Starting phenix.real_space_refine
on Wed Mar 12 08:55:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5u1d_8482/03_2025/5u1d_8482.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5u1d_8482/03_2025/5u1d_8482.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5u1d_8482/03_2025/5u1d_8482.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5u1d_8482/03_2025/5u1d_8482.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5u1d_8482/03_2025/5u1d_8482.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5u1d_8482/03_2025/5u1d_8482.cif"
  }
  resolution = 3.97
  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=   0.036 sd=   0.252
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: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    4900      2.51       5
     N    1426      2.21       5
     O    1458      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7815
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 561, 3635
          Classifications: {'peptide': 561}
          Incomplete info: {'truncation_to_alanine': 214}
          Link IDs: {'PTRANS': 18, 'TRANS': 542}
          Chain breaks: 2
          Unresolved chain link angles: 13
          Unresolved non-hydrogen bonds: 744
          Unresolved non-hydrogen angles: 962
          Unresolved non-hydrogen dihedrals: 594
          Unresolved non-hydrogen chiralities: 81
          Planarities with less than four sites: {'GLN:plan1': 26, 'ASP:plan': 9, 'TYR:plan': 8, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 19, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 411
    Chain: "B"
      Number of atoms: 3732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 552, 3732
          Classifications: {'peptide': 552}
          Incomplete info: {'truncation_to_alanine': 186}
          Link IDs: {'PTRANS': 20, 'TRANS': 531}
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 612
          Unresolved non-hydrogen angles: 790
          Unresolved non-hydrogen dihedrals: 478
          Unresolved non-hydrogen chiralities: 71
          Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 327
    Chain: "X"
      Number of atoms: 448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 448
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   ARG A 529 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  ARG A 529 " occ=0.50
    residue:
      pdb=" N   ARG B 494 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  ARG B 494 " occ=0.50
  Time building chain proxies: 5.16, per 1000 atoms: 0.66
  Number of scatterers: 7815
  At special positions: 0
  Unit cell: (92.8618, 120.53, 116.905, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1458      8.00
     N    1426      7.00
     C    4900      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.00
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2158

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 5 sheets defined
      73.8% alpha, 4.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 173 through 181
    Processing helix  chain 'A' and resid 185 through 202
      removed outlier: 4.083A  pdb=" N   GLY A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 217
      removed outlier: 3.637A  pdb=" N   PHE A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 271
      removed outlier: 3.871A  pdb=" N   PHE A 224 " --> pdb=" O   SER A 220 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL A 268 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU A 269 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLN A 271 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 279
      removed outlier: 4.230A  pdb=" N   PHE A 276 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 287
      removed outlier: 4.009A  pdb=" N   ILE A 284 " --> pdb=" O   GLN A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 320
      removed outlier: 3.564A  pdb=" N   LEU A 305 " --> pdb=" O   GLU A 301 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 373
      removed outlier: 3.648A  pdb=" N   ILE A 333 " --> pdb=" O   MET A 329 " (cutoff:3.500A)
      Proline residue:  A 336  - end of helix
      removed outlier: 4.223A  pdb=" N   LEU A 341 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      Proline residue:  A 342  - end of helix
      removed outlier: 4.023A  pdb=" N   TRP A 348 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   LEU A 352 " --> pdb=" O   TRP A 348 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLU A 353 " --> pdb=" O   TYR A 349 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLN A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ALA A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 380
      removed outlier: 3.659A  pdb=" N   VAL A 377 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   PHE A 380 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 437
      removed outlier: 3.640A  pdb=" N   ALA A 387 " --> pdb=" O   GLU A 383 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLN A 388 " --> pdb=" O   GLU A 384 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLN A 402 " --> pdb=" O   LYS A 398 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   LYS A 403 " --> pdb=" O   THR A 399 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA A 409 " --> pdb=" O   ALA A 405 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   GLY A 419 " --> pdb=" O   THR A 415 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   MET A 420 " --> pdb=" O   SER A 416 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU A 433 " --> pdb=" O   ILE A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 462
      removed outlier: 3.809A  pdb=" N   VAL A 460 " --> pdb=" O   GLN A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 483
      removed outlier: 4.162A  pdb=" N   ARG A 467 " --> pdb=" O   SER A 463 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLY A 473 " --> pdb=" O   GLN A 469 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   SER A 474 " --> pdb=" O   LYS A 470 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LYS A 477 " --> pdb=" O   GLY A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 553
      removed outlier: 3.505A  pdb=" N   ALA A 548 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 572
    Processing helix  chain 'A' and resid 573 through 580
    Processing helix  chain 'A' and resid 594 through 600
    Processing helix  chain 'A' and resid 608 through 619
    Processing helix  chain 'A' and resid 621 through 628
    Processing helix  chain 'A' and resid 630 through 634
      removed outlier: 3.751A  pdb=" N   THR A 634 " --> pdb=" O   GLY A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 660
      removed outlier: 4.055A  pdb=" N   ARG A 659 " --> pdb=" O   ARG A 655 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LYS A 660 " --> pdb=" O   ALA A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 686
    Processing helix  chain 'A' and resid 688 through 694
    Processing helix  chain 'A' and resid 702 through 708
      removed outlier: 3.662A  pdb=" N   VAL A 706 " --> pdb=" O   HIS A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 733
    Processing helix  chain 'A' and resid 734 through 742
    Processing helix  chain 'B' and resid 131 through 145
      removed outlier: 3.648A  pdb=" N   LYS B 143 " --> pdb=" O   TRP B 139 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU B 144 " --> pdb=" O   ARG B 140 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   SER B 145 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 167
      removed outlier: 4.073A  pdb=" N   LEU B 152 " --> pdb=" O   ASP B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 183
      removed outlier: 4.414A  pdb=" N   HIS B 171 " --> pdb=" O   THR B 167 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR B 172 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   GLY B 182 " --> pdb=" O   ASP B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 236
      removed outlier: 3.678A  pdb=" N   GLY B 211 " --> pdb=" O   ALA B 207 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER B 219 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLU B 227 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ARG B 235 " --> pdb=" O   SER B 231 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLN B 236 " --> pdb=" O   SER B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 244
