Starting phenix.real_space_refine on Sat Jul 4 12:07:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r83_18993/07_2026/8r83_18993.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r83_18993/07_2026/8r83_18993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r83_18993/07_2026/8r83_18993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r83_18993/07_2026/8r83_18993.map" model { file = "/net/cci-nas-00/data/ceres_data/8r83_18993/07_2026/8r83_18993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r83_18993/07_2026/8r83_18993.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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 110 5.16 5 C 12818 2.51 5 N 3487 2.21 5 O 3998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20415 Number of models: 1 Model: "" Number of chains: 20 Chain: "N" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1686 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain: "B" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 208} Chain: "C" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1757 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 207} Chain: "D" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1757 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 207} Chain: "L" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 213} Chain: "K" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "H" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "G" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "A" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 213} Chain: "J" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain breaks: 1 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: "N" 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 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: "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: "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: "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 Time building chain proxies: 5.17, per 1000 atoms: 0.25 Number of scatterers: 20415 At special positions: 0 Unit cell: (72.756, 177.66, 202.194, 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 110 16.00 O 3998 8.00 N 3487 7.00 C 12818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS N 147 " - pdb=" SG CYS N 181 " distance=2.03 Simple disulfide: pdb=" SG CYS N 163 " - pdb=" SG CYS N 228 " distance=2.03 Simple disulfide: pdb=" SG CYS N 176 " - pdb=" SG CYS N 238 " distance=2.03 Simple disulfide: pdb=" SG CYS N 191 " - pdb=" SG CYS L 414 " distance=2.07 Simple disulfide: pdb=" SG CYS N 208 " - pdb=" SG CYS N 218 " distance=2.04 Simple disulfide: pdb=" SG CYS N 253 " - pdb=" SG CYS N 287 " distance=2.03 Simple disulfide: pdb=" SG CYS N 269 " - pdb=" SG CYS N 335 " distance=2.03 Simple disulfide: pdb=" SG CYS N 282 " - pdb=" SG CYS N 345 " distance=2.03 Simple disulfide: pdb=" SG CYS N 315 " - pdb=" SG CYS N 325 " 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.04 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 575 " - pdb=" SG CYS J 14 " distance=2.19 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 414 " - pdb=" SG CYS H 414 " distance=2.04 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 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 474 " - pdb=" SG CYS H 536 " distance=2.04 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 414 " - pdb=" SG CYS F 414 " distance=2.04 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 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 474 " - pdb=" SG CYS F 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 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=2.00 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " 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 B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 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 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 965.3 milliseconds 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4978 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 66 sheets defined 13.0% alpha, 42.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'N' and resid 168 through 180 removed outlier: 3.638A pdb=" N ALA N 172 " --> pdb=" O SER N 168 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU N 179 " --> pdb=" O VAL N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 285 removed outlier: 3.699A pdb=" N VAL N 280 " --> pdb=" O LYS N 276 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL N 281 " --> pdb=" O GLU N 277 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN N 284 " --> pdb=" O VAL N 280 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU N 285 " --> pdb=" O VAL N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 297 through 301 removed outlier: 3.683A pdb=" N CYS N 300 " --> pdb=" O ASP N 297 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR N 301 " --> pdb=" O ARG N 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 297 through 301' Processing helix chain 'N' and resid 