal weight:    0.4980
   chunk 60 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0170
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.5276

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 ASN
** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
V 157 HIS
** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.208421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.167283 restraints weight = 14069.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.174713 restraints weight = 9540.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.180622 restraints weight = 6909.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.4366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5743
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8053  Z= 0.167
  Angle     :  0.600   9.885  10954  Z= 0.295
  Chirality :  0.044   0.325   1209
  Planarity :  0.004   0.057   1352
  Dihedral  :  6.230 125.240   1159
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.32 %
    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: -2.73 (0.24), residues: 978
  helix: -2.41 (0.23), residues: 336
  sheet: -0.79 (0.37), residues: 183
  loop : -1.65 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP V  62 
 HIS   0.002   0.001   HIS A 240 
 PHE   0.020   0.001   PHE A 170 
 TYR   0.016   0.001   TYR H 120 
 ARG   0.003   0.000   ARG H  69 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.874 
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   80 GLU cc_start: 0.7161 (mp0) cc_final: 0.5906 (tt0)
REVERT: A   98 ASP cc_start: 0.9552 (p0) cc_final: 0.9307 (p0)
REVERT: A  104 ARG cc_start: 0.8553 (tpt170) cc_final: 0.8088 (ttm-80)
REVERT: A  111 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7635 (mm-40)
REVERT: A  136 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8191 (tm-30)
REVERT: A  166 CYS cc_start: 0.8638 (t) cc_final: 0.7350 (t)
REVERT: A  168 ILE cc_start: 0.9442 (mm) cc_final: 0.9241 (mm)
REVERT: A  172 ILE cc_start: 0.9351 (mt) cc_final: 0.8717 (tt)
REVERT: A  223 HIS cc_start: 0.7676 (m170) cc_final: 0.7422 (m-70)
REVERT: A  238 GLN cc_start: 0.8256 (mt0) cc_final: 0.7776 (mt0)
REVERT: A  253 TRP cc_start: 0.5515 (m100) cc_final: 0.4684 (p-90)
REVERT: A  317 TRP cc_start: 0.7604 (p-90) cc_final: 0.6971 (m-10)
REVERT: A  358 TYR cc_start: 0.7757 (t80) cc_final: 0.6811 (t80)
REVERT: A  408 ILE cc_start: 0.9416 (mm) cc_final: 0.9137 (mm)
REVERT: A  430 MET cc_start: 0.7664 (ttt) cc_final: 0.6769 (ttp)
REVERT: A  528 MET cc_start: 0.4220 (ppp) cc_final: 0.4004 (ppp)
REVERT: A  595 TYR cc_start: 0.6401 (t80) cc_final: 0.5552 (t80)
REVERT: V   45 THR cc_start: 0.7567 (p) cc_final: 0.6553 (t)
REVERT: V   63 ILE cc_start: 0.8125 (mt) cc_final: 0.7576 (mt)
REVERT: V  159 PHE cc_start: 0.6470 (m-10) cc_final: 0.6268 (m-10)
REVERT: V  176 GLN cc_start: 0.7245 (mt0) cc_final: 0.6965 (mt0)
REVERT: V  241 TYR cc_start: 0.8112 (t80) cc_final: 0.7871 (t80)
REVERT: H   21 VAL cc_start: 0.7273 (t) cc_final: 0.5528 (t)
REVERT: H   46 TYR cc_start: 0.8219 (p90) cc_final: 0.7939 (p90)
REVERT: H   52 TRP cc_start: 0.7792 (m100) cc_final: 0.7171 (m100)
REVERT: H   71 TYR cc_start: 0.8335 (t80) cc_final: 0.7982 (t80)
REVERT: L  100 HIS cc_start: 0.6107 (m170) cc_final: 0.5731 (m-70)
REVERT: L  102 MET cc_start: 0.4858 (ptt) cc_final: 0.4558 (ptt)
REVERT: L  110 TYR cc_start: 0.8101 (m-10) cc_final: 0.7894 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.1906
  time to fit residues: 62.7943
Evaluate side-chains
  195 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 88 optimal weight:    6.9990
   chunk 49 optimal weight:    0.0040
   chunk 21 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 38 optimal weight:    0.2980
   overall best weight:    3.0598

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 ASN
A 223 HIS
** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
V  54 GLN
** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 114 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.190805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.151939 restraints weight = 13916.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.158723 restraints weight = 9266.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.164034 restraints weight = 6657.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.4213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6105
moved from start:          0.4792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8053  Z= 0.284