      removed outlier: 4.134A  pdb=" N   PHE B 241 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLN B 242 " --> pdb=" O   LEU B 238 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   GLU B 243 " --> pdb=" O   GLY B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 289
      removed outlier: 4.797A  pdb=" N   THR B 257 " --> pdb=" O   LEU B 253 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   THR B 258 " --> pdb=" O   SER B 254 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LEU B 264 " --> pdb=" O   MET B 260 " (cutoff:3.500A)
      Proline residue:  B 265  - end of helix
      removed outlier: 3.549A  pdb=" N   ILE B 288 " --> pdb=" O   PHE B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 299
      removed outlier: 3.791A  pdb=" N   SER B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 338
      removed outlier: 3.685A  pdb=" N   ALA B 306 " --> pdb=" O   PHE B 302 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   VAL B 309 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU B 316 " --> pdb=" O   THR B 312 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   VAL B 332 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 346
    Processing helix  chain 'B' and resid 347 through 401
      removed outlier: 3.538A  pdb=" N   GLN B 361 " --> pdb=" O   GLU B 357 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LEU B 365 " --> pdb=" O   GLN B 361 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   TYR B 366 " --> pdb=" O   CYS B 362 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU B 385 " --> pdb=" O   ARG B 381 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   CYS B 394 " --> pdb=" O   LEU B 390 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   MET B 399 " --> pdb=" O   GLY B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 433
      removed outlier: 3.790A  pdb=" N   LEU B 409 " --> pdb=" O   THR B 405 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   LEU B 410 " --> pdb=" O   GLN B 406 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   SER B 418 " --> pdb=" O   ILE B 414 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLY B 420 " --> pdb=" O   GLN B 416 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   SER B 421 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   THR B 425 " --> pdb=" O   SER B 421 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   TYR B 430 " --> pdb=" O   LEU B 426 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   GLY B 431 " --> pdb=" O   VAL B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 449
      removed outlier: 3.896A  pdb=" N   ALA B 440 " --> pdb=" O   ASN B 436 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   LYS B 442 " --> pdb=" O   GLY B 438 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL B 443 " --> pdb=" O   ALA B 439 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   TYR B 446 " --> pdb=" O   LYS B 442 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   MET B 447 " --> pdb=" O   VAL B 443 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ARG B 449 " --> pdb=" O   SER B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 518
    Processing helix  chain 'B' and resid 538 through 546
    Processing helix  chain 'B' and resid 559 through 565
    Processing helix  chain 'B' and resid 572 through 584
    Processing helix  chain 'B' and resid 585 through 592
    Processing helix  chain 'B' and resid 594 through 598
    Processing helix  chain 'B' and resid 608 through 624
      removed outlier: 3.529A  pdb=" N   ALA B 616 " --> pdb=" O   LYS B 612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 638 through 646
      removed outlier: 4.359A  pdb=" N   GLU B 642 " --> pdb=" O   ASP B 638 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   GLN B 643 " --> pdb=" O   VAL B 639 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ALA B 644 " --> pdb=" O   GLN B 640 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU B 645 " --> pdb=" O   CYS B 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 647 through 654
      removed outlier: 3.760A  pdb=" N   SER B 650 " --> pdb=" O   ASP B 647 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ARG B 654 " --> pdb=" O   ARG B 651 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 669
    Processing helix  chain 'X' and resid 2 through 14
      removed outlier: 3.883A  pdb=" N   GLU X   6 " --> pdb=" O   SER X   2 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 20 through 44
      removed outlier: 3.845A  pdb=" N   ASP X  24 " --> pdb=" O   ARG X  20 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   VAL X  25 " --> pdb=" O   THR X  21 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ASP X  27 " --> pdb=" O   ALA X  23 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ARG X  41 " --> pdb=" O   ARG X  37 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   VAL X  44 " --> pdb=" O   ALA X  40 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 521 through 527
      removed outlier: 5.019A  pdb=" N   GLN A 522 " --> pdb=" O   PHE A 510 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   PHE A 510 " --> pdb=" O   GLN A 522 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   PHE A 526 " --> pdb=" O   GLN A 506 " (cutoff:3.500A)
      removed outlier: 4.972A  pdb=" N   GLN A 506 " --> pdb=" O   PHE A 526 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 533 through 535
      removed outlier: 6.903A  pdb=" N   THR A 534 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   LEU A 664 " --> pdb=" O   LEU A 697 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 714 through 716
      removed outlier: 3.727A  pdb=" N   GLU A 722 " --> pdb=" O   PHE A 714 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   GLU A 716 " --> pdb=" O   ILE A 720 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   ILE A 720 " --> pdb=" O   GLU A 716 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 486 through 489
      removed outlier: 5.093A  pdb=" N   LYS B 487 " --> pdb=" O   PHE B 475 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   PHE B 475 " --> pdb=" O   LYS B 487 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   VAL B 473 " --> pdb=" O   GLY B 524 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   GLY B 524 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 548 through 549
      removed outlier: 6.559A  pdb=" N   ALA B 500 " --> pdb=" O   LEU B 673 " (cutoff:3.500A)

    584 hydrogen bonds defined for protein.
    1707 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: 2.32

  Time building geometry restraints manager: 2.21 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: 2692
        1.34 -     1.46: 649
        1.46 -     1.58: 4523
        1.58 -     1.69: 0
        1.69 -     1.81: 55
  Bond restraints: 7919
  Sorted by residual:
  bond pdb=" CA  ILE A 204 "
       pdb=" CB  ILE A 204 "
    ideal  model  delta    sigma   weight residual
    1.534  1.565 -0.031 6.80e-03 2.16e+04 2.05e+01
  bond pdb=" CA  ILE A 204 "
       pdb=" C   ILE A 204 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 8.80e-03 1.29e+04 8.27e+00
  bond pdb=" N   LEU A 335 "
       pdb=" CA  LEU A 335 "
    ideal  model  delta    sigma   weight residual
    1.462  1.484 -0.023 9.50e-03 1.11e+04 5.67e+00
  bond pdb=" N   GLY B 524 "
       pdb=" CA  GLY B 524 "
    ideal  model  delta    sigma   weight residual
    1.446  1.469 -0.023 9.50e-03 1.11e+04 5.62e+00
  bond pdb=" N   ASP B 130 "
       pdb=" CA  ASP B 130 "
    ideal  model  delta    sigma   weight residual
    1.458  1.500 -0.042 1.90e-02 2.77e+03 4.87e+00
  ... (remaining 7914 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 9939
        2.08 -     4.16: 812
        4.16 -     6.23: 37
        6.23 -     8.31: 3
        8.31 -    10.39: 3
  Bond angle restraints: 10794
  Sorted by residual:
  angle pdb=" C   ASP B 624 "
        pdb=" N   PRO B 625 "
        pdb=" CA  PRO B 625 "
      ideal   model   delta    sigma   weight residual
     120.11  130.50  -10.39 1.12e+00 7.97e-01 8.61e+01
  angle pdb=" C   SER A 688 "
        pdb=" N   PRO A 689 "
        pdb=" CA  PRO A 689 "
      ideal   model   delta    sigma   weight residual
     119.05  129.31  -10.26 1.11e+00 8.12e-01 8.54e+01
  angle pdb=" C   LYS A 660 "
        pdb=" N   PRO A 661 "
        pdb=" CA  PRO A 661 "
      ideal   model   delta    sigma   weight residual
     120.31  128.17   -7.86 9.80e-01 1.04e+00 6.44e+01
  angle pdb=" C   LEU A 569 "
        pdb=" N   PRO A 570 "