321 through 325 Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.537A pdb=" N LEU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 531 removed outlier: 3.630A pdb=" N GLY B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.842A pdb=" N TRP C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 524 through 531 removed outlier: 3.705A pdb=" N GLY C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 419 removed outlier: 3.644A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 414 through 419' Processing helix chain 'D' and resid 460 through 467 Processing helix chain 'D' and resid 525 through 531 removed outlier: 3.862A pdb=" N GLY D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 361 removed outlier: 3.568A pdb=" N LEU L 359 " --> pdb=" O ALA L 355 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 419 removed outlier: 3.781A pdb=" N TRP L 418 " --> pdb=" O CYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 463 through 467 Processing helix chain 'L' and resid 496 through 498 No H-bonds generated for 'chain 'L' and resid 496 through 498' Processing helix chain 'L' and resid 524 through 531 removed outlier: 3.530A pdb=" N GLY L 531 " --> pdb=" O GLU L 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 353 through 361 Processing helix chain 'K' and resid 414 through 420 removed outlier: 4.323A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 466 Processing helix chain 'K' and resid 496 through 498 No H-bonds generated for 'chain 'K' and resid 496 through 498' Processing helix chain 'K' and resid 525 through 530 Processing helix chain 'H' and resid 353 through 357 Processing helix chain 'H' and resid 414 through 420 removed outlier: 3.520A pdb=" N TRP H 418 " --> pdb=" O CYS H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 467 Processing helix chain 'H' and resid 524 through 530 Processing helix chain 'G' and resid 353 through 360 Processing helix chain 'G' and resid 414 through 421 removed outlier: 3.771A pdb=" N TRP G 418 " --> pdb=" O CYS G 414 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY G 421 " --> pdb=" O ASP G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 466 removed outlier: 3.981A pdb=" N LEU G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 531 removed outlier: 3.965A pdb=" N GLY G 531 " --> pdb=" O GLU G 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 361 Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.657A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 466 Processing helix chain 'E' and resid 524 through 529 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 415 through 421 removed outlier: 3.565A pdb=" N ASN F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER F 420 " --> pdb=" O ASP F 416 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY F 421 " --> pdb=" O ASP F 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 415 through 421' Processing helix chain 'F' and resid 460 through 467 Processing helix chain 'F' and resid 525 through 531 removed outlier: 3.979A pdb=" N GLY F 531 " --> pdb=" O GLU F 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 414 through 420 removed outlier: 3.676A pdb=" N TRP A 418 " --> pdb=" O CYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.696A pdb=" N LEU A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN A 465 " --> pdb=" O ARG A 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 465' Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.758A pdb=" N GLY A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 148 through 150 removed outlier: 3.563A pdb=" N ASP N 233 " --> pdb=" O ARG N 190 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN N 188 " --> pdb=" O TRP N 235 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU N 186 " --> pdb=" O GLU N 237 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 152 through 153 Processing sheet with id=AA3, first strand: chain 'N' and resid 243 through 248 removed outlier: 4.246A pdb=" N ASP N 243 " --> pdb=" O LEU N 260 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU N 257 " --> pdb=" O VAL N 268 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL N 268 " --> pdb=" O LEU N 257 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TRP N 309 " --> pdb=" O TRP N 265 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N SER N 267 " --> pdb=" O TRP N 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 347 removed outlier: 4.019A pdb=" N ARG B 346 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 370 " --> pdb=" O ARG B 346 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR B 370 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 407 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 411 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR B 363 " --> pdb=" O ILE B 413 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 347 removed outlier: 4.019A pdb=" N ARG B 346 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 370 " --> pdb=" O ARG B 346 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR B 370 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 407 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 410 " --> pdb=" O HIS B 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 380 through 383 removed outlier: 3.761A pdb=" N CYS B 426 " --> pdb=" O GLN B 439 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN B 439 " --> pdb=" O CYS B 426 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 428 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 437 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.552A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.552A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.524A pdb=" N VAL B 537 " --> pdb=" O GLN B 487 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 565 through 566 removed outlier: 3.545A pdb=" N SER B 569 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A 565 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N TYR J 62 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 567 " --> pdb=" O TYR J 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 346 through 348 removed outlier: 3.629A pdb=" N ASP C 371 " --> pdb=" O PHE C 405 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE C 405 " --> pdb=" O ASP C 371 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N SER C 406 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 397 " --> pdb=" O SER C 406 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 389 through 390 removed outlier: 4.351A pdb=" N TRP C 382 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR C 425 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN C 439 " --> pdb=" O CYS C 426 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 453 through 457 removed outlier: 6.125A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 453 through 457 removed outlier: 6.125A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB7, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.770A pdb=" N THR D 366 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR D 363 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE D 413 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N PHE D 405 " --> pdb=" O ASP D 371 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER D 406 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 397 " --> pdb=" O SER D 406 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 410 " --> pdb=" O HIS D 393 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 389 through 390 removed outlier: 3.908A pdb=" N TRP D 382 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE D 441 " --> pdb=" O PHE D 424 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.509A pdb=" N SER D 519 " --> pdb=" O CYS D 474 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 520 " --> pdb=" O VAL D 501 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 501 " --> pdb=" O ILE D 520 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.509A pdb=" N SER D 519 " --> pdb=" O CYS D 474 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 493 through 494 removed outlier: 3.525A pdb=" N GLN D 493 " --> pdb=" O GLN D 490 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS D 536 " --> pdb=" O ARG D 550 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 550 " --> pdb=" O CYS D 536 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 346 through 350 removed outlier: 4.102A pdb=" N THR L 366 " --> pdb=" O ILE L 350 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY L 409 " --> pdb=" O CYS L 367 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP L 371 " --> pdb=" O PHE L 405 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N PHE L 405 " --> pdb=" O ASP L 371 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 389 through 390 removed outlier: 4.485A pdb=" N TRP L 382 " --> pdb=" O VAL L 390 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR L 383 " --> pdb=" O THR L 425 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR L 425 " --> pdb=" O THR L 383 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 453 through 457 removed outlier: 6.046A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 453 through 457 removed outlier: 6.046A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 493 through 494 Processing sheet with id=AC8, first strand: chain 'H' and resid 561 through 567 removed outlier: 5.933A pdb=" N TYR K 562 " --> pdb=" O ASN H 563 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER H 565 " --> pdb=" O TYR K 562 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL K 564 " --> pdb=" O SER H 565 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL H 567 " --> pdb=" O VAL K 564 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU K 566 " --> pdb=" O VAL H 567 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TYR L 562 " --> pdb=" O ASN K 563 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N SER K 565 " --> pdb=" O TYR L 562 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL L 564 " --> pdb=" O SER K 565 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL K 567 " --> pdb=" O VAL L 564 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU L 566 " --> pdb=" O VAL K 567 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER L 569 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE J 32 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE J 22 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA J 15 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP J 9 " --> pdb=" O ALA J 15 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE J 17 " --> pdb=" O LEU J 7 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 574 through 575 Processing sheet with id=AD1, first strand: chain 'K' and resid 347 through 348 removed outlier: 6.191A pdb=" N LEU K 368 " --> pdb=" O GLY K 409 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLY K 409 " --> pdb=" O LEU K 368 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR K 370 " --> pdb=" O ALA K 407 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ALA K 407 " --> pdb=" O THR K 370 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU K 372 " --> pdb=" O PHE K 405 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA K 411 " --> pdb=" O LEU K 365 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR K 363 " --> pdb=" O ILE K 413 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 347 through 348 removed outlier: 6.191A pdb=" N LEU K 368 " --> pdb=" O GLY K 409 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLY K 409 " --> pdb=" O LEU K 368 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR K 370 " --> pdb=" O ALA K 407 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ALA K 407 " --> pdb=" O THR K 370 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU K 372 " --> pdb=" O PHE K 405 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 389 through 390 removed outlier: 3.687A pdb=" N VAL K 390 " --> pdb=" O TRP K 382 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TRP K 382 " --> pdb=" O VAL K 390 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN K 439 " --> pdb=" O CYS K 426 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL K 428 " --> pdb=" O LEU K 437 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU K 437 " --> pdb=" O VAL K 428 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.526A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE K 472 " --> pdb=" O LEU K 521 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY K 478 " --> pdb=" O TYR K 515 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 485 through 486 removed outlier: 3.507A pdb=" N PHE K 485 " --> pdb=" O ALA K 539 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 489 through 490 Processing sheet with id=AD7, first strand: chain 'K' and resid 534 through 535 removed outlier: 4.260A pdb=" N TYR K 534 " --> pdb=" O VAL K 552 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL K 552 " --> pdb=" O TYR K 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'H' and resid 346 through 350 removed outlier: 3.705A pdb=" N ARG H 346 " --> pdb=" O THR H 370 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR H 366 " --> pdb=" O ILE H 350 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS H 364 " --> pdb=" O ILE H 413 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE H 413 " --> pdb=" O LYS H 364 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N THR H 366 " --> pdb=" O ALA H 411 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA H 411 " --> pdb=" O THR H 366 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU H 368 " --> pdb=" O GLY H 409 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLY H 409 " --> pdb=" O LEU H 368 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N THR H 370 " --> pdb=" O ALA H 407 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA H 407 " --> pdb=" O THR H 370 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 389 through 390 removed outlier: 4.413A pdb=" N TRP H 382 " --> pdb=" O VAL H 390 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER H 381 " --> pdb=" O THR H 427 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE H 424 " --> pdb=" O ILE H 441 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN H 439 " --> pdb=" O CYS H 426 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.614A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.614A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 493 through 494 removed outlier: 3.611A pdb=" N ARG H 550 " --> pdb=" O CYS H 536 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 346 through 347 removed outlier: 3.836A pdb=" N ARG G 346 " --> pdb=" O THR G 370 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N THR G 370 " --> pdb=" O ALA G 407 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA G 407 " --> pdb=" O THR G 370 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA G 411 " --> pdb=" O LEU G 365 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 346 through 347 removed outlier: 3.836A pdb=" N ARG G 346 " --> pdb=" O THR G 370 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N