Starting phenix.real_space_refine on Sat Jul 4 12:10:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wyr_37936/07_2026/8wyr_37936.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wyr_37936/07_2026/8wyr_37936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wyr_37936/07_2026/8wyr_37936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wyr_37936/07_2026/8wyr_37936.map" model { file = "/net/cci-nas-00/data/ceres_data/8wyr_37936/07_2026/8wyr_37936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wyr_37936/07_2026/8wyr_37936.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 112 5.16 5 C 12931 2.51 5 N 3512 2.21 5 O 4055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20612 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "B" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 18, 'TRANS': 211} Chain: "C" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1757 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 18, 'TRANS': 207} Chain: "D" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain: "E" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1757 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 18, 'TRANS': 207} Chain: "F" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain: "G" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 18, 'TRANS': 206} Chain: "H" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "J" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain breaks: 1 Chain: "K" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "L" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "M" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1669 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 8, 'TRANS': 204} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 4.50, per 1000 atoms: 0.22 Number of scatterers: 20612 At special positions: 0 Unit cell: (67.23, 170.15, 193.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 112 16.00 O 4055 8.00 N 3512 7.00 C 12931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.04 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS J 68 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS C 414 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.04 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.01 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS E 414 " distance=2.02 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.14 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 414 " - pdb=" SG CYS G 414 " distance=2.39 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.02 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.04 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 414 " - pdb=" SG CYS K 414 " distance=2.02 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 575 " - pdb=" SG CYS K 575 " distance=2.03 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=2.02 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 91 " distance=2.02 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.04 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 414 " - pdb=" SG CYS M 191 " distance=2.04 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.03 Simple disulfide: pdb=" SG CYS M 147 " - pdb=" SG CYS M 181 " distance=2.04 Simple disulfide: pdb=" SG CYS M 163 " - pdb=" SG CYS M 228 " distance=2.04 Simple disulfide: pdb=" SG CYS M 176 " - pdb=" SG CYS M 238 " distance=2.02 Simple disulfide: pdb=" SG CYS M 208 " - pdb=" SG CYS M 218 " distance=2.05 Simple disulfide: pdb=" SG CYS M 253 " - pdb=" SG CYS M 287 " distance=2.02 Simple disulfide: pdb=" SG CYS M 269 " - pdb=" SG CYS M 335 " distance=2.03 Simple disulfide: pdb=" SG CYS M 282 " - pdb=" SG CYS M 345 " distance=2.03 Simple disulfide: pdb=" SG CYS M 315 " - pdb=" SG CYS M 325 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG I 1 " - " ASN J 48 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 944.6 milliseconds 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5016 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 66 sheets defined 13.4% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 353 through 360 removed outlier: 3.525A pdb=" N ILE A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 414 through 421 removed outlier: 3.881A pdb=" N TRP B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 466 Processing helix chain 'B' and resid 524 through 531 removed outlier: 3.968A pdb=" N GLY B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 460 through 467 Processing helix chain 'C' and resid 524 through 530 Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 460 through 465 Processing helix chain 'D' and resid 524 through 530 Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.828A pdb=" N GLY D 557 " --> pdb=" O LYS D 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 414 through 421 removed outlier: 4.315A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 467 removed outlier: 3.622A pdb=" N LEU E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 531 removed outlier: 3.796A pdb=" N GLY E 531 " --> pdb=" O GLU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 557 removed outlier: 4.153A pdb=" N GLY E 557 " --> pdb=" O LYS E 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 Processing helix chain 'F' and resid 414 through 421 removed outlier: 3.994A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 467 Processing helix chain 'F' and resid 524 through 530 removed outlier: 3.523A pdb=" N THR F 530 " --> pdb=" O GLU F 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 361 removed outlier: 3.629A pdb=" N THR G 360 " --> pdb=" O SER G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 420 removed outlier: 3.707A pdb=" N TRP G 418 " --> pdb=" O CYS G 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 467 removed outlier: 3.549A pdb=" N ARG G 467 " --> pdb=" O GLN G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 531 removed outlier: 3.842A pdb=" N GLY G 531 " --> pdb=" O GLU G 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 558 removed outlier: 4.070A pdb=" N GLY G 557 " --> pdb=" O ASP G 553 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS G 558 " --> pdb=" O LYS G 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 553 through 558' Processing helix chain 'H' and resid 355 through 360 Processing helix chain 'H' and resid 415 through 420 Processing helix chain 'H' and resid 460 through 466 Processing helix chain 'H' and resid 525 through 531 removed outlier: 3.669A pdb=" N THR H 530 " --> pdb=" O GLU H 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 68 Processing helix chain 'K' and resid 353 through 361 removed outlier: 3.572A pdb=" N THR K 360 " --> pdb=" O SER K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 419 Processing helix chain 'K' and resid 460 through 467 Processing helix chain 'K' and resid 524 through 531 removed outlier: 3.619A pdb=" N GLY K 531 " --> pdb=" O GLU K 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 359 Processing helix chain 'L' and resid 416 through 421 Processing helix chain 'L' and resid 460 through 465 Processing helix chain 'L' and resid 524 through 530 removed outlier: 3.540A pdb=" N TRP L 528 " --> pdb=" O SER L 524 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR L 530 " --> pdb=" O GLU L 526 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 3.730A pdb=" N ALA M 172 " --> pdb=" O SER M 168 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG M 177 " --> pdb=" O LYS M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 197 removed outlier: 4.056A pdb=" N GLY M 197 " --> pdb=" O HIS M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 286 Processing helix chain 'M' and resid 295 through 301 Processing helix chain 'M' and resid 336 through 340 removed outlier: 3.514A pdb=" N GLU M 339 " --> pdb=" O THR M 336 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP M 340 " --> pdb=" O HIS M 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 336 through 340' Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 347 removed outlier: 3.595A pdb=" N ARG A 346 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 363 through 364 removed outlier: 4.260A pdb=" N THR A 363 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 413 " --> pdb=" O THR A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 380 removed outlier: 3.690A pdb=" N THR A 379 " --> pdb=" O THR A 429 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.592A pdb=" N THR A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.929A pdb=" N GLN A 439 " --> pdb=" O CYS A 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 453 through 457 removed outlier: 5.608A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 453 through 457 removed outlier: 5.608A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.769A pdb=" N THR A 535 " --> pdb=" O MET A 489 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 548 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AB1, first strand: chain 'C' and resid 565 through 566 removed outlier: 6.913A pdb=" N LEU A 566 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N SER B 569 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N MET A 568 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AB3, first strand: chain 'B' and resid 381 through 382 Processing sheet with id=AB4, first strand: chain 'B' and resid 453 through 457 Processing sheet with id=AB5, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.642A pdb=" N VAL B 476 " --> pdb=" O ALA B 517 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AB7, first strand: chain 'C' and resid 346 through 348 Processing sheet with id=AB8, first strand: chain 'C' and resid 363 through 366 removed outlier: 4.198A pdb=" N THR C 363 " --> pdb=" O ILE C 413 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 389 through 390 removed outlier: 4.491A pdb=" N TRP C 382 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 424 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 441 " --> pdb=" O PHE C 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 456 through 457 Processing sheet with id=AC2, first strand: chain 'C' and resid 476 through 479 removed outlier: 5.696A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AC4, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AC5, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.647A pdb=" N LEU D 368 " --> pdb=" O PHE D 348 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR D 366 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 424 through 426 removed outlier: 3.575A pdb=" N GLN D 439 " --> pdb=" O CYS D 426 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 456 through 457 Processing sheet with id=AC8, first strand: chain 'D' and resid 470 through 471 Processing sheet with id=AC9, first strand: chain 'D' and resid 476 through 479 removed outlier: 5.219A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 493 through 494 removed outlier: 3.735A pdb=" N THR D 548 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 349 through 350 removed outlier: 3.803A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR E 363 " --> pdb=" O ILE E 413 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 379 through 380 Processing sheet with id=AD4, first strand: chain 'E' and resid 383 through 384 Processing sheet with id=AD5, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.695A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.695A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AD8, first strand: chain 'F' and resid 363 through 364 removed outlier: 3.896A pdb=" N THR F 363 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE F 413 " --> pdb=" O THR F 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'F' and resid 381 through 382 Processing sheet with id=AE1, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.780A pdb=" N THR F 477 " --> pdb=" O ASP F 453 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.780A pdb=" N THR F 477 " --> pdb=" O ASP F 453 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 493 through 494 removed outlier: 3.580A pdb=" N GLN F 493 " --> pdb=" O GLN F 490 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 565 through 568 removed outlier: 6.596A pdb=" N SER F 565 " --> pdb=" O LEU G 566 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N MET G 568 " --> pdb=" O SER F 565 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL F 567 " --> pdb=" O MET G 568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'G' and resid 346 through 349 removed outlier: 3.838A pdb=" N ARG G 346 " --> pdb=" O THR G 370 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR G 370 " --> pdb=" O ARG G 346 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 363 through 365 Processing sheet with id=AE7, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.641A pdb=" N THR G 477 " --> pdb=" O ASP G 453 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.641A pdb=" N THR G 477 " --> pdb=" O ASP G 453 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AF1, first strand: chain 'H' and resid 363 through 364 removed outlier: 4.045A pdb=" N THR H 363 " --> pdb=" O ILE H 413 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 424 through 425 removed outlier: 3.818A pdb=" N ILE H 441 " --> pdb=" O PHE H 424 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 455 through 457 Processing sheet with id=AF4, first strand: chain 'H' and resid 455 through 457 removed outlier: 5.283A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 493 through 494 removed outlier: 3.531A pdb=" N THR H 548 " --> pdb=" O VAL H 538 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 5 through 9 removed outlier: 5.670A pdb=" N VAL J 6 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER J 19 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL J 33 " --> pdb=" O LEU L 561 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASN L 563 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ARG J 35 " --> pdb=" O ASN L 563 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N SER L 565 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE J 37 " --> pdb=" O SER L 565 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL L 567 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE J 39 " --> pdb=" O VAL L 567 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER L 569 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL J 41 " --> pdb=" O SER L 569 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER K 565 " --> pdb=" O LEU L 566 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET L 568 " --> pdb=" O SER K 565 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL K 567 " --> pdb=" O MET L 568 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 74 through 77 removed outlier: 9.651A pdb=" N VAL L 547 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR J 84 " --> pdb=" O VAL L 547 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLU L 549 " --> pdb=" O THR J 84 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR J 86 " --> pdb=" O GLU L 549 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N THR L 551 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 112 through 115 Processing sheet with id=AF9, first strand: chain 'K' and resid 363 through 365 removed outlier: 3.792A pdb=" N ILE K 413 " --> pdb=" O THR K 363 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU K 365 " --> pdb=" O ALA K 411 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA K 411 " --> pdb=" O LEU K 365 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 382 through 383 Processing sheet with id=AG2, first strand: chain 'K' and resid 453 through 457 removed outlier: 5.628A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 453 through 457 removed outlier: 5.628A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 485 through 489 Processing sheet with id=AG5, first strand: chain 'L' and resid 347 through 