        pdb=" CA  PRO A 570 "
      ideal   model   delta    sigma   weight residual
     119.28  127.08   -7.80 1.10e+00 8.26e-01 5.03e+01
  angle pdb=" C   THR A 495 "
        pdb=" N   PRO A 496 "
        pdb=" CA  PRO A 496 "
      ideal   model   delta    sigma   weight residual
     119.84  128.32   -8.48 1.25e+00 6.40e-01 4.60e+01
  ... (remaining 10789 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.80: 4369
       15.80 -    31.60: 210
       31.60 -    47.40: 79
       47.40 -    63.20: 20
       63.20 -    79.00: 1
  Dihedral angle restraints: 4679
    sinusoidal: 1333
      harmonic: 3346
  Sorted by residual:
  dihedral pdb=" CA  SER A 182 "
           pdb=" C   SER A 182 "
           pdb=" N   GLU A 183 "
           pdb=" CA  GLU A 183 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.36  -19.64     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  GLU A 183 "
           pdb=" C   GLU A 183 "
           pdb=" N   THR A 184 "
           pdb=" CA  THR A 184 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.78  -19.22     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  THR A 184 "
           pdb=" C   THR A 184 "
           pdb=" N   ARG A 185 "
           pdb=" CA  ARG A 185 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.84  -19.16     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 4676 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 837
       0.038 -    0.076: 297
       0.076 -    0.114: 117
       0.114 -    0.152: 36
       0.152 -    0.190: 14
  Chirality restraints: 1301
  Sorted by residual:
  chirality pdb=" CA  HIS X  45 "
            pdb=" N   HIS X  45 "
            pdb=" C   HIS X  45 "
            pdb=" CB  HIS X  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.01e-01
  chirality pdb=" CA  ASP A 483 "
            pdb=" N   ASP A 483 "
            pdb=" C   ASP A 483 "
            pdb=" CB  ASP A 483 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.39e-01
  chirality pdb=" CA  ILE A 204 "
            pdb=" N   ILE A 204 "
            pdb=" C   ILE A 204 "
            pdb=" CB  ILE A 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.26    0.17 2.00e-01 2.50e+01 7.45e-01
  ... (remaining 1298 not shown)

  Planarity restraints: 1427
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 300 "   -0.030 5.00e-02 4.00e+02   4.59e-02 3.38e+00
        pdb=" N   PRO B 301 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 301 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 301 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 146 "   -0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO B 147 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 147 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 147 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 465 "   -0.023 5.00e-02 4.00e+02   3.43e-02 1.88e+00
        pdb=" N   PRO A 466 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 466 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 466 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1424 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 3099
        2.94 -     3.43: 8317
        3.43 -     3.92: 12011
        3.92 -     4.41: 12091
        4.41 -     4.90: 21589
  Nonbonded interactions: 57107
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 183 "
            pdb=" OG1 THR A 184 "
     model   vdw
     2.452 3.040
  nonbonded pdb=" O   MET B 218 "
            pdb=" OG  SER B 261 "
     model   vdw
     2.513 3.040
  nonbonded pdb=" O   ARG X  20 "
            pdb=" OG1 THR X  21 "
     model   vdw
     2.563 3.040
  nonbonded pdb=" O   SER B 255 "
            pdb=" OG1 THR B 258 "
     model   vdw
     2.571 3.040
  nonbonded pdb=" O   LEU A 360 "
            pdb=" OG  SER A 363 "
     model   vdw
     2.582 3.040
  ... (remaining 57102 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.860
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.450
  Find NCS groups from input model:        0.120
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5049
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      :  0.007   0.042   7919  Z= 0.493
  Angle     :  1.173  10.391  10794  Z= 0.861
  Chirality :  0.050   0.190   1301
  Planarity :  0.003   0.046   1427
  Dihedral  : 12.049  78.999   2521
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 0.07
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.70 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  1.69 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.21), residues: 1158
  helix: -0.58 (0.15), residues: 765
  sheet: -4.63 (0.65), residues: 37
  loop : -2.79 (0.29), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 214 
 HIS   0.002   0.001   HIS B 539 
 PHE   0.013   0.001   PHE B 240 
 TYR   0.014   0.001   TYR B 446 
 ARG   0.005   0.001   ARG B 483 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 363
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.7526 (t60) cc_final: 0.7319 (t60)
REVERT: A  304 SER cc_start: 0.8176 (t) cc_final: 0.7835 (p)
REVERT: A  317 LEU cc_start: 0.8945 (mt) cc_final: 0.8468 (mt)
REVERT: A  351 LEU cc_start: 0.8574 (tt) cc_final: 0.8295 (pp)
REVERT: A  374 MET cc_start: 0.6740 (tpt) cc_final: 0.5995 (tpt)
REVERT: A  383 GLU cc_start: 0.7744 (pt0) cc_final: 0.7504 (pt0)
REVERT: A  392 GLU cc_start: 0.7150 (tt0) cc_final: 0.6871 (mm-30)
REVERT: A  417 ILE cc_start: 0.7832 (mm) cc_final: 0.7611 (mm)
REVERT: A  439 VAL cc_start: 0.6634 (t) cc_final: 0.6243 (m)
REVERT: A  443 ASN cc_start: 0.9299 (m-40) cc_final: 0.9075 (t0)
REVERT: A  452 MET cc_start: 0.7528 (ttt) cc_final: 0.7199 (tpp)
REVERT: A  655 ARG cc_start: 0.7559 (ttp-170) cc_final: 0.6995 (ptm160)
REVERT: A  660 LYS cc_start: 0.7518 (mttt) cc_final: 0.7258 (mmtm)
REVERT: A  702 HIS cc_start: 0.7329 (m-70) cc_final: 0.6930 (m-70)
REVERT: B  218 MET cc_start: 0.7298 (ttm) cc_final: 0.7032 (mtt)
REVERT: B  243 GLU cc_start: 0.8711 (tp30) cc_final: 0.8492 (tt0)
REVERT: B  248 GLU cc_start: 0.7216 (tp30) cc_final: 0.6960 (tp30)
REVERT: B  267 ASN cc_start: 0.6832 (m-40) cc_final: 0.6604 (m-40)
REVERT: B  292 LEU cc_start: 0.8587 (mt) cc_final: 0.8273 (mt)
REVERT: B  316 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7032 (tp30)
REVERT: B  345 PHE cc_start: 0.7333 (m-80) cc_final: 0.6845 (m-80)
REVERT: B  360 GLU cc_start: 0.7579 (tt0) cc_final: 0.7370 (tm-30)
REVERT: B  372 GLU cc_start: 0.6172 (tp30) cc_final: 0.5885 (tp30)
REVERT: B  389 MET cc_start: 0.9184 (mmt) cc_final: 0.8666 (tmm)
REVERT: B  416 GLN cc_start: 0.7558 (tp40) cc_final: 0.7284 (tp40)
REVERT: B  428 TYR cc_start: 0.7588 (t80) cc_final: 0.7366 (t80)
REVERT: B  430 TYR cc_start: 0.7824 (t80) cc_final: 0.7617 (t80)
REVERT: B  446 TYR cc_start: 0.6981 (m-80) cc_final: 0.6772 (m-10)
REVERT: B  452 ASN cc_start: 0.3719 (m-40) cc_final: 0.3458 (m-40)
REVERT: X    1 MET cc_start: 0.4101 (ttm) cc_final: 0.3416 (ttt)
REVERT: X    3 TRP cc_start: 0.6559 (t60) cc_final: 0.5842 (t60)
REVERT: X    5 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6242 (tt)
REVERT: X   46 ASP cc_start: 0.6712 (p0) cc_final: 0.6489 (p0)
  outliers start: 5
  outliers final: 2
  residues processed: 366
  average time/residue: 0.2149
  time to fit residues: 102.1778
Evaluate side-chains
  279 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 276
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  449 ARG
Chi-restraints excluded: chain B residue  450 GLN
Chi-restraints excluded: chain X residue    5 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 87 optimal weight:    5.9990
   chunk 48 optimal weight:   40.0000
   chunk 30 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 46 optimal weight:   20.0000
   chunk 90 optimal weight:   20.0000
   chunk 35 optimal weight:    0.6980
   chunk 55 optimal weight:   40.0000
   chunk 67 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   overall best weight:    4.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 227 ASN
A 251 ASN
A 257 HIS
A 382 ASN
A 701 GLN
B 171 HIS
B 539 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.160533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.139763 restraints weight = 19557.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.142825 restraints weight = 12900.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.145066 restraints weight = 9442.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3867