THR G 370 " --> pdb=" O ALA G 407 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA G 407 " --> pdb=" O THR G 370 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 389 through 390 removed outlier: 4.284A pdb=" N TRP G 382 " --> pdb=" O VAL G 390 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR G 379 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE G 424 " --> pdb=" O ILE G 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS G 426 " --> pdb=" O GLN G 439 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN G 439 " --> pdb=" O CYS G 426 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL G 428 " --> pdb=" O LEU G 437 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU G 437 " --> pdb=" O VAL G 428 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.652A pdb=" N SER G 519 " --> pdb=" O CYS G 474 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 501 " --> pdb=" O ILE G 520 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.652A pdb=" N SER G 519 " --> pdb=" O CYS G 474 " (cutoff:3.500A) removed outlier: 6.080A 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 'G' and resid 493 through 494 Processing sheet with id=AF2, first strand: chain 'G' and resid 565 through 567 Processing sheet with id=AF3, first strand: chain 'E' and resid 346 through 348 removed outlier: 6.014A pdb=" N LEU E 368 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLY E 409 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR E 370 " --> pdb=" O ALA E 407 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA E 407 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA E 411 " --> pdb=" O LEU E 365 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 346 through 348 removed outlier: 6.014A pdb=" N LEU E 368 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLY E 409 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR E 370 " --> pdb=" O ALA E 407 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA E 407 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR E 404 " --> pdb=" O HIS E 400 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER E 406 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLU E 398 " --> pdb=" O SER E 406 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL E 408 " --> pdb=" O ILE E 396 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ILE E 396 " --> pdb=" O VAL E 408 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLU E 410 " --> pdb=" O THR E 394 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N THR E 394 " --> pdb=" O GLU E 410 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 379 through 383 removed outlier: 3.641A pdb=" N THR E 379 " --> pdb=" O THR E 429 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR E 429 " --> pdb=" O THR E 379 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER E 381 " --> pdb=" O THR E 427 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR E 383 " --> pdb=" O THR E 425 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR E 425 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN E 439 " --> pdb=" O CYS E 426 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL E 428 " --> pdb=" O LEU E 437 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.560A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.560A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AF9, first strand: chain 'F' and resid 347 through 350 removed outlier: 3.973A pdb=" N THR F 366 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS F 364 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE F 413 " --> pdb=" O LYS F 364 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR F 366 " --> pdb=" O ALA F 411 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA F 411 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU F 368 " --> pdb=" O GLY F 409 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY F 409 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR F 370 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ALA F 407 " --> pdb=" O THR F 370 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 379 through 383 removed outlier: 3.504A pdb=" N THR F 379 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 429 " --> pdb=" O THR F 379 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN F 439 " --> pdb=" O CYS F 426 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 453 through 457 removed outlier: 6.013A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE F 520 " --> pdb=" O VAL F 501 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 501 " --> pdb=" O ILE F 520 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 453 through 457 removed outlier: 6.013A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AG5, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.690A pdb=" N THR A 366 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR A 363 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS A 367 " --> pdb=" O GLY A 409 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLY A 409 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 371 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE A 405 " --> pdb=" O ASP A 371 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER A 406 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 389 through 390 removed outlier: 3.524A pdb=" N VAL A 390 " --> pdb=" O TRP A 382 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP A 382 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 425 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS A 426 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 439 " --> pdb=" O CYS A 426 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 428 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.630A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.630A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 516 " --> pdb=" O MET A 506 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.631A pdb=" N PHE A 485 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 74 through 77 Processing sheet with id=AH2, first strand: chain 'J' and resid 110 through 113 removed outlier: 3.591A pdb=" N ALA J 111 " --> pdb=" O THR J 126 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 116 through 117 removed outlier: 3.619A pdb=" N GLU J 120 " --> pdb=" O TYR J 117 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2019 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: 4.79 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6142 1.34 - 1.46: 4123 1.46 - 1.58: 10512 1.58 - 1.70: 1 1.70 - 1.82: 142 Bond restraints: 20920 Sorted by residual: bond pdb=" N VAL E 567 " pdb=" CA VAL E 567 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.18e-02 7.18e+03 1.33e+01 bond pdb=" N ILE A 413 " pdb=" CA ILE A 413 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.24e+01 bond pdb=" N ILE G 413 " pdb=" CA ILE G 413 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.14e-02 7.69e+03 1.23e+01 bond pdb=" CA PRO K 458 " pdb=" C PRO K 458 " ideal model delta sigma weight residual 1.514 1.533 -0.019 5.50e-03 3.31e+04 1.21e+01 bond pdb=" N VAL C 567 " pdb=" CA VAL C 567 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.19e-02 7.06e+03 1.20e+01 ... (remaining 20915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 24910 1.14 - 2.27: 2663 2.27 - 3.41: 905 3.41 - 4.55: 110 4.55 - 5.68: 26 Bond angle restraints: 28614 Sorted by residual: angle pdb=" C ALA J 132 " pdb=" CA ALA J 132 " pdb=" CB ALA J 132 " ideal model delta sigma weight residual 116.54 111.45 5.09 1.15e+00 7.56e-01 1.96e+01 angle pdb=" N LYS K 361 " pdb=" CA LYS K 361 " pdb=" C LYS K 361 " ideal model delta sigma weight residual 112.86 108.02 4.84 1.22e+00 6.72e-01 1.58e+01 angle pdb=" N VAL E 567 " pdb=" CA VAL E 567 " pdb=" C VAL E 567 " ideal model delta sigma weight residual 112.96 109.00 3.96 1.00e+00 1.00e+00 1.57e+01 angle pdb=" N THR E 530 " pdb=" CA THR E 530 " pdb=" C THR E 530 " ideal model delta sigma weight residual 113.30 108.15 5.15 1.34e+00 5.57e-01 1.48e+01 angle pdb=" CA ILE K 413 " pdb=" C ILE K 413 " pdb=" O ILE K 413 " ideal model delta sigma weight residual 121.09 117.96 3.13 8.20e-01 1.49e+00 1.46e+01 ... (remaining 28609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 11569 17.45 - 34.91: 966 34.91 - 52.36: 230 52.36 - 69.81: 60 69.81 - 87.26: 13 Dihedral angle restraints: 12838 sinusoidal: 5194 harmonic: 7644 Sorted by residual: dihedral pdb=" CB CYS N 191 " pdb=" SG CYS N 191 " pdb=" SG CYS L 414 " pdb=" CB CYS L 414 " ideal model delta sinusoidal sigma weight residual 93.00 41.37 51.63 1 1.00e+01 1.00e-02 3.64e+01 dihedral pdb=" CB CYS G 367 " pdb=" SG CYS G 367 " pdb=" SG CYS G 426 " pdb=" CB CYS G 426 " ideal model delta sinusoidal sigma weight residual 93.00 49.24 43.76 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS J 108 " pdb=" SG CYS J 108 " pdb=" SG CYS J 133 " pdb=" CB CYS J 133 " ideal model delta sinusoidal sigma weight residual 93.00 130.47 -37.47 1 1.00e+01 1.00e-02 1.98e+01 ... (remaining 12835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.280: 3347 0.280 - 0.559: 2 0.559 - 0.839: 0 0.839 - 1.118: 1 1.118 - 1.398: 1 Chirality restraints: 3351 Sorted by residual: 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 -1.00 -1.40 2.00e-01 2.50e+01 4.88e+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 -1.29 -1.11 2.00e-01 2.50e+01 3.09e+01 chirality pdb=" C1 NAG H 601 " pdb=" ND2 ASN H 563 " pdb=" C2 NAG H 601 " pdb=" O5 NAG H 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.82 0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 3348 not shown) Planarity restraints: 3682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 563 " -0.078 2.00e-02 2.50e+03 1.61e-01 3.23e+02 pdb=" CG ASN K 563 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN K 563 " -0.077 2.00e-02 2.50e+03 pdb=" ND2 ASN K 563 " 0.289 2.00e-02 2.50e+03 pdb=" C1 NAG K 601 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 563 " -0.110 2.00e-02 2.50e+03 1.25e-01 1.94e+02 pdb=" CG ASN C 563 