  Angle     :  0.701  10.214  10954  Z= 0.363
  Chirality :  0.046   0.369   1209
  Planarity :  0.005   0.051   1352
  Dihedral  :  6.719 134.762   1159
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 16.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  4.81 %
    Favored  : 95.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.32 %
    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: -2.03 (0.25), residues: 978
  helix: -1.67 (0.25), residues: 327
  sheet: -0.60 (0.38), residues: 179
  loop : -1.30 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 204 
 HIS   0.010   0.002   HIS A 143 
 PHE   0.028   0.002   PHE A 170 
 TYR   0.020   0.002   TYR H 120 
 ARG   0.006   0.001   ARG V 113 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 231
  time to evaluate  : 0.803 
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: A  104 ARG cc_start: 0.8583 (tpt170) cc_final: 0.8109 (ttm-80)
REVERT: A  133 PHE cc_start: 0.7919 (m-80) cc_final: 0.7543 (m-80)
REVERT: A  136 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8602 (tm-30)
REVERT: A  166 CYS cc_start: 0.8683 (t) cc_final: 0.8375 (p)
REVERT: A  168 ILE cc_start: 0.9447 (mm) cc_final: 0.9160 (mm)
REVERT: A  172 ILE cc_start: 0.9468 (mt) cc_final: 0.8890 (tt)
REVERT: A  229 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8814 (tm-30)
REVERT: A  238 GLN cc_start: 0.8582 (mt0) cc_final: 0.7737 (mt0)
REVERT: A  241 ARG cc_start: 0.8125 (mmm-85) cc_final: 0.7886 (mmt90)
REVERT: A  302 LEU cc_start: 0.8321 (mt) cc_final: 0.7933 (mt)
REVERT: A  317 TRP cc_start: 0.7631 (p-90) cc_final: 0.7031 (m-10)
REVERT: A  341 PHE cc_start: 0.8351 (t80) cc_final: 0.7797 (t80)
REVERT: A  343 VAL cc_start: 0.9158 (t) cc_final: 0.8868 (t)
REVERT: A  358 TYR cc_start: 0.7913 (t80) cc_final: 0.7146 (t80)
REVERT: A  407 PHE cc_start: 0.9281 (m-10) cc_final: 0.8584 (m-80)
REVERT: A  417 MET cc_start: 0.7522 (mmp) cc_final: 0.7271 (tpp)
REVERT: A  430 MET cc_start: 0.7774 (ttp) cc_final: 0.6903 (ttp)
REVERT: A  444 GLU cc_start: 0.8772 (pt0) cc_final: 0.8226 (pt0)
REVERT: A  473 CYS cc_start: 0.8154 (p) cc_final: 0.7933 (p)
REVERT: A  528 MET cc_start: 0.5203 (ppp) cc_final: 0.4849 (ppp)
REVERT: V   35 ILE cc_start: 0.8528 (tp) cc_final: 0.8274 (mp)
REVERT: V   49 MET cc_start: 0.8943 (tpt) cc_final: 0.8548 (tpt)
REVERT: V   63 ILE cc_start: 0.8624 (mt) cc_final: 0.7916 (mt)
REVERT: V   65 ASN cc_start: 0.8768 (m110) cc_final: 0.8408 (m-40)
REVERT: V  109 TYR cc_start: 0.7943 (m-10) cc_final: 0.7734 (m-10)
REVERT: V  151 ILE cc_start: 0.7908 (mt) cc_final: 0.7600 (mt)
REVERT: H   21 VAL cc_start: 0.7536 (t) cc_final: 0.5900 (t)
REVERT: H   46 TYR cc_start: 0.8462 (p90) cc_final: 0.8178 (p90)
REVERT: H   52 TRP cc_start: 0.8342 (m100) cc_final: 0.8048 (m100)
REVERT: L   97 LEU cc_start: 0.4622 (pt) cc_final: 0.4245 (pt)
REVERT: L  100 HIS cc_start: 0.6492 (m170) cc_final: 0.6104 (m-70)
REVERT: L  127 LYS cc_start: 0.7364 (mttt) cc_final: 0.6635 (tttt)
  outliers start: 1
  outliers final: 0
  residues processed: 232
  average time/residue: 0.1915
  time to fit residues: 60.8529
Evaluate side-chains
  189 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 89 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 54 optimal weight:    0.1980
   chunk 85 optimal weight:    7.9990
   chunk 90 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0070
   chunk 35 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 114 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.198790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.159476 restraints weight = 14142.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.166457 restraints weight = 9533.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.171966 restraints weight = 6886.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5943
moved from start:          0.4802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8053  Z= 0.157
  Angle     :  0.588  10.173  10954  Z= 0.291
  Chirality :  0.044   0.322   1209
  Planarity :  0.004   0.046   1352
  Dihedral  :  6.344 128.932   1159