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3867 r_free = 0.3867    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3860 r_free = 0.3860    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3860
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7919  Z= 0.226
  Angle     :  0.582  10.623  10794  Z= 0.310
  Chirality :  0.039   0.192   1301
  Planarity :  0.004   0.051   1427
  Dihedral  :  4.358  47.533   1248
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.20 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 15.88 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.24), residues: 1158
  helix:  1.62 (0.17), residues: 789
  sheet: -4.00 (0.98), residues: 25
  loop : -2.28 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 413 
 HIS   0.005   0.001   HIS B 299 
 PHE   0.018   0.002   PHE B 240 
 TYR   0.021   0.002   TYR X  22 
 ARG   0.007   0.001   ARG A 186 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 292
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.9073 (t60) cc_final: 0.8526 (t60)
REVERT: A  223 THR cc_start: 0.7829 (p) cc_final: 0.7613 (t)
REVERT: A  224 PHE cc_start: 0.8013 (t80) cc_final: 0.7587 (t80)
REVERT: A  227 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8368 (t0)
REVERT: A  285 MET cc_start: 0.7752 (tpp) cc_final: 0.7507 (tpp)
REVERT: A  392 GLU cc_start: 0.8085 (tt0) cc_final: 0.7484 (mt-10)
REVERT: A  417 ILE cc_start: 0.9146 (mm) cc_final: 0.8875 (mm)
REVERT: A  420 MET cc_start: 0.8854 (mpp) cc_final: 0.8654 (mpp)
REVERT: A  439 VAL cc_start: 0.6854 (t) cc_final: 0.6304 (t)
REVERT: A  443 ASN cc_start: 0.9024 (m-40) cc_final: 0.8801 (t0)
REVERT: A  466 PRO cc_start: 0.9245 (Cg_exo) cc_final: 0.9041 (Cg_endo)
REVERT: A  660 LYS cc_start: 0.8335 (mttt) cc_final: 0.8130 (mmtm)
REVERT: B  131 GLN cc_start: 0.6675 (pm20) cc_final: 0.6437 (pm20)
REVERT: B  243 GLU cc_start: 0.8993 (tp30) cc_final: 0.8745 (tt0)
REVERT: B  248 GLU cc_start: 0.8750 (tp30) cc_final: 0.8422 (tp30)
REVERT: B  300 MET cc_start: 0.9011 (mmt) cc_final: 0.8570 (mmp)
REVERT: B  316 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6589 (tp30)
REVERT: B  320 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8572 (mm-30)
REVERT: B  351 GLU cc_start: 0.8755 (tp30) cc_final: 0.8420 (tp30)
REVERT: B  360 GLU cc_start: 0.8556 (tt0) cc_final: 0.8263 (tm-30)
REVERT: B  370 ASP cc_start: 0.8877 (m-30) cc_final: 0.8602 (m-30)
REVERT: B  372 GLU cc_start: 0.6921 (tp30) cc_final: 0.6576 (tp30)
REVERT: B  373 ARG cc_start: 0.9179 (tmm-80) cc_final: 0.8832 (ttm170)
REVERT: B  391 MET cc_start: 0.9056 (ttm) cc_final: 0.8150 (ttt)
REVERT: B  416 GLN cc_start: 0.8772 (tp40) cc_final: 0.8486 (tp40)
REVERT: B  428 TYR cc_start: 0.9437 (t80) cc_final: 0.9166 (t80)
REVERT: B  430 TYR cc_start: 0.8576 (t80) cc_final: 0.8192 (t80)
REVERT: X   46 ASP cc_start: 0.8277 (p0) cc_final: 0.7950 (p0)
REVERT: X   53 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7372 (mtt180)
  outliers start: 35
  outliers final: 20
  residues processed: 305
  average time/residue: 0.1941
  time to fit residues: 80.7953
Evaluate side-chains
  263 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 242
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 ASN
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain B residue  139 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  244 THR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  344 SER
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  411 SER
Chi-restraints excluded: chain B residue  449 ARG
Chi-restraints excluded: chain B residue  450 GLN
Chi-restraints excluded: chain X residue   25 VAL
Chi-restraints excluded: chain X residue   45 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 50 optimal weight:   30.0000
   chunk 66 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 90 optimal weight:   30.0000
   chunk 93 optimal weight:   20.0000
   chunk 63 optimal weight:    8.9990
   chunk 68 optimal weight:    6.9990
   chunk 96 optimal weight:   30.0000
   chunk 6 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 365 GLN
B 171 HIS
B 452 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.155312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.134570 restraints weight = 19710.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.137669 restraints weight = 12836.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.139888 restraints weight = 9296.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.4508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7919  Z= 0.260
  Angle     :  0.605  10.008  10794  Z= 0.317
  Chirality :  0.040   0.250   1301
  Planarity :  0.004   0.035   1427
  Dihedral  :  4.235  34.546   1246
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.66 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  7.60 %
    Allowed  : 19.09 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.25), residues: 1158
  helix:  1.91 (0.18), residues: 806
  sheet: -3.80 (0.81), residues: 34
  loop : -2.09 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 348 
 HIS   0.003   0.001   HIS B 171 
 PHE   0.028   0.002   PHE A 190 
 TYR   0.017   0.002   TYR A 349 
 ARG   0.005   0.001   ARG A 659 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 270
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.9133 (t60) cc_final: 0.8867 (t60)
REVERT: A  224 PHE cc_start: 0.8114 (t80) cc_final: 0.7762 (t80)
REVERT: A  250 ASN cc_start: 0.9219 (m110) cc_final: 0.8998 (m-40)
REVERT: A  344 LYS cc_start: 0.8047 (tttt) cc_final: 0.7274 (ttpt)
REVERT: A  382 ASN cc_start: 0.8953 (t0) cc_final: 0.8673 (t0)
REVERT: A  392 GLU cc_start: 0.8255 (tt0) cc_final: 0.7643 (mm-30)
REVERT: A  417 ILE cc_start: 0.9171 (mm) cc_final: 0.8896 (mm)
REVERT: A  420 MET cc_start: 0.8792 (mpp) cc_final: 0.8543 (mpp)
REVERT: A  443 ASN cc_start: 0.9017 (m-40) cc_final: 0.8745 (t0)
REVERT: A  601 TYR cc_start: 0.8785 (t80) cc_final: 0.8321 (t80)
REVERT: B  131 GLN cc_start: 0.6676 (pm20) cc_final: 0.6431 (pm20)
REVERT: B  151 LEU cc_start: 0.8527 (mt) cc_final: 0.8229 (mt)
REVERT: B  172 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.7563 (m-10)
REVERT: B  248 GLU cc_start: 0.8837 (tp30) cc_final: 0.8627 (tp30)
REVERT: B  254 SER cc_start: 0.7463 (t) cc_final: 0.7058 (m)
REVERT: B  285 MET cc_start: 0.8302 (mtm) cc_final: 0.7764 (mtm)
REVERT: B  316 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6551 (tp30)
REVERT: B  320 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8419 (mm-30)
REVERT: B  351 GLU cc_start: 0.8765 (tp30) cc_final: 0.8448 (tp30)
REVERT: B  360 GLU cc_start: 0.8614 (tt0) cc_final: 0.8234 (tm-30)
REVERT: B  372 GLU cc_start: 0.7258 (tp30) cc_final: 0.6902 (tp30)
REVERT: B  373 ARG cc_start: 0.9142 (tmm-80) cc_final: 0.8787 (ttm170)
REVERT: B  391 MET cc_start: 0.9039 (ttm) cc_final: 0.8627 (ttt)
REVERT: B  416 GLN cc_start: 0.8938 (tp40) cc_final: 0.8435 (tp40)
REVERT: B  430 TYR cc_start: 0.8668 (t80) cc_final: 0.8338 (t80)
REVERT: B  477 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.6451 (m-10)
REVERT: X   41 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8442 (ttp80)
REVERT: X   46 ASP cc_start: 0.8328 (p0) cc_final: 0.7994 (p0)
REVERT: X   53 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7405 (mtt180)
  outliers start: 45
  outliers final: 34
  residues processed: 288
  average time/residue: 0.1769
  time to fit residues: 69.9594
Evaluate side-chains
  265 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 229
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  331 THR
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  374 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain B residue  139 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  172 TYR
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  244 THR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  344 SER
Chi-restraints excluded: chain B residue  425 THR
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain B residue  449 ARG
Chi-restraints excluded: chain B residue  450 GLN
Chi-restraints excluded: chain B residue  477 TYR
Chi-restraints excluded: chain X residue    5 LEU
Chi-restraints excluded: chain X residue   14 ASN
Chi-restraints excluded: chain X residue   25 VAL
Chi-restraints excluded: chain X residue   45 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 10 optimal weight:   30.0000
   chunk 91 optimal weight:    0.2980
   chunk 97 optimal weight:    8.9990
   chunk 83 optimal weight:   30.0000