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN C 563 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 563 " 0.205 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 48 " 0.108 2.00e-02 2.50e+03 1.16e-01 1.69e+02 pdb=" CG ASN J 48 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN J 48 " -0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN J 48 " -0.179 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.145 2.00e-02 2.50e+03 ... (remaining 3679 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2879 2.77 - 3.30: 18072 3.30 - 3.84: 30354 3.84 - 4.37: 34911 4.37 - 4.90: 61188 Nonbonded interactions: 147404 Sorted by model distance: nonbonded pdb=" ND2 ASN C 563 " pdb=" N2 NAG C 601 " model vdw 2.239 2.560 nonbonded pdb=" O SER G 353 " pdb=" OG SER G 356 " model vdw 2.283 3.040 nonbonded pdb=" OD1 ASN G 402 " pdb=" OG1 THR G 404 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASN F 402 " pdb=" OG1 THR F 404 " model vdw 2.297 3.040 nonbonded pdb=" OD1 ASN C 402 " pdb=" OG1 THR C 404 " model vdw 2.319 3.040 ... (remaining 147399 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 568) selection = (chain 'B' and resid 345 through 568) selection = (chain 'C' and resid 345 through 568) selection = (chain 'D' and resid 345 through 568) selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 345 through 568) selection = (chain 'H' and resid 345 through 568) selection = (chain 'K' and resid 345 through 568) selection = (chain 'L' and resid 345 through 568) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 22.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.580 Find NCS groups from input model: 0.490 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: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.158 20966 Z= 0.511 Angle : 0.946 36.122 28714 Z= 0.588 Chirality : 0.068 1.398 3351 Planarity : 0.006 0.118 3675 Dihedral : 13.920 87.263 7746 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.13 % Allowed : 17.59 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.06 (0.16), residues: 2582 helix: -0.76 (0.31), residues: 252 sheet: 0.94 (0.17), residues: 919 loop : -0.37 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 546 TYR 0.014 0.001 TYR L 515 PHE 0.029 0.001 PHE H 354 TRP 0.012 0.001 TRP K 418 HIS 0.007 0.001 HIS H 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.51 (20920) covalent geometry : angle 0.81763 / 0.57 (28614) SS BOND : bond 0.02691 / 0.91 ( 38) SS BOND : angle 1.13411 / 0.86 ( 76) hydrogen bonds : bond 0.29130 / 19.38 ( 648) hydrogen bonds : angle 9.24858 / 6.45 ( 2019) link_BETA1-4 : bond 0.02198 / 1.16 ( 1) link_BETA1-4 : angle 4.42802 / 2.32 ( 3) link_NAG-ASN : bond 0.04310 / 2.41 ( 7) link_NAG-ASN : angle 17.46076 / 12.51 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 284 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 154 LYS cc_start: 0.6512 (tttm) cc_final: 0.6085 (mmtm) REVERT: N 214 THR cc_start: 0.4991 (m) cc_final: 0.4160 (t) REVERT: B 489 MET cc_start: 0.7942 (mtp) cc_final: 0.7604 (mtt) REVERT: B 506 MET cc_start: 0.5631 (mtt) cc_final: 0.5347 (mtm) REVERT: B 532 GLU cc_start: 0.7692 (mp0) cc_final: 0.6914 (mp0) REVERT: C 451 ARG cc_start: 0.7098 (ptp90) cc_final: 0.6523 (ptm-80) REVERT: D 384 ARG cc_start: 0.6469 (mtt180) cc_final: 0.6237 (ttm170) REVERT: D 568 MET cc_start: 0.6412 (ptp) cc_final: 0.6047 (pmm) REVERT: H 415 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6916 (tm-30) REVERT: H 558 LYS cc_start: 0.7733 (mtpp) cc_final: 0.7399 (mtmm) REVERT: E 451 ARG cc_start: 0.7582 (ptp-110) cc_final: 0.7185 (ptm-80) REVERT: F 393 HIS cc_start: 0.7151 (t70) cc_final: 0.6814 (t70) REVERT: F 450 HIS cc_start: 0.7078 (m-70) cc_final: 0.6394 (m-70) REVERT: F 544 PRO cc_start: 0.5474 (Cg_exo) cc_final: 0.5273 (Cg_endo) REVERT: J 70 LYS cc_start: 0.5117 (mttm) cc_final: 0.4915 (mtmt) outliers start: 3 outliers final: 1 residues processed: 286 average time/residue: 0.1849 time to fit residues: 77.0053 Evaluate side-chains 191 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 568 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 465 ASN D 545 ASN L 545 ASN ** K 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 HIS F 518 HIS A 465 ASN J 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.243108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.183937 restraints weight = 26263.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.183118 restraints weight = 37479.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.179881 restraints weight = 36190.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.179490 restraints weight = 34788.