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  1.93 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.32 %
    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: -1.77 (0.26), residues: 978
  helix: -1.46 (0.26), residues: 328
  sheet: -0.34 (0.39), residues: 178
  loop : -1.19 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 541 
 HIS   0.004   0.001   HIS A 235 
 PHE   0.024   0.001   PHE A 170 
 TYR   0.017   0.001   TYR H 120 
 ARG   0.006   0.000   ARG A 596 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 235
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLU cc_start: 0.7311 (mp0) cc_final: 0.5919 (tt0)
REVERT: A   90 LEU cc_start: 0.9471 (tp) cc_final: 0.9222 (tp)
REVERT: A  104 ARG cc_start: 0.8601 (tpt170) cc_final: 0.8191 (ttm-80)
REVERT: A  112 ASN cc_start: 0.7703 (OUTLIER) cc_final: 0.7460 (m110)
REVERT: A  133 PHE cc_start: 0.7720 (m-80) cc_final: 0.7341 (m-80)
REVERT: A  136 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8586 (tm-30)
REVERT: A  166 CYS cc_start: 0.8622 (t) cc_final: 0.8335 (p)
REVERT: A  168 ILE cc_start: 0.9490 (mm) cc_final: 0.9211 (mm)
REVERT: A  172 ILE cc_start: 0.9426 (mt) cc_final: 0.8854 (tt)
REVERT: A  182 TRP cc_start: 0.8823 (m-10) cc_final: 0.7724 (m-90)
REVERT: A  185 TYR cc_start: 0.7929 (t80) cc_final: 0.7570 (t80)
REVERT: A  229 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8532 (tm-30)
REVERT: A  230 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8214 (mm-30)
REVERT: A  237 LEU cc_start: 0.9289 (mm) cc_final: 0.8892 (mm)
REVERT: A  238 GLN cc_start: 0.8421 (mt0) cc_final: 0.7951 (mt0)
REVERT: A  306 TRP cc_start: 0.8532 (p90) cc_final: 0.8175 (p90)
REVERT: A  307 ARG cc_start: 0.8248 (mtt180) cc_final: 0.7175 (mtt180)
REVERT: A  317 TRP cc_start: 0.7599 (p-90) cc_final: 0.7009 (m-10)
REVERT: A  341 PHE cc_start: 0.8156 (t80) cc_final: 0.7603 (t80)
REVERT: A  347 PHE cc_start: 0.8123 (m-80) cc_final: 0.7839 (m-80)
REVERT: A  358 TYR cc_start: 0.7468 (t80) cc_final: 0.6965 (t80)
REVERT: A  389 MET cc_start: 0.7198 (ttt) cc_final: 0.6978 (ttt)
REVERT: A  407 PHE cc_start: 0.9271 (m-10) cc_final: 0.8655 (m-10)
REVERT: A  417 MET cc_start: 0.7564 (mmp) cc_final: 0.7253 (tpp)
REVERT: A  430 MET cc_start: 0.7900 (ttt) cc_final: 0.7065 (ttp)
REVERT: A  444 GLU cc_start: 0.8600 (pt0) cc_final: 0.8109 (pt0)
REVERT: A  473 CYS cc_start: 0.8094 (p) cc_final: 0.7889 (p)
REVERT: A  595 TYR cc_start: 0.6583 (t80) cc_final: 0.5567 (t80)
REVERT: V   45 THR cc_start: 0.7398 (p) cc_final: 0.6557 (t)
REVERT: V   49 MET cc_start: 0.8712 (tpt) cc_final: 0.8133 (tpt)
REVERT: V   63 ILE cc_start: 0.8270 (mt) cc_final: 0.7858 (mt)
REVERT: V   65 ASN cc_start: 0.8558 (m110) cc_final: 0.8279 (m-40)
REVERT: V  109 TYR cc_start: 0.8031 (m-10) cc_final: 0.7731 (m-80)
REVERT: V  151 ILE cc_start: 0.7711 (mt) cc_final: 0.7459 (mt)
REVERT: V  241 TYR cc_start: 0.8292 (t80) cc_final: 0.8058 (t80)
REVERT: H   21 VAL cc_start: 0.7421 (t) cc_final: 0.5997 (t)
REVERT: H   52 TRP cc_start: 0.8282 (m100) cc_final: 0.8046 (m100)
REVERT: H   70 ILE cc_start: 0.7855 (mt) cc_final: 0.7594 (mt)
REVERT: H  100 MET cc_start: 0.4262 (tpp) cc_final: 0.3736 (tpp)
REVERT: H  117 ARG cc_start: 0.7560 (tmt170) cc_final: 0.7321 (tmt170)
REVERT: H  127 MET cc_start: 0.5785 (mpp) cc_final: 0.4824 (ptp)
REVERT: L   97 LEU cc_start: 0.4225 (pt) cc_final: 0.3902 (pt)
REVERT: L  100 HIS cc_start: 0.6356 (m170) cc_final: 0.5936 (m-70)
REVERT: L  113 GLN cc_start: 0.8080 (tt0) cc_final: 0.7624 (tm-30)
REVERT: L  127 LYS cc_start: 0.7181 (mttt) cc_final: 0.6460 (tttt)
  outliers start: 2
  outliers final: 0
  residues processed: 236
  average time/residue: 0.1966
  time to fit residues: 63.1484
Evaluate side-chains
  210 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 1 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0980
   chunk 37 optimal weight:    0.9980
   chunk 70 optimal weight:    6.9990
   chunk 93 optimal weight:    8.9990
   chunk 42 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0670
   chunk 67 optimal weight:    7.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A 211 ASN
A 368 ASN
** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V 239 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 = 0.4528 r_free = 0.4528 target = 0.200027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.160784 restraints weight = 14163.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.167782 restraints weight = 9523.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.173326 restraints weight = 6877.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.4275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5922
moved from start:          0.4952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8053  Z= 0.155
  Angle     :  0.575  10.350  10954  Z= 0.282
  Chirality :  0.043   0.280   1209
  Planarity :  0.004   0.042   1352
  Dihedral  :  6.166 125.217   1159
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.29 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.32 %
    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: -1.56 (0.26), residues: 978
  helix: -1.24 (0.26), residues: 328
  sheet: -0.18 (0.39), residues: 183
  loop : -1.12 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 204 
 HIS   0.003   0.001   HIS V 240 
 PHE   0.023   0.001   PHE A 170 
 TYR   0.012   0.001   TYR A 312 
 ARG   0.005   0.000   ARG A 596 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 237
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 GLU cc_start: 0.7216 (mp0) cc_final: 0.5869 (tt0)
REVERT: A   90 LEU cc_start: 0.9482 (tp) cc_final: 0.9243 (tp)
REVERT: A  104 ARG cc_start: 0.8687 (tpt170) cc_final: 0.8184 (ttm-80)
REVERT: A  133 PHE cc_start: 0.7740 (m-80) cc_final: 0.7475 (m-80)
REVERT: A  135 MET cc_start: 0.8791 (ppp) cc_final: 0.8387 (ppp)
REVERT: A  136 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8456 (tm-30)
REVERT: A  166 CYS cc_start: 0.8624 (t) cc_final: 0.8371 (p)
REVERT: A  168 ILE cc_start: 0.9501 (mm) cc_final: 0.9210 (mm)
REVERT: A  172 ILE cc_start: 0.9408 (mt) cc_final: 0.8834 (tt)
REVERT: A  185 TYR cc_start: 0.7951 (t80) cc_final: 0.7407 (t80)
REVERT: A  229 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8476 (tm-30)
REVERT: A  230 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8201 (mm-30)
REVERT: A  238 GLN cc_start: 0.8394 (mt0) cc_final: 0.7909 (mt0)
REVERT: A  260 MET cc_start: 0.5417 (ttt) cc_final: 0.5164 (ttt)
REVERT: A  306 TRP cc_start: 0.8434 (p90) cc_final: 0.8063 (p90)
REVERT: A  317 TRP cc_start: 0.7578 (p-90) cc_final: 0.6946 (m-10)
REVERT: A  341 PHE cc_start: 0.8132 (t80) cc_final: 0.7538 (t80)
REVERT: A  358 TYR cc_start: 0.7586 (t80) cc_final: 0.6832 (t80)
REVERT: A  407 PHE cc_start: 0.9294 (m-10) cc_final: 0.8761 (m-10)
REVERT: A  408 ILE cc_start: 0.9299 (mm) cc_final: 0.9049 (mm)
REVERT: A  417 MET cc_start: 0.7473 (mmp) cc_final: 0.7172 (tpp)
REVERT: A  430 MET cc_start: 0.7875 (ttt) cc_final: 0.7107 (ttp)
REVERT: A  444 GLU cc_start: 0.8619 (pt0) cc_final: 0.8184 (pt0)
REVERT: A  473 CYS cc_start: 0.8054 (p) cc_final: 0.7840 (p)
REVERT: A  595 TYR cc_start: 0.6779 (t80) cc_final: 0.5766 (t80)
REVERT: V   35 ILE cc_start: 0.8290 (tp) cc_final: 0.8030 (mp)
REVERT: V   45 THR cc_start: 0.7423 (p) cc_final: 0.6584 (t)
REVERT: V   63 ILE cc_start: 0.8369 (mt) cc_final: 0.7578 (mt)
REVERT: V  241 TYR cc_start: 0.8156 (t80) cc_final: 0.7859 (t80)
REVERT: H   21 VAL cc_start: 0.7541 (t) cc_final: 0.5329 (t)
REVERT: H   46 TYR cc_start: 0.8441 (p90) cc_final: 0.8110 (p90)
REVERT: H   70 ILE cc_start: 0.7942 (mt) cc_final: 0.7706 (mt)
REVERT: H  100 MET cc_start: 0.4200 (tpp) cc_final: 0.3698 (tpp)
REVERT: H  117 ARG cc_start: 0.7442 (tmt170) cc_final: 0.7163 (tmt170)
REVERT: H  127 MET cc_start: 0.5714 (mpp) cc_final: 0.4518 (ptp)
REVERT: L   57 LEU cc_start: 0.9456 (tp) cc_final: 0.8972 (tp)
REVERT: L   85 ARG cc_start: 0.7893 (ptm160) cc_final: 0.7505 (ptm160)
REVERT: L   97 LEU cc_start: 0.4259 (pt) cc_final: 0.3910 (pt)
REVERT: L  100 HIS cc_start: 0.6462 (m170) cc_final: 0.6026 (m-70)
REVERT: L  113 GLN cc_start: 0.8106 (tt0) cc_final: 0.7446 (tm-30)
REVERT: L  127 LYS cc_start: 0.7154 (mttt) cc_final: 0.6454 (tttt)
  outliers start: 1
  outliers final: 1
  residues processed: 237
  average time/residue: 0.2095
  time to fit residues: 66.8131
Evaluate side-chains
  208 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 63 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 70 optimal weight:    0.2980
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.0588