   chunk 4 optimal weight:   20.0000
   chunk 8 optimal weight:    8.9990
   chunk 21 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   chunk 69 optimal weight:   10.0000
   chunk 63 optimal weight:    8.9990
   overall best weight:    6.6588

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

Flipped N/Q/H residues before XYZ refinement:
** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 424 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.154278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.133494 restraints weight = 20050.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.136417 restraints weight = 13412.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.138630 restraints weight = 9907.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.5297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7919  Z= 0.255
  Angle     :  0.618   9.897  10794  Z= 0.319
  Chirality :  0.040   0.230   1301
  Planarity :  0.003   0.039   1427
  Dihedral  :  4.367  38.358   1246
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.97 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  8.95 %
    Allowed  : 23.48 %
    Favored  : 67.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.25), residues: 1158
  helix:  1.92 (0.18), residues: 808
  sheet: -3.73 (0.78), residues: 34
  loop : -2.12 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 348 
 HIS   0.005   0.001   HIS B 299 
 PHE   0.028   0.002   PHE A 447 
 TYR   0.016   0.002   TYR A 249 
 ARG   0.006   0.001   ARG A 378 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 243
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.9215 (t60) cc_final: 0.8913 (t60)
REVERT: A  224 PHE cc_start: 0.8061 (t80) cc_final: 0.7758 (t80)
REVERT: A  285 MET cc_start: 0.8042 (tpp) cc_final: 0.7773 (tpp)
REVERT: A  344 LYS cc_start: 0.8077 (tttt) cc_final: 0.7307 (ttpt)
REVERT: A  374 MET cc_start: 0.8708 (tpt) cc_final: 0.8334 (tmm)
REVERT: A  378 ARG cc_start: 0.9355 (mmm-85) cc_final: 0.8912 (mmm-85)
REVERT: A  382 ASN cc_start: 0.8932 (t0) cc_final: 0.8682 (t0)
REVERT: A  392 GLU cc_start: 0.8324 (tt0) cc_final: 0.7676 (mt-10)
REVERT: A  420 MET cc_start: 0.8789 (mpp) cc_final: 0.8536 (mpp)
REVERT: A  443 ASN cc_start: 0.8949 (m-40) cc_final: 0.8666 (t0)
REVERT: A  601 TYR cc_start: 0.8736 (t80) cc_final: 0.8368 (t80)
REVERT: B  131 GLN cc_start: 0.6652 (pm20) cc_final: 0.6406 (pm20)
REVERT: B  151 LEU cc_start: 0.8602 (mt) cc_final: 0.8338 (mt)
REVERT: B  172 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7561 (m-10)
REVERT: B  248 GLU cc_start: 0.8832 (tp30) cc_final: 0.8468 (tp30)
REVERT: B  254 SER cc_start: 0.7651 (t) cc_final: 0.7329 (m)
REVERT: B  285 MET cc_start: 0.8193 (mtm) cc_final: 0.7669 (mtm)
REVERT: B  300 MET cc_start: 0.8876 (mmm) cc_final: 0.8329 (mmp)
REVERT: B  316 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6879 (tp30)
REVERT: B  320 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8548 (mm-30)
REVERT: B  343 ARG cc_start: 0.8974 (mtp85) cc_final: 0.8626 (tpp80)
REVERT: B  351 GLU cc_start: 0.8761 (tp30) cc_final: 0.8445 (tp30)
REVERT: B  372 GLU cc_start: 0.7456 (tp30) cc_final: 0.7040 (tp30)
REVERT: B  373 ARG cc_start: 0.9078 (tmm-80) cc_final: 0.8699 (ttm170)
REVERT: B  391 MET cc_start: 0.8942 (ttm) cc_final: 0.8461 (ttm)
REVERT: B  416 GLN cc_start: 0.8993 (tp40) cc_final: 0.8396 (tp40)
REVERT: B  430 TYR cc_start: 0.8673 (t80) cc_final: 0.8357 (t80)
REVERT: B  450 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6587 (pp30)
REVERT: B  477 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6444 (m-10)
REVERT: X   46 ASP cc_start: 0.8393 (p0) cc_final: 0.8081 (p0)
REVERT: X   53 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7389 (mtt180)
  outliers start: 53
  outliers final: 42
  residues processed: 272
  average time/residue: 0.1734
  time to fit residues: 65.4149
Evaluate side-chains
  278 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 233
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  242 GLU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain B residue  139 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  172 TYR
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  244 THR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  344 SER
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain B residue  449 ARG
Chi-restraints excluded: chain B residue  450 GLN
Chi-restraints excluded: chain B residue  477 TYR
Chi-restraints excluded: chain X residue   10 THR
Chi-restraints excluded: chain X residue   12 LEU
Chi-restraints excluded: chain X residue   14 ASN
Chi-restraints excluded: chain X residue   25 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 33 optimal weight:   30.0000
   chunk 14 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 29 optimal weight:    0.4980
   chunk 60 optimal weight:    0.6980
   chunk 67 optimal weight:   10.0000
   chunk 31 optimal weight:   50.0000
   chunk 8 optimal weight:    7.9990
   overall best weight:    3.2386

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

Flipped N/Q/H residues before XYZ refinement:
B 388 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.156715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.135368 restraints weight = 19764.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.138477 restraints weight = 13210.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.140671 restraints weight = 9730.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.5489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7919  Z= 0.180
  Angle     :  0.572  10.339  10794  Z= 0.288
  Chirality :  0.038   0.162   1301
  Planarity :  0.003   0.035   1427
  Dihedral  :  4.130  41.839   1246
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.02 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  6.93 %
    Allowed  : 26.69 %
    Favored  : 66.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.34 (0.26), residues: 1158
  helix:  2.12 (0.18), residues: 808
  sheet: -3.65 (0.78), residues: 34
  loop : -1.97 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 348 
 HIS   0.003   0.001   HIS B 299 
 PHE   0.020   0.002   PHE A 390 
 TYR   0.028   0.002   TYR A 249 
 ARG   0.006   0.000   ARG X  41 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 256
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.9208 (t60) cc_final: 0.8910 (t60)
REVERT: A  224 PHE cc_start: 0.8005 (t80) cc_final: 0.7638 (t80)
REVERT: A  344 LYS cc_start: 0.8072 (tttt) cc_final: 0.7412 (pttt)
REVERT: A  349 TYR cc_start: 0.8602 (t80) cc_final: 0.8167 (t80)
REVERT: A  350 GLN cc_start: 0.8590 (mm110) cc_final: 0.8300 (mp10)
REVERT: A  374 MET cc_start: 0.8788 (tpt) cc_final: 0.8370 (tmm)
REVERT: A  378 ARG cc_start: 0.9367 (mmm-85) cc_final: 0.8908 (mmm-85)
REVERT: A  382 ASN cc_start: 0.8908 (t0) cc_final: 0.8662 (t0)
REVERT: A  388 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8495 (mm-40)
REVERT: A  392 GLU cc_start: 0.8298 (tt0) cc_final: 0.7623 (mt-10)
REVERT: A  420 MET cc_start: 0.8860 (mpp) cc_final: 0.8576 (mpp)
REVERT: A  429 ILE cc_start: 0.9279 (mm) cc_final: 0.8737 (mt)
REVERT: A  443 ASN cc_start: 0.8924 (m-40) cc_final: 0.8705 (t0)
REVERT: A  601 TYR cc_start: 0.8690 (t80) cc_final: 0.8344 (t80)
REVERT: B  131 GLN cc_start: 0.6616 (pm20) cc_final: 0.6375 (pm20)
REVERT: B  228 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8320 (tt0)
REVERT: B  248 GLU cc_start: 0.8772 (tp30) cc_final: 0.8480 (tp30)
REVERT: B  254 SER cc_start: 0.7657 (t) cc_final: 0.7346 (m)
REVERT: B  285 MET cc_start: 0.8058 (mtm) cc_final: 0.7646 (mtm)
REVERT: B  316 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6788 (tp30)
REVERT: B  320 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8609 (mm-30)
REVERT: B  343 ARG cc_start: 0.8945 (mtp85) cc_final: 0.8559 (tpp80)
REVERT: B  351 GLU cc_start: 0.8747 (tp30) cc_final: 0.8435 (tp30)
REVERT: B  372 GLU cc_start: 0.7516 (tp30) cc_final: 0.6955 (tp30)
REVERT: B  373 ARG cc_start: 0.9027 (tmm-80) cc_final: 0.8674 (ttm170)
REVERT: B  391 MET cc_start: 0.9000 (ttm) cc_final: 0.8353 (ttm)
REVERT: B  416 GLN cc_start: 0.8884 (tp40) cc_final: 0.8337 (tp40)
REVERT: B  450 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6778 (pp30)
REVERT: B  477 TYR cc_start: 0.6723 (OUTLIER) cc_final: 0.6334 (m-10)
REVERT: X   38 GLU cc_start: 0.8702 (tp30) cc_final: 0.8255 (tp30)
REVERT: X   46 ASP cc_start: 0.8390 (p0) cc_final: 0.8035 (p0)