348 removed outlier: 3.789A pdb=" N PHE L 348 " --> pdb=" O LEU L 368 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS L 367 " --> pdb=" O GLY L 409 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY L 409 " --> pdb=" O CYS L 367 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL L 369 " --> pdb=" O ALA L 407 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA L 407 " --> pdb=" O VAL L 369 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE L 396 " --> pdb=" O VAL L 408 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 389 through 390 removed outlier: 3.527A pdb=" N VAL L 390 " --> pdb=" O TRP L 382 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TRP L 382 " --> pdb=" O VAL L 390 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER L 381 " --> pdb=" O THR L 427 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS L 426 " --> pdb=" O GLN L 439 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN L 439 " --> pdb=" O CYS L 426 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 453 through 457 Processing sheet with id=AG8, first strand: chain 'L' and resid 453 through 457 removed outlier: 5.399A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'M' and resid 140 through 141 Processing sheet with id=AH1, first strand: chain 'M' and resid 140 through 141 Processing sheet with id=AH2, first strand: chain 'M' and resid 243 through 251 removed outlier: 4.138A pdb=" N ASP M 243 " --> pdb=" O LEU M 260 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY M 249 " --> pdb=" O SER M 254 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER M 254 " --> pdb=" O GLY M 249 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU M 257 " --> pdb=" O VAL M 268 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL M 268 " --> pdb=" O LEU M 257 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP M 309 " --> pdb=" O TRP M 265 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N SER M 267 " --> pdb=" O TRP M 309 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 243 through 251 removed outlier: 4.138A pdb=" N ASP M 243 " --> pdb=" O LEU M 260 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY M 249 " --> pdb=" O SER M 254 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER M 254 " --> pdb=" O GLY M 249 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY M 255 " --> pdb=" O VAL M 343 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3615 1.32 - 1.45: 5596 1.45 - 1.58: 11760 1.58 - 1.70: 3 1.70 - 1.83: 144 Bond restraints: 21118 Sorted by residual: bond pdb=" CA THR F 535 " pdb=" C THR F 535 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.19e-02 7.06e+03 2.48e+01 bond pdb=" CA LEU C 475 " pdb=" C LEU C 475 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.11e-02 8.12e+03 2.35e+01 bond pdb=" N VAL F 484 " pdb=" CA VAL F 484 " ideal model delta sigma weight residual 1.457 1.397 0.060 1.25e-02 6.40e+03 2.33e+01 bond pdb=" CA TYR F 534 " pdb=" C TYR F 534 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.20e-02 6.94e+03 2.17e+01 bond pdb=" CA CYS D 474 " pdb=" C CYS D 474 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.23e-02 6.61e+03 2.16e+01 ... (remaining 21113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 28013 2.72 - 5.44: 732 5.44 - 8.16: 112 8.16 - 10.88: 21 10.88 - 13.60: 4 Bond angle restraints: 28882 Sorted by residual: angle pdb=" N SER F 480 " pdb=" CA SER F 480 " pdb=" C SER F 480 " ideal model delta sigma weight residual 109.83 97.52 12.31 1.27e+00 6.20e-01 9.40e+01 angle pdb=" N ASP E 483 " pdb=" CA ASP E 483 " pdb=" C ASP E 483 " ideal model delta sigma weight residual 109.76 123.36 -13.60 1.59e+00 3.96e-01 7.32e+01 angle pdb=" N ASP D 483 " pdb=" CA ASP D 483 " pdb=" C ASP D 483 " ideal model delta sigma weight residual 110.24 121.28 -11.04 1.30e+00 5.92e-01 7.21e+01 angle pdb=" N PHE F 479 " pdb=" CA PHE F 479 " pdb=" C PHE F 479 " ideal model delta sigma weight residual 109.07 120.58 -11.51 1.52e+00 4.33e-01 5.73e+01 angle pdb=" N ALA F 482 " pdb=" CA ALA F 482 " pdb=" C ALA F 482 " ideal model delta sigma weight residual 112.97 105.12 7.85 1.06e+00 8.90e-01 5.49e+01 ... (remaining 28877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11296 17.76 - 35.53: 1315 35.53 - 53.29: 323 53.29 - 71.06: 53 71.06 - 88.82: 16 Dihedral angle restraints: 13003 sinusoidal: 5298 harmonic: 7705 Sorted by residual: dihedral pdb=" CB CYS M 269 " pdb=" SG CYS M 269 " pdb=" SG CYS M 335 " pdb=" CB CYS M 335 " ideal model delta sinusoidal sigma weight residual 93.00 173.35 -80.35 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS M 208 " pdb=" SG CYS M 208 " pdb=" SG CYS M 218 " pdb=" CB CYS M 218 " ideal model delta sinusoidal sigma weight residual -86.00 -6.70 -79.30 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS J 12 " pdb=" SG CYS J 12 " pdb=" SG CYS J 100 " pdb=" CB CYS J 100 " ideal model delta sinusoidal sigma weight residual -86.00 -154.00 68.00 1 1.00e+01 1.00e-02 6.00e+01 ... (remaining 13000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 3264 0.139 - 0.279: 119 0.279 - 0.418: 10 0.418 - 0.557: 2 0.557 - 0.697: 1 Chirality restraints: 3396 Sorted by residual: chirality pdb=" CA THR G 427 " pdb=" N THR G 427 " pdb=" C THR G 427 " pdb=" CB THR G 427 " both_signs ideal model delta sigma weight residual False 2.53 1.83 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" C1 NAG K 601 " pdb=" ND2 ASN K 563 " pdb=" C2 NAG K 601 " pdb=" O5 NAG K 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 563 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.48e+00 ... (remaining 3393 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 424 " 0.024 2.00e-02 2.50e+03 3.30e-02 1.90e+01 pdb=" CG PHE F 424 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE F 424 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE F 424 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE F 424 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 424 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE F 424 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 354 " 0.018 2.00e-02 2.50e+03 3.19e-02 1.79e+01 pdb=" CG PHE A 354 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 354 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 354 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 354 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 354 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 354 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO F 351 " 0.065 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO F 352 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO F 352 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 352 " 0.052 5.00e-02 4.00e+02 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4431 2.78 - 3.31: 18561 3.31 - 3.84: 34916 3.84 - 4.37: 39283 4.37 - 4.90: 68304 Nonbonded interactions: 165495 Sorted by model distance: nonbonded pdb=" OG SER K 565 " pdb=" O7 NAG K 601 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR F 363 " pdb=" O ILE F 413 " model vdw 2.265 3.040 nonbonded pdb=" O ASP G 416 " pdb=" OG SER G 420 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASP M 250 " pdb=" OH TYR M 301 " model vdw 2.289 3.040 nonbonded pdb=" O ALA D 448 " pdb=" OG SER D 480 " model vdw 2.299 3.040 ... (remaining 165490 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 345 through 569 or resid 601)) selection = (chain 'B' and (resid 345 through 569 or resid 601)) selection = (chain 'C' and (resid 345 through 569 or resid 601)) selection = (chain 'D' and (resid 345 through 569 or resid 601)) selection = (chain 'E' and (resid 345 through 569 or resid 601)) selection = (chain 'F' and (resid 345 through 569 or resid 601)) selection = chain 'G' selection = (chain 'H' and (resid 345 through 569 or resid 601)) selection = (chain 'K' and (resid 345 through 569 or resid 601)) selection = (chain 'L' and (resid 345 through 569 