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 239 GLN
L 100 HIS
L 114 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.187555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.149763 restraints weight = 14342.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.156498 restraints weight = 9652.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.161719 restraints weight = 6952.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6136
moved from start:          0.5538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8053  Z= 0.219
  Angle     :  0.623  10.572  10954  Z= 0.317
  Chirality :  0.044   0.309   1209
  Planarity :  0.004   0.043   1352
  Dihedral  :  6.425 131.216   1159
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  1.81 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.32 %
    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: -1.53 (0.26), residues: 978
  helix: -1.21 (0.26), residues: 332
  sheet: -0.42 (0.37), residues: 187
  loop : -0.99 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 541 
 HIS   0.006   0.002   HIS L 100 
 PHE   0.023   0.002   PHE A 133 
 TYR   0.018   0.001   TYR H 120 
 ARG   0.017   0.001   ARG H  69 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 240
  time to evaluate  : 0.971 
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   80 GLU cc_start: 0.7472 (mp0) cc_final: 0.5945 (tt0)
REVERT: A   90 LEU cc_start: 0.9513 (tp) cc_final: 0.9259 (tp)
REVERT: A   98 ASP cc_start: 0.9563 (p0) cc_final: 0.9363 (p0)
REVERT: A  104 ARG cc_start: 0.8813 (tpt170) cc_final: 0.8287 (ttm-80)
REVERT: A  132 LEU cc_start: 0.9094 (tp) cc_final: 0.8888 (tp)
REVERT: A  133 PHE cc_start: 0.7869 (m-80) cc_final: 0.7558 (m-80)
REVERT: A  136 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: A  166 CYS cc_start: 0.8674 (t) cc_final: 0.8382 (p)
REVERT: A  168 ILE cc_start: 0.9471 (mm) cc_final: 0.9230 (mm)
REVERT: A  172 ILE cc_start: 0.9439 (mt) cc_final: 0.8875 (tt)
REVERT: A  185 TYR cc_start: 0.8362 (t80) cc_final: 0.8037 (t80)
REVERT: A  229 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8838 (tm-30)
REVERT: A  238 GLN cc_start: 0.8674 (mt0) cc_final: 0.8235 (mt0)
REVERT: A  260 MET cc_start: 0.5246 (ttt) cc_final: 0.5021 (ttt)
REVERT: A  306 TRP cc_start: 0.8492 (p90) cc_final: 0.8066 (p90)
REVERT: A  317 TRP cc_start: 0.7516 (p-90) cc_final: 0.7105 (m-10)
REVERT: A  343 VAL cc_start: 0.9281 (t) cc_final: 0.9068 (t)
REVERT: A  358 TYR cc_start: 0.7446 (t80) cc_final: 0.6925 (t80)
REVERT: A  407 PHE cc_start: 0.9348 (m-10) cc_final: 0.8798 (m-10)
REVERT: A  417 MET cc_start: 0.7664 (mmp) cc_final: 0.7327 (tpp)
REVERT: A  430 MET cc_start: 0.7949 (ttt) cc_final: 0.7207 (ttp)
REVERT: A  444 GLU cc_start: 0.8875 (pt0) cc_final: 0.8270 (pt0)
REVERT: A  473 CYS cc_start: 0.8061 (p) cc_final: 0.7848 (p)
REVERT: V   45 THR cc_start: 0.7467 (p) cc_final: 0.6670 (t)
REVERT: V   63 ILE cc_start: 0.8567 (mt) cc_final: 0.8107 (mt)
REVERT: V  158 LYS cc_start: 0.8259 (ptmm) cc_final: 0.7755 (tmtt)
REVERT: V  241 TYR cc_start: 0.8326 (t80) cc_final: 0.8033 (t80)
REVERT: H   38 ARG cc_start: 0.7673 (ttm170) cc_final: 0.7227 (ttt-90)
REVERT: H  100 MET cc_start: 0.5171 (tpp) cc_final: 0.4561 (tpp)
REVERT: H  117 ARG cc_start: 0.7740 (tmt170) cc_final: 0.7404 (tmt170)
REVERT: H  127 MET cc_start: 0.6005 (mpp) cc_final: 0.4619 (ptp)
REVERT: L   95 PHE cc_start: 0.6634 (m-10) cc_final: 0.6061 (m-80)
REVERT: L   97 LEU cc_start: 0.4920 (pt) cc_final: 0.4502 (pt)
REVERT: L  100 HIS cc_start: 0.5947 (OUTLIER) cc_final: 0.5544 (m90)
REVERT: L  113 GLN cc_start: 0.8087 (tt0) cc_final: 0.7284 (tm-30)
REVERT: L  127 LYS cc_start: 0.7502 (mttt) cc_final: 0.6792 (tttt)
  outliers start: 3
  outliers final: 0
  residues processed: 241
  average time/residue: 0.1948
  time to fit residues: 64.0219
Evaluate side-chains
  204 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 203
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 17 optimal weight:    8.9990
   chunk 44 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 46 optimal weight:    8.9990
   chunk 70 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 80 optimal weight:    0.5980
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
V  21 GLN
** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 239 GLN
L  78 GLN
** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 114 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.173047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.137303 restraints weight = 14892.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.143462 restraints weight = 9935.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.148334 restraints weight = 7154.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6275
moved from start:          0.6215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8053  Z= 0.252
  Angle     :  0.676  10.565  10954  Z= 0.348
  Chirality :  0.045   0.308   1209
  Planarity :  0.005   0.050   1352
  Dihedral  :  6.832 137.088   1159
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  1.44 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.32 %
    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: -1.50 (0.26), residues: 978
  helix: -1.18 (0.26), residues: 329
  sheet: -0.45 (0.37), residues: 186
  loop : -0.95 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.074   0.003   TRP A 541 
 HIS   0.007   0.002   HIS L 100 
 PHE   0.026   0.002   PHE A 170 
 TYR   0.029   0.002   TYR L 110 
 ARG   0.007   0.001   ARG A 241 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 240
  time to evaluate  : 0.994 
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: A   80 GLU cc_start: 0.7394 (mp0) cc_final: 0.5994 (tt0)
REVERT: A  104 ARG cc_start: 0.8702 (tpt170) cc_final: 0.8282 (ttm-80)
REVERT: A  132 LEU cc_start: 0.9200 (tp) cc_final: 0.8875 (tp)
REVERT: A  136 GLU cc_start: 0.8706 (tm-30) cc_final: 0.7952 (tt0)
REVERT: A  166 CYS cc_start: 0.8746 (t) cc_final: 0.8430 (p)
REVERT: A  229 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8731 (tm-30)
REVERT: A  238 GLN cc_start: 0.8804 (mt0) cc_final: 0.8359 (mt0)
REVERT: A  260 MET cc_start: 0.5393 (ttt) cc_final: 0.5177 (ttt)
REVERT: A  317 TRP cc_start: 0.7553 (p-90) cc_final: 0.7305 (m-10)
REVERT: A  326 TRP cc_start: 0.7006 (m100) cc_final: 0.6027 (m-10)
REVERT: A  343 VAL cc_start: 0.9253 (t) cc_final: 0.8922 (t)
REVERT: A  347 PHE cc_start: 0.8532 (m-80) cc_final: 0.8327 (m-80)
REVERT: A  407 PHE cc_start: 0.9406 (m-10) cc_final: 0.8819 (m-80)
REVERT: A  408 ILE cc_start: 0.9341 (mm) cc_final: 0.9050 (mm)
REVERT: A  430 MET cc_start: 0.8056 (ttt) cc_final: 0.7324 (ttp)
REVERT: A  444 GLU cc_start: 0.9098 (pt0) cc_final: 0.8711 (pt0)
REVERT: A  507 ILE cc_start: 0.8943 (tp) cc_final: 0.8734 (tp)
REVERT: A  595 TYR cc_start: 0.6835 (t80) cc_final: 0.6593 (t80)
REVERT: V   45 THR cc_start: 0.7384 (p) cc_final: 0.6503 (t)
REVERT: V   49 MET cc_start: 0.8930 (tpt) cc_final: 0.8534 (tpt)
REVERT: H   21 VAL cc_start: 0.7640 (t) cc_final: 0.6070 (t)
REVERT: H   38 ARG cc_start: 0.7980 (ttm170) cc_final: 0.7627 (ttt180)
REVERT: H   46 TYR cc_start: 0.8439 (p90) cc_final: 0.8199 (p90)
REVERT: H  100 MET cc_start: 0.5547 (tpp) cc_final: 0.4943 (tpp)
REVERT: H  117 ARG cc_start: 0.7834 (tmt170) cc_final: 0.7617 (tmt170)
REVERT: H  127 MET cc_start: 0.6222 (mpp) cc_final: 0.5479 (mpp)
REVERT: L   51 ASN cc_start: 0.7871 (t0) cc_final: 0.7554 (t0)
REVERT: L   85 ARG cc_start: 0.7947 (ptm160) cc_final: 0.6698 (mpt90)
REVERT: L   95 PHE cc_start: 0.6793 (m-10) cc_final: 0.6182 (m-80)
REVERT: L  100 HIS cc_start: 0.6584 (m90) cc_final: 0.6117 (m90)
REVERT: L  102 MET cc_start: 0.6324 (ptt) cc_final: 0.5794 (ptt)
REVERT: L  103 GLU cc_start: 0.7910 (mp0) cc_final: 0.7427 (mp0)
REVERT: L  113 GLN cc_start: 0.7691 (tt0) cc_final: 0.7369 (tm-30)
REVERT: L  127 LYS cc_start: 0.7610 (mttt) cc_final: 0.7246 (mtpt)
  outliers start: 2
  outliers final: 0
  residues processed: 241
  average time/residue: 0.1981
  time to fit residues: 65.0547
Evaluate side-chains
  205 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 90 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 85 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 155 GLN
** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 239 GLN
** L 114 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 = 0.4265 r_free = 0.4265 target = 0.168058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.132366 restraints weight = 15305.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.138560 restraints weight = 10147.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.143498 restraints weight = 7282.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6375
moved from start:          0.6746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8053  Z= 0.270