REVERT: X   53 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7373 (mtt180)
  outliers start: 41
  outliers final: 28
  residues processed: 276
  average time/residue: 0.1811
  time to fit residues: 68.3464
Evaluate side-chains
  274 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 244
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  242 GLU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain B residue  139 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  244 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  344 SER
Chi-restraints excluded: chain B residue  424 GLN
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain B residue  449 ARG
Chi-restraints excluded: chain B residue  450 GLN
Chi-restraints excluded: chain B residue  477 TYR
Chi-restraints excluded: chain X residue    5 LEU
Chi-restraints excluded: chain X residue   25 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 114 optimal weight:    9.9990
   chunk 97 optimal weight:   10.0000
   chunk 35 optimal weight:    0.0470
   chunk 69 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 32 optimal weight:   50.0000
   chunk 29 optimal weight:    4.9990
   chunk 73 optimal weight:    9.9990
   chunk 31 optimal weight:   50.0000
   overall best weight:    4.4086

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.155955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.134826 restraints weight = 19732.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.137742 restraints weight = 13186.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.139958 restraints weight = 9750.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.5742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7919  Z= 0.193
  Angle     :  0.585   9.941  10794  Z= 0.297
  Chirality :  0.039   0.175   1301
  Planarity :  0.003   0.038   1427
  Dihedral  :  4.188  44.841   1246
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.63 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  7.94 %
    Allowed  : 26.01 %
    Favored  : 66.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.26), residues: 1158
  helix:  2.18 (0.18), residues: 805
  sheet: -3.46 (0.79), residues: 34
  loop : -1.90 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 348 
 HIS   0.003   0.001   HIS B 299 
 PHE   0.012   0.002   PHE B 195 
 TYR   0.026   0.002   TYR B 310 
 ARG   0.006   0.000   ARG X  41 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 238
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.9239 (t60) cc_final: 0.9033 (t60)
REVERT: A  224 PHE cc_start: 0.8019 (t80) cc_final: 0.7658 (t80)
REVERT: A  344 LYS cc_start: 0.8099 (tttt) cc_final: 0.7434 (pttt)
REVERT: A  349 TYR cc_start: 0.8586 (t80) cc_final: 0.8149 (t80)
REVERT: A  350 GLN cc_start: 0.8572 (mm110) cc_final: 0.8267 (mp10)
REVERT: A  382 ASN cc_start: 0.8849 (t0) cc_final: 0.8592 (t0)
REVERT: A  392 GLU cc_start: 0.8260 (tt0) cc_final: 0.7612 (mt-10)
REVERT: A  420 MET cc_start: 0.8854 (mpp) cc_final: 0.8555 (mpp)
REVERT: A  429 ILE cc_start: 0.8951 (mm) cc_final: 0.8657 (mt)
REVERT: A  443 ASN cc_start: 0.8958 (m-40) cc_final: 0.8757 (t0)
REVERT: A  601 TYR cc_start: 0.8682 (t80) cc_final: 0.8295 (t80)
REVERT: B  131 GLN cc_start: 0.6549 (pm20) cc_final: 0.6323 (pm20)
REVERT: B  172 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7556 (m-10)
REVERT: B  228 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8370 (tt0)
REVERT: B  248 GLU cc_start: 0.8796 (tp30) cc_final: 0.8522 (tp30)
REVERT: B  285 MET cc_start: 0.8099 (mtm) cc_final: 0.7648 (mtm)
REVERT: B  300 MET cc_start: 0.8892 (mmt) cc_final: 0.8213 (mmp)
REVERT: B  316 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6775 (tp30)
REVERT: B  320 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8511 (mm-30)
REVERT: B  343 ARG cc_start: 0.8955 (mtp85) cc_final: 0.8495 (tpp80)
REVERT: B  349 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7481 (tm-30)
REVERT: B  351 GLU cc_start: 0.8708 (tp30) cc_final: 0.8424 (tp30)
REVERT: B  372 GLU cc_start: 0.7512 (tp30) cc_final: 0.6913 (tp30)
REVERT: B  373 ARG cc_start: 0.9062 (tmm-80) cc_final: 0.8691 (ttm170)
REVERT: B  391 MET cc_start: 0.9025 (ttm) cc_final: 0.8376 (ttm)
REVERT: B  416 GLN cc_start: 0.8905 (tp40) cc_final: 0.8431 (tp40)
REVERT: B  450 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6821 (pp30)
REVERT: B  477 TYR cc_start: 0.6729 (OUTLIER) cc_final: 0.6292 (m-10)
REVERT: X   38 GLU cc_start: 0.8703 (tp30) cc_final: 0.8327 (tp30)
REVERT: X   46 ASP cc_start: 0.8415 (p0) cc_final: 0.8093 (p0)
REVERT: X   53 ARG cc_start: 0.7764 (mtt180) cc_final: 0.7316 (mtt180)
  outliers start: 47
  outliers final: 36
  residues processed: 261
  average time/residue: 0.1834
  time to fit residues: 66.1486
Evaluate side-chains
  275 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 236
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  242 GLU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain B residue  139 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  172 TYR
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  244 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  344 SER
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain B residue  449 ARG
Chi-restraints excluded: chain B residue  450 GLN
Chi-restraints excluded: chain B residue  477 TYR
Chi-restraints excluded: chain X residue   10 THR
Chi-restraints excluded: chain X residue   12 LEU
Chi-restraints excluded: chain X residue   25 VAL
Chi-restraints excluded: chain X residue   45 HIS
Chi-restraints excluded: chain X residue   51 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 52 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 93 optimal weight:   50.0000
   chunk 35 optimal weight:   50.0000
   chunk 61 optimal weight:   20.0000
   chunk 21 optimal weight:    5.9990
   chunk 80 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 ASN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 424 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.154401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.133181 restraints weight = 19755.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.136103 restraints weight = 13111.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.138281 restraints weight = 9663.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.6073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7919  Z= 0.216
  Angle     :  0.592  10.055  10794  Z= 0.306
  Chirality :  0.039   0.169   1301
  Planarity :  0.003   0.040   1427
  Dihedral  :  4.345  49.910   1246
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.97 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  8.61 %
    Allowed  : 26.18 %
    Favored  : 65.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.26), residues: 1158
  helix:  2.19 (0.18), residues: 801
  sheet: -3.16 (0.83), residues: 34
  loop : -1.76 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 308 
 HIS   0.004   0.001   HIS B 299 
 PHE   0.015   0.002   PHE A 339 
 TYR   0.037   0.002   TYR B 310 
 ARG   0.007   0.001   ARG X  41 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 236
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.9269 (t60) cc_final: 0.8980 (t60)
REVERT: A  224 PHE cc_start: 0.8055 (t80) cc_final: 0.7679 (t80)
REVERT: A  231 MET cc_start: 0.8182 (ttt) cc_final: 0.7744 (mtp)
REVERT: A  251 ASN cc_start: 0.9447 (m110) cc_final: 0.7860 (m110)
REVERT: A  309 TYR cc_start: 0.8798 (m-80) cc_final: 0.8596 (m-80)
REVERT: A  344 LYS cc_start: 0.8107 (tttt) cc_final: 0.7435 (pttt)
REVERT: A  349 TYR cc_start: 0.8604 (t80) cc_final: 0.8165 (t80)
REVERT: A  350 GLN cc_start: 0.8585 (mm110) cc_final: 0.8252 (mp10)
REVERT: A  383 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8669 (mt-10)
REVERT: A  392 GLU cc_start: 0.8317 (tt0) cc_final: 0.7664 (mt-10)
REVERT: A  420 MET cc_start: 0.8869 (mpp) cc_final: 0.8521 (mpp)
REVERT: A  429 ILE cc_start: 0.8960 (mm) cc_final: 0.8669 (mt)
REVERT: A  601 TYR cc_start: 0.8662 (t80) cc_final: 0.8188 (t80)
REVERT: B  131 GLN cc_start: 0.6465 (pm20) cc_final: 0.6259 (pm20)
REVERT: B  172 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7565 (m-10)
REVERT: B  187 HIS cc_start: 0.8367 (m-70) cc_final: 0.8082 (p90)
REVERT: B  228 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8378 (tt0)
REVERT: B  285 MET cc_start: 0.8106 (mtm) cc_final: 0.7600 (mtm)
REVERT: B  300 MET cc_start: 0.8965 (mmt) cc_final: 0.8250 (mmp)