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 18.520 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.360 21169 Z= 0.393 Angle : 1.078 17.938 28996 Z= 0.607 Chirality : 0.067 0.697 3396 Planarity : 0.010 0.120 3701 Dihedral : 15.720 88.822 7870 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.24 % Allowed : 23.67 % Favored : 75.10 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.15), residues: 2603 helix: -3.34 (0.19), residues: 292 sheet: -1.72 (0.18), residues: 700 loop : -1.59 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG H 461 TYR 0.058 0.003 TYR J 62 PHE 0.075 0.004 PHE F 424 TRP 0.052 0.003 TRP E 418 HIS 0.022 0.002 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.37 (21118) covalent geometry : angle 1.04879 / 0.60 (28882) SS BOND : bond 0.06058 / 2.20 ( 39) SS BOND : angle 2.16361 / 1.60 ( 78) hydrogen bonds : bond 0.25922 / 17.65 ( 522) hydrogen bonds : angle 10.06781 / 7.00 ( 1518) link_BETA1-4 : bond 0.00608 / 0.32 ( 1) link_BETA1-4 : angle 1.97249 / 0.93 ( 3) link_NAG-ASN : bond 0.00980 / 0.49 ( 11) link_NAG-ASN : angle 6.90278 / 4.64 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 303 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 PHE cc_start: 0.7232 (t80) cc_final: 0.6941 (t80) REVERT: D 358 PHE cc_start: 0.7998 (t80) cc_final: 0.7791 (t80) REVERT: E 453 ASP cc_start: 0.7556 (m-30) cc_final: 0.7322 (t70) REVERT: E 483 ASP cc_start: 0.7725 (p0) cc_final: 0.7188 (p0) REVERT: E 485 PHE cc_start: 0.8279 (t80) cc_final: 0.7693 (t80) REVERT: F 500 TYR cc_start: 0.8027 (p90) cc_final: 0.7763 (p90) REVERT: F 530 THR cc_start: 0.8289 (p) cc_final: 0.7671 (p) REVERT: L 380 ILE cc_start: 0.5061 (OUTLIER) cc_final: 0.4795 (mt) REVERT: M 240 ASP cc_start: 0.8471 (t0) cc_final: 0.7475 (p0) outliers start: 29 outliers final: 16 residues processed: 323 average time/residue: 0.1351 time to fit residues: 67.6004 Evaluate side-chains 293 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 276 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain H residue 553 ASP Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain M residue 134 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 490 GLN B 395 ASN ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS H 529 ASN ** K 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN M 272 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.176336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.119215 restraints weight = 30318.351| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.60 r_work: 0.3385 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21169 Z= 0.155 Angle : 0.641 15.026 28996 Z= 0.329 Chirality : 0.046 0.429 3396 Planarity : 0.006 0.064 3701 Dihedral : 6.474 56.672 3103 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.37 % Allowed : 22.43 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.16), residues: 2603 helix: -2.61 (0.21), residues: 317 sheet: -1.54 (0.18), residues: 726 loop : -1.28 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 461 TYR 0.021 0.001 TYR F 534 PHE 0.023 0.002 PHE L 479 TRP 0.011 0.001 TRP E 418 HIS 0.005 0.001 HIS F 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (21118) covalent geometry : angle 0.60847 / 0.32 (28882) SS BOND : bond 0.00279 / 0.19 ( 39) SS BOND : angle 1.08430 / 0.79 ( 78) hydrogen bonds : bond 0.04331 / 3.02 ( 522) hydrogen bonds : angle 6.76251 / 4.65 ( 1518) link_BETA1-4 : bond 0.00419 / 0.22 ( 1) link_BETA1-4 : angle 1.57921 / 0.69 ( 3) link_NAG-ASN : bond 0.00613 / 0.31 ( 11) link_NAG-ASN : angle 5.83778 / 3.88 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 317 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7643 (p0) cc_final: 0.7374 (p0) REVERT: A 487 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8025 (tm-30) REVERT: B 354 PHE cc_start: 0.7980 (t80) cc_final: 0.7751 (t80) REVERT: B 462 GLU cc_start: 0.8349 (mp0) cc_final: 0.7990 (mt-10) REVERT: B 490 GLN cc_start: 0.8331 (tm130) cc_final: 0.7930 (tm-30) REVERT: D 518 HIS cc_start: 0.7400 (m-70) cc_final: 0.7142 (m-70) REVERT: E 354 PHE cc_start: 0.7804 (t80) cc_final: 0.7574 (t80) REVERT: E 364 LYS cc_start: 0.7454 (mmtt) cc_final: 0.7239 (tppt) REVERT: E 418 TRP cc_start: 0.6620 (t60) cc_final: 0.6337 (t60) REVERT: E 453 ASP cc_start: 0.8152 (m-30) cc_final: 0.7340 (t70) REVERT: E 483 ASP cc_start: 0.7934 (p0) cc_final: 0.7415 (p0) REVERT: E 485 PHE cc_start: 0.8343 (t80) cc_final: 0.7555 (t80) REVERT: F 530 THR cc_start: 0.8639 (p) cc_final: 0.8398 (p) REVERT: G 388 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.6184 (mp0) REVERT: H 525 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7442 (tm-30) REVERT: H 529 ASN cc_start: 0.8498 (m-40) cc_final: 0.7384 (m-40) REVERT: J 104 ASP cc_start: 0.8343 (t0) cc_final: 0.8118 (t0) REVERT: K 415 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8247 (mm-30) REVERT: K 476 VAL cc_start: 0.9162 (t) cc_final: 0.8921 (m) REVERT: L 382 TRP cc_start: 0.5343 (m100) cc_final: 0.5078 (m100) outliers start: 79 outliers final: 43 residues processed: 383 average time/residue: 0.1445 time to fit residues: 86.3086 Evaluate side-chains 326 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 388 GLU Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 365 LEU Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 155 HIS Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 92 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 68 optimal weight: 30.0000 chunk 190 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 159 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 55 optimal weight: 0.3980 chunk 167 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 430 HIS B 395 ASN C 385 GLN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS H 529 ASN ** K 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.176352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115312 restraints weight = 31198.393| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.94 r_work: 0.3349 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21169 Z= 0.171 Angle : 0.633 15.182 28996 Z= 0.321 Chirality : 0.046 0.450 3396 Planarity : 0.005 0.060 3701 Dihedral : 5.921 50.987 3089 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.06 % Allowed : 22.60 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.16), residues: 2603 helix: -2.10 (0.23), residues: 316 sheet: -1.38 (0.19), residues: 719 loop : -1.16 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 461 TYR 0.016 0.001 TYR M 196 PHE 0.020 0.002 PHE D 354 TRP 0.016 0.001 TRP F 418 HIS 0.007 0.001 HIS G 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (21118) covalent geometry : angle 0.59978 / 0.31 (28882) SS BOND : bond 0.00375 / 0.22 ( 39) SS BOND : angle 1.21150 / 0.91 ( 78) hydrogen bonds : bond 0.03934 / 2.71 ( 522) hydrogen bonds : angle 6.19614 / 4.24 ( 1518) link_BETA1-4 : bond 0.00367 / 0.19 ( 1) link_BETA1-4 : angle 1.48252 / 0.61 ( 3) link_NAG-ASN : bond 0.00656 / 0.34 ( 11) link_NAG-ASN : angle 5.76212 / 3.85 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 295 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7804 (p0) cc_final: 0.7580 (p0) REVERT: A 487 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8148 (tm-30) REVERT: B 462 GLU cc_start: 0.8287 (mp0) cc_final: 0.7993 (mt-10) REVERT: B 490 GLN cc_start: 0.8395 (tm130) cc_final: 0.7949 (tm-30) REVERT: D 450 HIS cc_start: 0.7890 (m170) cc_final: 0.7621 (m90) REVERT: E 354 PHE cc_start: 0.7681 (t80) cc_final: 0.7181 (t80) REVERT: E 364 LYS cc_start: 0.7445 (mmtt) cc_final: 0.7194 (tppt) REVERT: E 483 ASP cc_start: 0.7973 (p0) cc_final: 0.7626 (p0) REVERT: E 485 PHE cc_start: 0.8393 (t80) cc_final: 0.7514 (t80) REVERT: F 388 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: F 530 THR cc_start: 0.8676 (p) cc_final: 0.8446 (p) REVERT: H 525 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7440 (tm-30) REVERT: H 529 ASN cc_start: 0.8269 (m110) cc_final: 0.7279 (m110) REVERT: J 104 ASP cc_start: 0.8459 (t0) cc_final: 0.8143 (t0) REVERT: K 443 ARG cc_start: 0.5756 (ttp-110) cc_final: 0.5367 (ttp-110) REVERT: L 382 TRP cc_start: 0.5383 (m100) cc_final: 0.5095 (m100) outliers start: 95 outliers final: 68 residues processed: 369 average time/residue: 0.1333 time to fit residues: 76.4188 Evaluate side-chains 338 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 269 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 526 GLU Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 480 SER Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 413 ILE Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 221 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 28 optimal weight: 40.0000 chunk 23 optimal weight: 20.0000 chunk 167 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 490 GLN ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** K 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.174685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.112812 restraints weight = 31189.947| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.59 r_work: 0.3326 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21169 Z= 0.209 Angle : 0.643 15.224 28996 Z= 0.324 Chirality : 0.047 0.460 3396 Planarity : 0.005 0.061 3701 Dihedral : 5.795 49.691 3089 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 5.47 % Allowed : 21.32 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.16), residues: 2603 helix: -1.81 (0.25), residues: 316 sheet: -1.29 (0.19), residues: 730 loop : -1.17 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 461 TYR 0.016 0.002 TYR M 196 PHE 0.019 0.002 PHE A 354 TRP 0.034 0.001 TRP K 418 HIS 0.019 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (21118) covalent geometry : angle 0.61087 / 0.32 (28882) SS BOND : bond 0.00397 / 0.24 ( 39) SS BOND : angle 1.19305 / 0.86 ( 78) hydrogen bonds : bond 0.03645 / 2.51 ( 522) hydrogen bonds : angle 6.05356 / 4.13 ( 1518) link_BETA1-4 : bond 0.00134 / 0.07 ( 1) link_BETA1-4 : angle 1.39341 / 0.56 ( 3) link_NAG-ASN : bond 0.00632 / 0.31 ( 11) link_NAG-ASN : angle 5.77924 / 3.88 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 288 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 487 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8130 (tm-30) REVERT: B 462 GLU cc_start: 0.8327 (mp0) cc_final: 0.8091 (mt-10) REVERT: B 480 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.7947 (p) REVERT: B 490 GLN cc_start: 0.8412 (tm130) cc_final: 0.7941 (tm-30) REVERT: C 553 ASP cc_start: 0.8159 (t0) cc_final: 0.7737 (m-30) REVERT: D 450 HIS cc_start: 0.7949 (m170) cc_final: 0.7629 (m90) REVERT: D 468 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7688 (tm-30) REVERT: E 354 PHE cc_start: 0.7723 (t80) cc_final: 0.7253 (t80) REVERT: E 364 LYS cc_start: 0.7475 (mmtt) cc_final: 0.7235 (tppt) REVERT: E 483 ASP cc_start: 0.7850 (p0) cc_final: 0.7526 (p0) REVERT: E 485 PHE cc_start: 0.8398 (t80) cc_final: 0.7523 (t80) REVERT: F 388 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: H 382 TRP cc_start: 0.2856 (OUTLIER) cc_final: -0.0751 (m100) REVERT: H 525 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7539 (tm-30) REVERT: H 529 ASN cc_start: 0.8206 (m110) cc_final: 0.7255 (m110) REVERT: J 104 ASP cc_start: 0.8531 (t0) cc_final: 0.8183 (t0) REVERT: K 443 ARG cc_start: 0.5630 (ttp-110) cc_final: 0.5328 (ttp-110) REVERT: K 489 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8259 (mtp) REVERT: L 380 ILE cc_start: 0.4785 (OUTLIER) cc_final: 0.4196 (mt) REVERT: L 382 TRP cc_start: 0.5401 (m100) cc_final: 0.5069 (m100) REVERT: M 169 LEU cc_start: 0.8023 (tt) cc_final: 0.7675 (tp) outliers start: 128 outliers final: 87 residues processed: 394 average time/residue: 0.1357 time to fit residues: 84.1551 Evaluate side-chains 355 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 263 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 382 TRP Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 480 SER Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain L residue 413 ILE Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 201 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 104 optimal weight: 0.0980 chunk 74 optimal weight: 40.0000 chunk 212 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 140 optimal weight: 30.0000 chunk 155 optimal weight: 0.0980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 490 GLN ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN D 545 ASN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN H 430 HIS ** K 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.177524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.116750 restraints weight = 31173.550| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.62 r_work: 0.3393 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21169 Z= 0.119 Angle : 0.600 15.075 28996 Z= 0.300 Chirality : 0.045 0.430 3396 Planarity : 0.005 0.055 3701 Dihedral : 5.699 56.297 3089 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.49 % Allowed : 22.90 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.16), residues: 2603 helix: -1.55 (0.26), residues: 310 sheet: -1.09 (0.19), residues: 743 loop : -1.11 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 461 TYR 0.021 0.001 TYR J 62 PHE 0.024 0.001 PHE A 354 TRP 0.031 0.001 TRP K 418 HIS 0.005 0.001 HIS F 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (21118) covalent geometry : angle 0.56757 / 0.29 (28882) SS BOND : bond 0.00222 / 0.15 ( 39) SS BOND : angle 0.99672 / 0.74 ( 78) hydrogen bonds : bond 0.03272 / 2.26 ( 522) hydrogen bonds : angle 5.71002 / 3.91 ( 1518) link_BETA1-4 : bond 0.00269 / 0.14 ( 1) link_BETA1-4 : angle 1.08870 / 0.46 ( 3) link_NAG-ASN : bond 0.00722 / 0.36 ( 11) link_NAG-ASN : angle 5.66243 / 3.79 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 320 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7683 (p0) cc_final: 0.7270 (p0) REVERT: A 455 TYR cc_start: 0.8288 (m-80) cc_final: 0.7936 (m-80) REVERT: A 570 ASP cc_start: 0.8499 (t0) cc_final: 0.7778 (t0) REVERT: B 354 PHE cc_start: 0.8132 (t80) cc_final: 0.7769 (t80) REVERT: B 462 GLU cc_start: 0.8265 (mp0) cc_final: 0.7971 (mt-10) REVERT: B 490 GLN cc_start: 0.8478 (tm130) cc_final: 0.7960 (tm-30) REVERT: C 553 ASP cc_start: 0.8130 (t0) cc_final: 0.7699 (m-30) REVERT: D 450 HIS cc_start: 0.7987 (m170) cc_final: 0.7655 (m170) REVERT: D 466 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8442 (mp) REVERT: D 468 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7625 (tm-30) REVERT: E 354 PHE cc_start: 0.7514 (t80) cc_final: 0.7248 (t80) REVERT: E 364 LYS cc_start: 0.7438 (mmtt) cc_final: 0.7210 (tppt) REVERT: E 483 ASP cc_start: 0.7910 (p0) cc_final: 0.7602 (p0) REVERT: E 485 PHE cc_start: 0.8335 (t80) cc_final: 0.7505 (t80) REVERT: F 388 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8188 (tp30) REVERT: F 541 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7869 (mp0) REVERT: G 545 ASN cc_start: 0.8612 (t0) cc_final: 0.8264 (t0) REVERT: H 525 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7771 (tm-30) REVERT: H 534 TYR cc_start: 0.8357 (m-80) cc_final: 0.8142 (m-10) REVERT: J 16 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.7943 (ttp80) REVERT: J 104 ASP cc_start: 0.8580 (t0) cc_final: 0.8178 (t0) REVERT: J 123 MET cc_start: 0.8455 (mmm) cc_final: 0.8239 (mmm) REVERT: K 443 ARG cc_start: 0.5668 (ttp-110) cc_final: 0.5376 (ttp-110) REVERT: K 476 VAL cc_start: 0.9130 (t) cc_final: 0.8891 (m) REVERT: K 489 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8248 (mtp) REVERT: K 508 GLU cc_start: 0.7464 (tp30) cc_final: 0.7173 (tt0) REVERT: L 380 ILE cc_start: 0.4961 (OUTLIER) cc_final: 0.4519 (mt) REVERT: L 382 TRP cc_start: 0.5415 (m100) cc_final: 0.5101 (m100) REVERT: L 532 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7211 (mp0) outliers start: 105 outliers final: 67 residues processed: 407 average time/residue: 0.1300 time to fit residues: 82.4875 Evaluate side-chains 358 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 286 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 480 SER Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 532 GLU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 157 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 chunk 249 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 255 optimal weight: 0.0670 chunk 90 optimal weight: 0.