  Angle     :  0.704  10.322  10954  Z= 0.363
  Chirality :  0.046   0.368   1209
  Planarity :  0.004   0.044   1352
  Dihedral  :  7.189 140.297   1159
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 18.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.36 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.32 %
    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: -1.51 (0.26), residues: 978
  helix: -1.14 (0.26), residues: 327
  sheet: -0.60 (0.36), residues: 188
  loop : -0.94 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP H  52 
 HIS   0.006   0.002   HIS A 143 
 PHE   0.024   0.002   PHE A 170 
 TYR   0.023   0.002   TYR H 120 
 ARG   0.016   0.001   ARG H  69 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 234
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 ARG cc_start: 0.8766 (tpt170) cc_final: 0.8434 (ttm-80)
REVERT: A  105 PHE cc_start: 0.9110 (t80) cc_final: 0.8874 (t80)
REVERT: A  136 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8131 (tm-30)
REVERT: A  166 CYS cc_start: 0.8751 (t) cc_final: 0.8428 (p)
REVERT: A  182 TRP cc_start: 0.8961 (m-10) cc_final: 0.7820 (m-10)
REVERT: A  229 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8314 (tm-30)
REVERT: A  230 GLU cc_start: 0.8735 (mm-30) cc_final: 0.7972 (mm-30)
REVERT: A  237 LEU cc_start: 0.9296 (mm) cc_final: 0.8936 (mm)
REVERT: A  238 GLN cc_start: 0.8878 (mt0) cc_final: 0.8408 (mt0)
REVERT: A  260 MET cc_start: 0.5229 (ttt) cc_final: 0.5018 (ttt)
REVERT: A  326 TRP cc_start: 0.7079 (m100) cc_final: 0.6047 (m-10)
REVERT: A  343 VAL cc_start: 0.9238 (t) cc_final: 0.8867 (t)
REVERT: A  347 PHE cc_start: 0.8507 (m-80) cc_final: 0.8148 (m-80)
REVERT: A  358 TYR cc_start: 0.7640 (t80) cc_final: 0.6755 (t80)
REVERT: A  407 PHE cc_start: 0.9430 (m-10) cc_final: 0.8820 (m-80)
REVERT: A  430 MET cc_start: 0.8413 (ttp) cc_final: 0.7699 (ttp)
REVERT: A  444 GLU cc_start: 0.9106 (pt0) cc_final: 0.8418 (pt0)
REVERT: A  507 ILE cc_start: 0.8981 (tp) cc_final: 0.8759 (tp)
REVERT: V   49 MET cc_start: 0.9029 (tpt) cc_final: 0.8721 (tpt)
REVERT: V  151 ILE cc_start: 0.7658 (mt) cc_final: 0.7324 (tt)
REVERT: V  158 LYS cc_start: 0.8039 (ptmm) cc_final: 0.7516 (tmtt)
REVERT: H   21 VAL cc_start: 0.7143 (t) cc_final: 0.6635 (t)
REVERT: H   38 ARG cc_start: 0.8274 (ttm170) cc_final: 0.7716 (ttt-90)
REVERT: H  100 MET cc_start: 0.5590 (tpp) cc_final: 0.4886 (tpp)
REVERT: H  127 MET cc_start: 0.6243 (mpp) cc_final: 0.5981 (ptp)
REVERT: L   85 ARG cc_start: 0.8118 (ptm160) cc_final: 0.6906 (ptp-170)
REVERT: L  100 HIS cc_start: 0.7040 (m90) cc_final: 0.6100 (m90)
REVERT: L  103 GLU cc_start: 0.7993 (mp0) cc_final: 0.7596 (mp0)
REVERT: L  127 LYS cc_start: 0.7706 (mttt) cc_final: 0.7250 (mtpt)
  outliers start: 1
  outliers final: 0
  residues processed: 234
  average time/residue: 0.1959
  time to fit residues: 63.2490
Evaluate side-chains
  190 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 89 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 59 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   chunk 22 optimal weight:    0.0980
   chunk 64 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9980
   chunk 32 optimal weight:    0.4980
   chunk 43 optimal weight:    0.0670
   overall best weight:    1.1320

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

Flipped N/Q/H residues before XYZ refinement:
A 211 ASN
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 155 GLN
V 176 GLN
** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 239 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.173592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.137493 restraints weight = 14473.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.143870 restraints weight = 9673.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.148865 restraints weight = 6958.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6187
moved from start:          0.6808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8053  Z= 0.174
  Angle     :  0.639  10.204  10954  Z= 0.315