REVERT: B  316 GLU cc_start: 0.7380 (tm-30) cc_final: 0.7140 (tp30)
REVERT: B  343 ARG cc_start: 0.8821 (mtp85) cc_final: 0.8537 (tpp80)
REVERT: B  351 GLU cc_start: 0.8739 (tp30) cc_final: 0.8482 (tp30)
REVERT: B  367 TRP cc_start: 0.9286 (t-100) cc_final: 0.8168 (t-100)
REVERT: B  373 ARG cc_start: 0.9071 (tmm-80) cc_final: 0.8675 (ttm170)
REVERT: B  391 MET cc_start: 0.9091 (ttm) cc_final: 0.8556 (ttm)
REVERT: B  416 GLN cc_start: 0.9008 (tp40) cc_final: 0.8496 (tp40)
REVERT: B  477 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6311 (m-10)
REVERT: X   38 GLU cc_start: 0.8707 (tp30) cc_final: 0.8343 (tp30)
REVERT: X   46 ASP cc_start: 0.8437 (p0) cc_final: 0.8213 (p0)
REVERT: X   53 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7347 (mtt180)
  outliers start: 51
  outliers final: 43
  residues processed: 262
  average time/residue: 0.1793
  time to fit residues: 64.8897
Evaluate side-chains
  284 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 239
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  242 GLU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  374 MET
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain B residue  139 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  172 TYR
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  244 THR
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  344 SER
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  424 GLN
Chi-restraints excluded: chain B residue  425 THR
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain B residue  449 ARG
Chi-restraints excluded: chain B residue  477 TYR
Chi-restraints excluded: chain X residue   10 THR
Chi-restraints excluded: chain X residue   12 LEU
Chi-restraints excluded: chain X residue   14 ASN
Chi-restraints excluded: chain X residue   25 VAL
Chi-restraints excluded: chain X residue   51 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 46 optimal weight:   50.0000
   chunk 35 optimal weight:   50.0000
   chunk 98 optimal weight:   20.0000
   chunk 79 optimal weight:    6.9990
   chunk 88 optimal weight:    0.4980
   chunk 48 optimal weight:   50.0000
   chunk 59 optimal weight:   20.0000
   chunk 77 optimal weight:   20.0000
   chunk 27 optimal weight:    7.9990
   chunk 103 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    5.2988

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 451 GLN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.153584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.132500 restraints weight = 19626.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.135428 restraints weight = 12971.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.137587 restraints weight = 9528.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.6320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7919  Z= 0.221
  Angle     :  0.615   9.884  10794  Z= 0.318
  Chirality :  0.039   0.169   1301
  Planarity :  0.003   0.039   1427
  Dihedral  :  4.146  32.184   1243
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.71 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  7.60 %
    Allowed  : 28.38 %
    Favored  : 64.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.26), residues: 1158
  helix:  2.08 (0.18), residues: 811
  sheet: -2.96 (0.85), residues: 34
  loop : -1.83 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 139 
 HIS   0.004   0.001   HIS B 299 
 PHE   0.038   0.002   PHE A 306 
 TYR   0.037   0.002   TYR B 310 
 ARG   0.008   0.000   ARG X  41 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 244
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.9212 (t60) cc_final: 0.8933 (t60)
REVERT: A  224 PHE cc_start: 0.8087 (t80) cc_final: 0.7765 (t80)
REVERT: A  251 ASN cc_start: 0.9441 (m110) cc_final: 0.7854 (m110)
REVERT: A  344 LYS cc_start: 0.8107 (tttt) cc_final: 0.7436 (pttt)
REVERT: A  349 TYR cc_start: 0.8606 (t80) cc_final: 0.8123 (t80)
REVERT: A  350 GLN cc_start: 0.8579 (mm110) cc_final: 0.8233 (mp10)
REVERT: A  392 GLU cc_start: 0.8310 (tt0) cc_final: 0.7633 (mt-10)
REVERT: A  420 MET cc_start: 0.8866 (mpp) cc_final: 0.8514 (mpp)
REVERT: A  429 ILE cc_start: 0.8938 (mm) cc_final: 0.8634 (mt)
REVERT: A  601 TYR cc_start: 0.8624 (t80) cc_final: 0.8131 (t80)
REVERT: B  172 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7587 (m-10)
REVERT: B  187 HIS cc_start: 0.8371 (m-70) cc_final: 0.8097 (p90)
REVERT: B  228 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8402 (tt0)
REVERT: B  248 GLU cc_start: 0.8782 (tp30) cc_final: 0.8506 (tp30)
REVERT: B  285 MET cc_start: 0.8104 (mtm) cc_final: 0.7634 (mtm)
REVERT: B  300 MET cc_start: 0.8969 (mmt) cc_final: 0.8272 (mmp)
REVERT: B  316 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6867 (tp30)
REVERT: B  320 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8550 (mm-30)
REVERT: B  343 ARG cc_start: 0.8923 (mtp85) cc_final: 0.8570 (tpp80)
REVERT: B  351 GLU cc_start: 0.8751 (tp30) cc_final: 0.8512 (tp30)
REVERT: B  367 TRP cc_start: 0.9263 (t-100) cc_final: 0.8779 (t-100)
REVERT: B  373 ARG cc_start: 0.9035 (tmm-80) cc_final: 0.8685 (ttm170)
REVERT: B  391 MET cc_start: 0.9156 (ttm) cc_final: 0.8657 (ttm)
REVERT: B  416 GLN cc_start: 0.9011 (tp40) cc_final: 0.8531 (tp40)
REVERT: B  477 TYR cc_start: 0.6790 (OUTLIER) cc_final: 0.6221 (m-10)
REVERT: X   38 GLU cc_start: 0.8730 (tp30) cc_final: 0.8379 (tp30)
REVERT: X   46 ASP cc_start: 0.8452 (p0) cc_final: 0.8240 (p0)
REVERT: X   53 ARG cc_start: 0.7801 (mtt180) cc_final: 0.7330 (mtt180)
  outliers start: 45
  outliers final: 37
  residues processed: 265
  average time/residue: 0.1789
  time to fit residues: 65.5806
Evaluate side-chains
  269 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 230
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  374 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain B residue  139 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  172 TYR
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  244 THR
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain B residue  449 ARG
Chi-restraints excluded: chain B residue  477 TYR
Chi-restraints excluded: chain X residue   10 THR
Chi-restraints excluded: chain X residue   12 LEU
Chi-restraints excluded: chain X residue   14 ASN
Chi-restraints excluded: chain X residue   25 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 48 optimal weight:   50.0000
   chunk 38 optimal weight:    8.9990
   chunk 90 optimal weight:   40.0000
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 94 optimal weight:   30.0000
   chunk 34 optimal weight:   50.0000
   chunk 6 optimal weight:    8.9990
   chunk 71 optimal weight:    5.9990
   chunk 86 optimal weight:    7.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.152594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.131462 restraints weight = 20032.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.134511 restraints weight = 13192.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.136598 restraints weight = 9649.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.6543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   7919  Z= 0.248
  Angle     :  0.661  11.474  10794  Z= 0.339
  Chirality :  0.041   0.195   1301
  Planarity :  0.004   0.051   1427
  Dihedral  :  4.281  33.562   1243
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.40 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  7.77 %
    Allowed  : 28.89 %
    Favored  : 63.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.25), residues: 1158
  helix:  1.95 (0.18), residues: 812
  sheet: -2.91 (0.85), residues: 34
  loop : -1.86 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP B 367 
 HIS   0.004   0.001   HIS A 255 
 PHE   0.043   0.002   PHE A 306 
 TYR   0.035   0.002   TYR B 310 
 ARG   0.008   0.001   ARG X  41 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 245
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.9208 (t60) cc_final: 0.8897 (t60)
REVERT: A  224 PHE cc_start: 0.8099 (t80) cc_final: 0.7620 (t80)
REVERT: A  253 MET cc_start: 0.9009 (mtp) cc_final: 0.8560 (mtp)
REVERT: A  344 LYS cc_start: 0.8104 (tttt) cc_final: 0.7392 (tttt)
REVERT: A  349 TYR cc_start: 0.8612 (t80) cc_final: 0.8157 (t80)
REVERT: A  350 GLN cc_start: 0.8599 (mm110) cc_final: 0.8242 (mp10)
REVERT: A  392 GLU cc_start: 0.8350 (tt0) cc_final: 0.7773 (mm-30)
REVERT: A  420 MET cc_start: 0.8880 (mpp) cc_final: 0.8512 (mpp)