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 490 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** K 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.172997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.114295 restraints weight = 30199.620| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.37 r_work: 0.3347 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21169 Z= 0.216 Angle : 0.648 14.970 28996 Z= 0.324 Chirality : 0.047 0.476 3396 Planarity : 0.005 0.057 3701 Dihedral : 5.687 55.909 3088 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 5.08 % Allowed : 22.98 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.16), residues: 2603 helix: -1.50 (0.27), residues: 311 sheet: -1.05 (0.19), residues: 732 loop : -1.09 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 190 TYR 0.020 0.002 TYR F 534 PHE 0.019 0.002 PHE D 354 TRP 0.017 0.001 TRP F 418 HIS 0.006 0.001 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (21118) covalent geometry : angle 0.61630 / 0.32 (28882) SS BOND : bond 0.00427 / 0.27 ( 39) SS BOND : angle 1.17888 / 0.85 ( 78) hydrogen bonds : bond 0.03432 / 2.35 ( 522) hydrogen bonds : angle 5.82244 / 3.99 ( 1518) link_BETA1-4 : bond 0.00169 / 0.09 ( 1) link_BETA1-4 : angle 1.47748 / 0.57 ( 3) link_NAG-ASN : bond 0.00653 / 0.32 ( 11) link_NAG-ASN : angle 5.71016 / 3.84 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 278 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7674 (p0) cc_final: 0.7202 (p0) REVERT: A 455 TYR cc_start: 0.8301 (m-80) cc_final: 0.7847 (m-80) REVERT: A 487 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8093 (tm-30) REVERT: B 462 GLU cc_start: 0.8365 (mp0) cc_final: 0.8091 (mt-10) REVERT: B 480 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.8020 (p) REVERT: B 490 GLN cc_start: 0.8429 (tm130) cc_final: 0.7968 (tm-30) REVERT: B 491 ARG cc_start: 0.8492 (ttm110) cc_final: 0.8176 (ttm110) REVERT: C 475 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8290 (pt) REVERT: C 553 ASP cc_start: 0.8119 (t0) cc_final: 0.7653 (m-30) REVERT: D 450 HIS cc_start: 0.7975 (m170) cc_final: 0.7615 (m170) REVERT: D 466 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8567 (mp) REVERT: E 354 PHE cc_start: 0.7552 (t80) cc_final: 0.7241 (t80) REVERT: E 364 LYS cc_start: 0.7442 (mmtt) cc_final: 0.7175 (tppt) REVERT: E 483 ASP cc_start: 0.7876 (p0) cc_final: 0.7571 (p0) REVERT: E 485 PHE cc_start: 0.8383 (t80) cc_final: 0.7519 (t80) REVERT: F 388 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: F 410 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.5714 (mp0) REVERT: H 382 TRP cc_start: 0.3178 (OUTLIER) cc_final: -0.0326 (m100) REVERT: J 16 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.7868 (ttp80) REVERT: J 104 ASP cc_start: 0.8644 (t0) cc_final: 0.8238 (t0) REVERT: K 379 THR cc_start: 0.4537 (OUTLIER) cc_final: 0.4289 (m) REVERT: K 415 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8188 (mm-30) REVERT: K 489 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8207 (mtp) REVERT: K 508 GLU cc_start: 0.7597 (tp30) cc_final: 0.7315 (tt0) REVERT: L 380 ILE cc_start: 0.4987 (OUTLIER) cc_final: 0.3831 (mt) REVERT: L 382 TRP cc_start: 0.5494 (m100) cc_final: 0.4938 (m100) REVERT: L 532 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: M 318 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8272 (mp0) outliers start: 119 outliers final: 87 residues processed: 380 average time/residue: 0.1289 time to fit residues: 76.4376 Evaluate side-chains 356 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 258 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 382 TRP Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 379 THR Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 413 ILE Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 532 GLU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 205 optimal weight: 0.2980 chunk 133 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 257 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 246 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 430 HIS A 490 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.175327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.117420 restraints weight = 30343.559| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.58 r_work: 0.3362 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21169 Z= 0.135 Angle : 0.610 15.155 28996 Z= 0.304 Chirality : 0.046 0.440 3396 Planarity : 0.005 0.054 3701 Dihedral : 5.550 58.252 3088 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.66 % Allowed : 23.02 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.16), residues: 2603 helix: -1.44 (0.26), residues: 321 sheet: -0.93 (0.19), residues: 741 loop : -1.05 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 190 TYR 0.020 0.001 TYR F 500 PHE 0.029 0.002 PHE A 354 TRP 0.018 0.001 TRP F 418 HIS 0.006 0.001 HIS G 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (21118) covalent geometry : angle 0.57802 / 0.30 (28882) SS BOND : bond 0.00244 / 0.17 ( 39) SS BOND : angle 0.94340 / 0.68 ( 78) hydrogen bonds : bond 0.03170 / 2.20 ( 522) hydrogen bonds : angle 5.55774 / 3.80 ( 1518) link_BETA1-4 : bond 0.00198 / 0.10 ( 1) link_BETA1-4 : angle 1.04175 / 0.44 ( 3) link_NAG-ASN : bond 0.00708 / 0.34 ( 11) link_NAG-ASN : angle 5.66159 / 3.80 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 299 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7776 (p0) cc_final: 0.7284 (p0) REVERT: A 455 TYR cc_start: 0.8291 (m-80) cc_final: 0.7799 (m-80) REVERT: A 487 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8064 (tm-30) REVERT: A 570 ASP cc_start: 0.8561 (t0) cc_final: 0.7896 (t0) REVERT: B 354 PHE cc_start: 0.8069 (t80) cc_final: 0.7672 (t80) REVERT: B 462 GLU cc_start: 0.8275 (mp0) cc_final: 0.7999 (mt-10) REVERT: B 480 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7865 (p) REVERT: B 490 GLN cc_start: 0.8461 (tm130) cc_final: 0.7789 (tm-30) REVERT: B 491 ARG cc_start: 0.8466 (ttm110) cc_final: 0.8105 (ttm110) REVERT: C 363 THR cc_start: 0.7620 (m) cc_final: 0.6390 (m) REVERT: D 450 HIS cc_start: 0.7959 (m170) cc_final: 0.7596 (m170) REVERT: D 466 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8495 (mp) REVERT: E 354 PHE cc_start: 0.7364 (t80) cc_final: 0.7112 (t80) REVERT: E 364 LYS cc_start: 0.7422 (mmtt) cc_final: 0.7175 (tppt) REVERT: E 483 ASP cc_start: 0.7822 (p0) cc_final: 0.7530 (p0) REVERT: E 485 PHE cc_start: 0.8330 (t80) cc_final: 0.7437 (t80) REVERT: F 388 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8198 (tp30) REVERT: H 529 ASN cc_start: 0.8260 (m110) cc_final: 0.7685 (m110) REVERT: J 16 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.7878 (ttp80) REVERT: J 71 CYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5537 (m) REVERT: J 104 ASP cc_start: 0.8582 (t0) cc_final: 0.8148 (t0) REVERT: K 379 THR cc_start: 0.4412 (OUTLIER) cc_final: 0.4169 (m) REVERT: K 415 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8203 (mm-30) REVERT: K 476 VAL cc_start: 0.9116 (t) cc_final: 0.8852 (m) REVERT: K 489 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8316 (mtp) REVERT: K 508 GLU cc_start: 0.7566 (tp30) cc_final: 0.7268 (tt0) REVERT: L 380 ILE cc_start: 0.4971 (OUTLIER) cc_final: 0.4441 (mt) REVERT: L 382 TRP cc_start: 0.5502 (m100) cc_final: 0.5147 (m100) REVERT: L 532 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: M 246 