  Chirality :  0.044   0.304   1209
  Planarity :  0.004   0.040   1352
  Dihedral  :  6.916 137.467   1159
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.24 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.32 %
    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: -1.38 (0.26), residues: 978
  helix: -1.20 (0.26), residues: 334
  sheet: -0.43 (0.37), residues: 187
  loop : -0.73 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP A 541 
 HIS   0.007   0.002   HIS A 235 
 PHE   0.024   0.001   PHE A 133 
 TYR   0.020   0.001   TYR A  95 
 ARG   0.005   0.001   ARG H  69 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 227
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 ARG cc_start: 0.8766 (tpt170) cc_final: 0.8406 (ttm-80)
REVERT: A  132 LEU cc_start: 0.9231 (tp) cc_final: 0.8883 (tp)
REVERT: A  136 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8057 (tm-30)
REVERT: A  182 TRP cc_start: 0.8851 (m-10) cc_final: 0.7857 (m-10)
REVERT: A  229 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8337 (tm-30)
REVERT: A  230 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8016 (mm-30)
REVERT: A  237 LEU cc_start: 0.9189 (mm) cc_final: 0.8848 (mm)
REVERT: A  238 GLN cc_start: 0.8746 (mt0) cc_final: 0.8296 (mt0)
REVERT: A  302 LEU cc_start: 0.7964 (tp) cc_final: 0.7080 (mt)
REVERT: A  343 VAL cc_start: 0.9280 (t) cc_final: 0.8899 (t)
REVERT: A  347 PHE cc_start: 0.8465 (m-80) cc_final: 0.8163 (m-80)
REVERT: A  358 TYR cc_start: 0.7519 (t80) cc_final: 0.6686 (t80)
REVERT: A  407 PHE cc_start: 0.9397 (m-10) cc_final: 0.8865 (m-80)
REVERT: A  408 ILE cc_start: 0.9278 (mm) cc_final: 0.8992 (mm)
REVERT: A  430 MET cc_start: 0.8347 (ttp) cc_final: 0.7609 (ttp)
REVERT: A  444 GLU cc_start: 0.9085 (pt0) cc_final: 0.8353 (pt0)
REVERT: A  507 ILE cc_start: 0.8882 (tp) cc_final: 0.8668 (tp)
REVERT: A  563 LEU cc_start: 0.8199 (mt) cc_final: 0.7997 (mt)
REVERT: V  158 LYS cc_start: 0.8042 (ptmm) cc_final: 0.7504 (tmtt)
REVERT: H   38 ARG cc_start: 0.8240 (ttm170) cc_final: 0.7682 (ttt180)
REVERT: H  100 MET cc_start: 0.5223 (tpp) cc_final: 0.4390 (tpp)
REVERT: H  127 MET cc_start: 0.5905 (mpp) cc_final: 0.4715 (ptp)
REVERT: L   85 ARG cc_start: 0.7927 (ptm160) cc_final: 0.7012 (ptp-170)
REVERT: L  100 HIS cc_start: 0.6988 (m90) cc_final: 0.6089 (m90)
REVERT: L  103 GLU cc_start: 0.7846 (mp0) cc_final: 0.7504 (mp0)
REVERT: L  113 GLN cc_start: 0.8012 (tt0) cc_final: 0.7375 (tm-30)
REVERT: L  127 LYS cc_start: 0.7538 (mttt) cc_final: 0.7088 (mtpt)
  outliers start: 2
  outliers final: 0
  residues processed: 228
  average time/residue: 0.1886
  time to fit residues: 58.8995
Evaluate side-chains
  194 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 32 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0070
   chunk 40 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 95 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.0002

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 155 GLN
V 176 GLN
** V 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 239 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.179232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.143769 restraints weight = 14337.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.150424 restraints weight = 9367.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.155434 restraints weight = 6590.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6214
moved from start:          0.6876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8053  Z= 0.173
  Angle     :  0.637  10.220  10954  Z= 0.316
  Chirality :  0.044   0.290   1209
  Planarity :  0.004   0.046   1352
  Dihedral  :  6.752 133.911   1159
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.24 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.32 %
    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: -1.22 (0.27), residues: 978
  helix: -1.17 (0.26), residues: 331
  sheet: -0.20 (0.36), residues: 197
  loop : -0.64 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 204 
 HIS   0.005   0.001   HIS V 240 
 PHE   0.024   0.001   PHE A 133 
 TYR   0.015   0.001   TYR H 120 
 ARG   0.005   0.001   ARG A 241 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2796.28 seconds
wall clock time: 51 minutes 9.62 seconds (3069.62 seconds total)