REVERT: A  601 TYR cc_start: 0.8645 (t80) cc_final: 0.8138 (t80)
REVERT: B  172 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7614 (m-10)
REVERT: B  187 HIS cc_start: 0.8401 (m-70) cc_final: 0.8194 (p90)
REVERT: B  248 GLU cc_start: 0.8767 (tp30) cc_final: 0.8480 (tp30)
REVERT: B  285 MET cc_start: 0.8090 (mtm) cc_final: 0.7613 (mtm)
REVERT: B  300 MET cc_start: 0.8980 (mmt) cc_final: 0.8279 (mmp)
REVERT: B  316 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6712 (tm-30)
REVERT: B  320 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8524 (mm-30)
REVERT: B  343 ARG cc_start: 0.8938 (mtp85) cc_final: 0.8590 (tpp80)
REVERT: B  351 GLU cc_start: 0.8747 (tp30) cc_final: 0.8511 (tp30)
REVERT: B  372 GLU cc_start: 0.7450 (tp30) cc_final: 0.7081 (tp30)
REVERT: B  373 ARG cc_start: 0.8838 (tmm-80) cc_final: 0.8522 (ttm170)
REVERT: B  391 MET cc_start: 0.9121 (ttm) cc_final: 0.8657 (ttm)
REVERT: B  416 GLN cc_start: 0.9039 (tp40) cc_final: 0.8562 (tp40)
REVERT: B  477 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.6239 (m-10)
REVERT: X   38 GLU cc_start: 0.8730 (tp30) cc_final: 0.8403 (tp30)
REVERT: X   46 ASP cc_start: 0.8453 (p0) cc_final: 0.8249 (p0)
REVERT: X   53 ARG cc_start: 0.7808 (mtt180) cc_final: 0.7326 (mtt180)
  outliers start: 46
  outliers final: 43
  residues processed: 266
  average time/residue: 0.1852
  time to fit residues: 70.1842
Evaluate side-chains
  281 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 236
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  242 GLU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  374 MET
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain B residue  139 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  172 TYR
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  244 THR
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  344 SER
Chi-restraints excluded: chain B residue  424 GLN
Chi-restraints excluded: chain B residue  425 THR
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain B residue  449 ARG
Chi-restraints excluded: chain B residue  477 TYR
Chi-restraints excluded: chain X residue   10 THR
Chi-restraints excluded: chain X residue   12 LEU
Chi-restraints excluded: chain X residue   25 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 104 optimal weight:    6.9990
   chunk 115 optimal weight:    6.9990
   chunk 70 optimal weight:    7.9990
   chunk 64 optimal weight:   10.0000
   chunk 111 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 67 optimal weight:    5.9990
   chunk 102 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 100 optimal weight:   20.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 456 GLN
** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.155075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.134072 restraints weight = 19675.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.137103 restraints weight = 13006.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.139192 restraints weight = 9547.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.6664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7919  Z= 0.201
  Angle     :  0.632  11.662  10794  Z= 0.323
  Chirality :  0.040   0.178   1301
  Planarity :  0.003   0.055   1427
  Dihedral  :  4.103  34.758   1243
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.20 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  6.93 %
    Allowed  : 30.07 %
    Favored  : 63.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.26), residues: 1158
  helix:  2.00 (0.18), residues: 818
  sheet: -3.34 (0.72), residues: 45
  loop : -1.78 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP B 367 
 HIS   0.004   0.001   HIS B 299 
 PHE   0.042   0.002   PHE A 306 
 TYR   0.029   0.002   TYR B 310 
 ARG   0.009   0.001   ARG X  41 

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 256
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 TRP cc_start: 0.9190 (t60) cc_final: 0.8897 (t60)
REVERT: A  224 PHE cc_start: 0.8039 (t80) cc_final: 0.7637 (t80)
REVERT: A  253 MET cc_start: 0.8985 (mtp) cc_final: 0.8398 (mtp)
REVERT: A  344 LYS cc_start: 0.8120 (tttt) cc_final: 0.7434 (tttt)
REVERT: A  349 TYR cc_start: 0.8592 (t80) cc_final: 0.8104 (t80)
REVERT: A  350 GLN cc_start: 0.8537 (mm110) cc_final: 0.8213 (mp10)
REVERT: A  392 GLU cc_start: 0.8278 (tt0) cc_final: 0.7684 (mm-30)
REVERT: A  420 MET cc_start: 0.8901 (mpp) cc_final: 0.8532 (mpp)
REVERT: B  172 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7622 (m-10)
REVERT: B  187 HIS cc_start: 0.8391 (m-70) cc_final: 0.8188 (p90)
REVERT: B  228 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8366 (tt0)
REVERT: B  248 GLU cc_start: 0.8793 (tp30) cc_final: 0.8520 (tp30)
REVERT: B  285 MET cc_start: 0.8000 (mtm) cc_final: 0.7681 (mtm)
REVERT: B  300 MET cc_start: 0.8926 (mmt) cc_final: 0.8212 (mmp)
REVERT: B  316 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6660 (tm-30)
REVERT: B  320 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8523 (mm-30)
REVERT: B  322 GLN cc_start: 0.9181 (tp-100) cc_final: 0.8621 (tt0)
REVERT: B  343 ARG cc_start: 0.8901 (mtp85) cc_final: 0.8542 (tpp80)
REVERT: B  351 GLU cc_start: 0.8693 (tp30) cc_final: 0.8483 (tp30)
REVERT: B  370 ASP cc_start: 0.8813 (m-30) cc_final: 0.8536 (t0)
REVERT: B  372 GLU cc_start: 0.7544 (tp30) cc_final: 0.7188 (tp30)
REVERT: B  373 ARG cc_start: 0.8777 (tmm-80) cc_final: 0.8540 (ttm170)
REVERT: B  391 MET cc_start: 0.9125 (ttm) cc_final: 0.8642 (ttm)
REVERT: B  416 GLN cc_start: 0.8925 (tp40) cc_final: 0.8538 (tp40)
REVERT: B  477 TYR cc_start: 0.6819 (OUTLIER) cc_final: 0.6079 (m-10)
REVERT: X   38 GLU cc_start: 0.8719 (tp30) cc_final: 0.8387 (tp30)
REVERT: X   53 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7317 (mtt180)
  outliers start: 41
  outliers final: 38
  residues processed: 273
  average time/residue: 0.1718
  time to fit residues: 64.6772
Evaluate side-chains
  278 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 238
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  242 GLU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  374 MET
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain B residue  139 TRP
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  172 TYR
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  244 THR
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  344 SER
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  424 GLN
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain B residue  449 ARG
Chi-restraints excluded: chain B residue  477 TYR
Chi-restraints excluded: chain X residue   10 THR
Chi-restraints excluded: chain X residue   12 LEU
Chi-restraints excluded: chain X residue   25 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0570
   chunk 88 optimal weight:    0.0170
   chunk 2 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9980
   chunk 100 optimal weight:   30.0000
   chunk 96 optimal weight:    0.0370
   chunk 104 optimal weight:    7.9990
   chunk 50 optimal weight:   20.0000
   chunk 18 optimal weight:    9.9990
   overall best weight:    1.0216

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

Flipped N/Q/H residues before XYZ refinement:
B 384 HIS
B 388 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.159447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.137848 restraints weight = 19619.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.141052 restraints weight = 13064.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.143288 restraints weight = 9601.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.6738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7919  Z= 0.175
  Angle     :  0.624  11.878  10794  Z= 0.316
  Chirality :  0.039   0.188   1301
  Planarity :  0.003   0.059   1427
  Dihedral  :  3.838  33.602   1243
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.20 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 32.94 %
    Favored  : 62.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.26), residues: 1158
  helix:  2.16 (0.19), residues: 806
  sheet: -3.09 (0.73), residues: 44
  loop : -1.56 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 367 
 HIS   0.011   0.001   HIS B 384 
 PHE   0.041   0.002   PHE A 306 
 TYR   0.023   0.001   TYR A 249 
 ARG   0.009   0.000   ARG X  41 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4305.17 seconds
wall clock time: 74 minutes 52.02 seconds (4492.02 seconds total)