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7179 (tp) outliers start: 109 outliers final: 79 residues processed: 394 average time/residue: 0.1266 time to fit residues: 77.8229 Evaluate side-chains 367 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 278 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 529 ASN Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 379 THR Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 480 SER Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 532 GLU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 158 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 166 optimal weight: 0.0370 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 HIS A 490 GLN B 385 GLN C 385 GLN ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN F 490 GLN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.175689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.114188 restraints weight = 31044.356| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.62 r_work: 0.3359 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 21169 Z= 0.165 Angle : 0.625 14.887 28996 Z= 0.312 Chirality : 0.046 0.461 3396 Planarity : 0.005 0.054 3701 Dihedral : 5.478 59.079 3084 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 5.00 % Allowed : 22.85 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.16), residues: 2603 helix: -1.36 (0.26), residues: 322 sheet: -0.79 (0.19), residues: 703 loop : -1.05 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 514 TYR 0.024 0.002 TYR F 534 PHE 0.030 0.002 PHE A 354 TRP 0.023 0.001 TRP F 418 HIS 0.013 0.001 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (21118) covalent geometry : angle 0.59437 / 0.30 (28882) SS BOND : bond 0.00313 / 0.21 ( 39) SS BOND : angle 0.99616 / 0.73 ( 78) hydrogen bonds : bond 0.03198 / 2.20 ( 522) hydrogen bonds : angle 5.55217 / 3.80 ( 1518) link_BETA1-4 : bond 0.00222 / 0.12 ( 1) link_BETA1-4 : angle 1.28206 / 0.52 ( 3) link_NAG-ASN : bond 0.00678 / 0.34 ( 11) link_NAG-ASN : angle 5.62757 / 3.79 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 283 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7828 (p0) cc_final: 0.7372 (p0) REVERT: A 455 TYR cc_start: 0.8329 (m-80) cc_final: 0.7876 (m-80) REVERT: A 487 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8122 (tm-30) REVERT: A 570 ASP cc_start: 0.8596 (t0) cc_final: 0.7943 (t0) REVERT: B 354 PHE cc_start: 0.8136 (t80) cc_final: 0.7740 (t80) REVERT: B 462 GLU cc_start: 0.8326 (mp0) cc_final: 0.8052 (mt-10) REVERT: B 480 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.7903 (p) REVERT: B 490 GLN cc_start: 0.8426 (tm130) cc_final: 0.7884 (tm-30) REVERT: B 491 ARG cc_start: 0.8466 (ttm110) cc_final: 0.8170 (ttm110) REVERT: C 475 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8283 (pt) REVERT: C 529 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8529 (m110) REVERT: D 450 HIS cc_start: 0.8026 (m170) cc_final: 0.7666 (m170) REVERT: D 466 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8557 (mp) REVERT: D 468 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7614 (tm-30) REVERT: E 354 PHE cc_start: 0.7422 (t80) cc_final: 0.7156 (t80) REVERT: E 364 LYS cc_start: 0.7429 (mmtt) cc_final: 0.7125 (tppt) REVERT: E 483 ASP cc_start: 0.7834 (p0) cc_final: 0.7546 (p0) REVERT: E 485 PHE cc_start: 0.8361 (t80) cc_final: 0.7483 (t80) REVERT: F 388 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8216 (tp30) REVERT: H 382 TRP cc_start: 0.3168 (OUTLIER) cc_final: -0.0374 (m100) REVERT: H 529 ASN cc_start: 0.8254 (m110) cc_final: 0.7834 (m110) REVERT: J 16 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.7889 (ttp80) REVERT: J 71 CYS cc_start: 0.6081 (OUTLIER) cc_final: 0.5639 (m) REVERT: J 104 ASP cc_start: 0.8614 (t0) cc_final: 0.8192 (t0) REVERT: K 379 THR cc_start: 0.4510 (OUTLIER) cc_final: 0.4267 (m) REVERT: K 415 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8225 (mm-30) REVERT: K 489 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8238 (mtp) REVERT: K 500 TYR cc_start: 0.8596 (p90) cc_final: 0.7919 (p90) REVERT: K 508 GLU cc_start: 0.7593 (tp30) cc_final: 0.7284 (tt0) REVERT: L 380 ILE cc_start: 0.4905 (OUTLIER) cc_final: 0.4452 (mt) REVERT: L 532 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7243 (mp0) outliers start: 117 outliers final: 88 residues processed: 381 average time/residue: 0.1300 time to fit residues: 76.7360 Evaluate side-chains 374 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 274 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 382 TRP Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 379 THR Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 480 SER Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 532 GLU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 190 ARG Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 58 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 188 optimal weight: 3.9990 chunk 68 optimal weight: 30.0000 chunk 17 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 242 optimal weight: 0.0370 chunk 177 optimal weight: 0.0870 chunk 175 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 overall best weight: 0.9438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 490 GLN D 545 ASN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS H 463 GLN H 529 ASN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.176189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.114797 restraints weight = 30962.521| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.61 r_work: 0.3353 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21169 Z= 0.149 Angle : 0.632 14.975 28996 Z= 0.314 Chirality : 0.046 0.452 3396 Planarity : 0.005 0.066 3701 Dihedral : 5.472 59.552 3084 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.70 % Allowed : 23.32 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.16), residues: 2603 helix: -1.26 (0.27), residues: 321 sheet: -0.82 (0.19), residues: 719 loop : -1.04 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 461 TYR 0.023 0.001 TYR F 534 PHE 0.032 0.002 PHE A 354 TRP 0.035 0.001 TRP F 418 HIS 0.024 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (21118) covalent geometry : angle 0.60155 / 0.31 (28882) SS BOND : bond 0.00285 / 0.19 ( 39) SS BOND : angle 0.96008 / 0.70 ( 78) hydrogen bonds : bond 0.03155 / 2.17 ( 522) hydrogen bonds : angle 5.50089 / 3.77 ( 1518) link_BETA1-4 : bond 0.00332 / 0.17 ( 1) link_BETA1-4 : angle 1.20219 / 0.49 ( 3) link_NAG-ASN : bond 0.00699 / 0.34 ( 11) link_NAG-ASN : angle 5.62796 / 3.78 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 282 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7819 (p0) cc_final: 0.7352 (p0) REVERT: A 455 TYR cc_start: 0.8309 (m-80) cc_final: 0.7853 (m-80) REVERT: A 487 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8114 (tm-30) REVERT: A 570 ASP cc_start: 0.8557 (t0) cc_final: 0.7889 (t0) REVERT: B 354 PHE cc_start: 0.8099 (t80) cc_final: 0.7690 (t80) REVERT: B 462 GLU cc_start: 0.8274 (mp0) cc_final: 0.8001 (mt-10) REVERT: B 480 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.7894 (p) REVERT: B 490 GLN cc_start: 0.8479 (tm130) cc_final: 0.7776 (tm-30) REVERT: B 491 ARG cc_start: 0.8472 (ttm110) cc_final: 0.8095 (ttm110) REVERT: C 410 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6658 (pp20) REVERT: C 475 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8265 (pt) REVERT: C 529 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8550 (m110) REVERT: D 423 ARG cc_start: 0.8419 (mtp-110) cc_final: 0.8103 (mtp85) REVERT: D 450 HIS cc_start: 0.8028 (m170) cc_final: 0.7674 (m170) REVERT: D 466 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8568 (mp) REVERT: D 468 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7608 (tm-30) REVERT: E 364 LYS cc_start: 0.7419 (mmtt) cc_final: 0.7113 (tppt) REVERT: E 483 ASP cc_start: 0.7835 (p0) cc_final: 0.7424 (p0) REVERT: E 485 PHE cc_start: 0.8355 (t80) cc_final: 0.7470 (t80) REVERT: F 388 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8189 (tp30) REVERT: H 382 TRP cc_start: 0.3173 (OUTLIER) cc_final: -0.0362 (m100) REVERT: H 529 ASN cc_start: 0.8391 (m-40) cc_final: 0.7834 (m110) REVERT: J 16 ARG cc_start: 0.8392 (ttm-80) cc_final: 0.7889 (ttp80) REVERT: J 71 CYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5553 (m) REVERT: J 104 ASP cc_start: 0.8602 (t0) cc_final: 0.8167 (t0) REVERT: K 379 THR cc_start: 0.4441 (OUTLIER) cc_final: 0.4201 (m) REVERT: K 476 VAL cc_start: 0.9121 (t) cc_final: 0.8858 (m) REVERT: K 489 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8259 (mtp) REVERT: K 500 TYR cc_start: 0.8551 (p90) cc_final: 0.7855 (p90) REVERT: K 508 GLU cc_start: 0.7648 (tp30) cc_final: 0.7319 (tt0) REVERT: L 380 ILE cc_start: 0.4864 (OUTLIER) cc_final: 0.4359 (mt) REVERT: L 532 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7229 (mp0) outliers start: 110 outliers final: 86 residues processed: 374 average time/residue: 0.1271 time to fit residues: 74.4129 Evaluate side-chains 369 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 271 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 382 TRP Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 379 THR Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 480 SER Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 532 GLU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 190 ARG Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 64 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 226 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 HIS A 490 GLN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 GLN D 545 ASN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.175617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.114088 restraints weight = 31114.766| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.62 r_work: 0.3344 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21169 Z= 0.164 Angle : 0.641 14.923 28996 Z= 0.318 Chirality : 0.046 0.461 3396 Planarity : 0.005 0.057 3701 Dihedral : 5.486 59.264 3084 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.70 % Allowed : 23.41 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.17), residues: 2603 helix: -1.20 (0.27), residues: 321 sheet: -0.84 (0.19), residues: 729 loop : -1.01 (0.16), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 423 TYR 0.026 0.002 TYR F 534 PHE 0.019 0.002 PHE E 358 TRP 0.029 0.001 TRP F 418 HIS 0.013 0.001 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (21118) covalent geometry : angle 0.61140 / 0.31 (28882) SS BOND : bond 0.00317 / 0.21 ( 39) SS BOND : angle 0.99368 / 0.72 ( 78) hydrogen bonds : bond 0.03167 / 2.18 ( 522) hydrogen bonds : angle 5.46642 / 3.75 ( 1518) link_BETA1-4 : bond 0.00275 / 0.14 ( 1) link_BETA1-4 : angle 1.24590 / 0.50 ( 3) link_NAG-ASN : bond 0.00676 / 0.33 ( 11) link_NAG-ASN : angle 5.62005 / 3.78 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5206 Ramachandran restraints generated. 2603 Oldfield, 0 Emsley, 2603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 279 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7844 (p0) cc_final: 0.7361 (p0) REVERT: A 455 TYR cc_start: 0.8306 (m-80) cc_final: 0.7850 (m-80) REVERT: A 487 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8101 (tm-30) REVERT: B 354 PHE cc_start: 0.8120 (t80) cc_final: 0.7836 (t80) REVERT: B 462 GLU cc_start: 0.8285 (mp0) cc_final: 0.8021 (mt-10) REVERT: B 480 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.7943 (p) REVERT: B 490 GLN cc_start: 0.8385 (tm130) cc_final: 0.7440 (tm-30) REVERT: B 491 ARG cc_start: 0.8465 (ttm110) cc_final: 0.7992 (ttm110) REVERT: C 475 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8278 (pt) REVERT: C 529 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8577 (m110) REVERT: D 423 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.8071 (mtp85) REVERT: D 450 HIS cc_start: 0.8012 (m170) cc_final: 0.7656 (m170) REVERT: D 466 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8547 (mp) REVERT: D 468 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7597 (tm-30) REVERT: E 364 LYS cc_start: 0.7416 (mmtt) cc_final: 0.7110 (tppt) REVERT: E 483 ASP cc_start: 0.7773 (p0) cc_final: 0.7406 (p0) REVERT: E 485 PHE cc_start: 0.8347 (t80) cc_final: 0.7472 (t80) REVERT: F 388 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8210 (tp30) REVERT: F 410 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5865 (mp0) REVERT: H 382 TRP cc_start: 0.3232 (OUTLIER) cc_final: -0.0339 (m100) REVERT: H 529 ASN cc_start: 0.8479 (m-40) cc_final: 0.7962 (m110) REVERT: J 16 ARG cc_start: 0.8402 (ttm-80) cc_final: 0.7872 (ttp80) REVERT: J 71 CYS cc_start: 0.6100 (OUTLIER) cc_final: 0.5647 (m) REVERT: J 80 ASN cc_start: 0.8464 (m-40) cc_final: 0.7949 (m-40) REVERT: J 104 ASP cc_start: 0.8611 (t0) cc_final: 0.8194 (t0) REVERT: K 379 THR cc_start: 0.4456 (OUTLIER) cc_final: 0.4214 (m) REVERT: K 489 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8221 (mtp) REVERT: K 500 TYR cc_start: 0.8575 (p90) cc_final: 0.7899 (p90) REVERT: K 508 GLU cc_start: 0.7656 (tp30) cc_final: 0.7321 (tt0) REVERT: L 380 ILE cc_start: 0.4914 (OUTLIER) cc_final: 0.4406 (mt) REVERT: L 532 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7225 (mp0) outliers start: 110 outliers final: 93 residues processed: 371 average time/residue: 0.1247 time to fit residues: 72.3639 Evaluate side-chains 378 residues out of total 2341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 273 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 529 ASN Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 367 CYS Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 382 TRP Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 378 VAL Chi-restraints excluded: chain K residue 379 THR Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 480 SER Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 380 ILE Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 532 GLU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 160 TYR Chi-restraints excluded: chain M residue 163 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 190 ARG Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 34 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 145 optimal weight: 0.0870 chunk 111 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 131 optimal weight: 0.0980 chunk 147 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 518 HIS D 545 ASN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS K 419 ASN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.176922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115816 restraints weight = 31169.067| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.63 r_work: 0.3369 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21169 Z= 0.130 Angle : 0.630 14.898 28996 Z= 0.312 Chirality : 0.046 0.447 3396 Planarity : 0.005 0.056 3701 Dihedral : 5.427 56.193 3084 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.44 % Allowed : 23.79 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.17), residues: 2603 helix: -1.15 (0.27), residues: 321 sheet: -0.83 (0.19), residues: 732 loop : -0.98 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 105 TYR 0.026 0.001 TYR F 534 PHE 0.035 0.002 PHE A 354 TRP 0.044 0.001 TRP F 418 HIS 0.016 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (21118) covalent geometry : angle 0.60051 / 0.30 (28882) SS BOND : bond 0.00238 / 0.16 ( 39) SS BOND : angle 0.89553 / 0.65 ( 78) hydrogen bonds : bond 0.03064 / 2.12 ( 522) hydrogen bonds : angle 5.37392 / 3.68 ( 1518) link_BETA1-4 : bond 0.00335 / 0.18 ( 1) link_BETA1-4 : angle 1.12477 / 0.46 ( 3) link_NAG-ASN : bond 0.00726 / 0.36 ( 11) link_NAG-ASN : angle 5.57828 / 3.75 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5267.24 seconds wall clock time: 91 minutes 3.55 seconds (5463.55 seconds total)