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.179732 restraints weight = 31691.672| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20966 Z= 0.188 Angle : 0.647 20.939 28714 Z= 0.330 Chirality : 0.046 0.180 3351 Planarity : 0.005 0.071 3675 Dihedral : 4.136 53.242 2975 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.67 % Allowed : 16.90 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.38 (0.16), residues: 2582 helix: -0.05 (0.32), residues: 253 sheet: 1.18 (0.17), residues: 933 loop : -0.30 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 467 TYR 0.012 0.001 TYR L 562 PHE 0.030 0.002 PHE H 424 TRP 0.016 0.001 TRP N 235 HIS 0.010 0.001 HIS F 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (20920) covalent geometry : angle 0.61088 / 0.32 (28614) SS BOND : bond 0.00706 / 0.47 ( 38) SS BOND : angle 1.28646 / 0.90 ( 76) hydrogen bonds : bond 0.05015 / 3.34 ( 648) hydrogen bonds : angle 6.27053 / 4.35 ( 2019) link_BETA1-4 : bond 0.01280 / 0.67 ( 1) link_BETA1-4 : angle 1.61068 / 0.87 ( 3) link_NAG-ASN : bond 0.00621 / 0.31 ( 7) link_NAG-ASN : angle 7.60768 / 5.53 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 197 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: N 201 ILE cc_start: 0.8025 (mt) cc_final: 0.7774 (mt) REVERT: B 489 MET cc_start: 0.7701 (mtp) cc_final: 0.7476 (mtt) REVERT: H 415 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: G 418 TRP cc_start: 0.7475 (t-100) cc_final: 0.7065 (t-100) REVERT: E 416 ASP cc_start: 0.7535 (p0) cc_final: 0.6912 (p0) REVERT: F 568 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6677 (tmm) REVERT: J 70 LYS cc_start: 0.7122 (mttm) cc_final: 0.6912 (mtmt) outliers start: 62 outliers final: 25 residues processed: 247 average time/residue: 0.1749 time to fit residues: 64.0371 Evaluate side-chains 193 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 561 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 170 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 465 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN H 419 ASN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.195419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127137 restraints weight = 24765.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.119546 restraints weight = 23338.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121889 restraints weight = 20321.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122564 restraints weight = 16006.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122960 restraints weight = 14657.493| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20966 Z= 0.168 Angle : 0.594 14.939 28714 Z= 0.305 Chirality : 0.046 0.285 3351 Planarity : 0.005 0.056 3675 Dihedral : 3.910 25.316 2972 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.32 % Allowed : 17.63 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.41 (0.16), residues: 2582 helix: -0.03 (0.32), residues: 264 sheet: 1.26 (0.17), residues: 953 loop : -0.36 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 451 TYR 0.014 0.001 TYR F 515 PHE 0.022 0.002 PHE B 516 TRP 0.026 0.001 TRP E 418 HIS 0.010 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (20920) covalent geometry : angle 0.57201 / 0.30 (28614) SS BOND : bond 0.00487 / 0.36 ( 38) SS BOND : angle 1.27138 / 0.92 ( 76) hydrogen bonds : bond 0.04303 / 2.84 ( 648) hydrogen bonds : angle 5.69569 / 3.95 ( 2019) link_BETA1-4 : bond 0.01146 / 0.60 ( 1) link_BETA1-4 : angle 1.48239 / 0.78 ( 3) link_NAG-ASN : bond 0.00556 / 0.28 ( 7) link_NAG-ASN : angle 5.58945 / 3.89 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 182 time to evaluate : 0.817 Fit side-chains REVERT: N 154 LYS cc_start: 0.6600 (tttm) cc_final: 0.6024 (mmtm) REVERT: N 178 GLN cc_start: 0.6137 (OUTLIER) cc_final: 0.5898 (tp40) REVERT: B 423 ARG cc_start: 0.8351 (mtm110) cc_final: 0.7608 (mtm110) REVERT: B 489 MET cc_start: 0.8124 (mtp) cc_final: 0.7813 (mtt) REVERT: L 545 ASN cc_start: 0.6720 (OUTLIER) cc_final: 0.6437 (t0) REVERT: K 359 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.6005 (mm) REVERT: G 418 TRP cc_start: 0.7580 (t-100) cc_final: 0.6445 (t-100) REVERT: F 568 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6381 (tmm) REVERT: A 545 ASN cc_start: 0.7199 (t0) cc_final: 0.6824 (t0) outliers start: 54 outliers final: 34 residues processed: 222 average time/residue: 0.1735 time to fit residues: 57.3438 Evaluate side-chains 198 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 516 PHE Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 545 ASN Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 568 MET Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 83 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 133 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 400 HIS ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 GLN A 540 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.193832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.126107 restraints weight = 24838.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120287 restraints weight = 25062.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122670 restraints weight = 21754.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123163 restraints weight = 16261.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123478 restraints weight = 15208.142| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20966 Z= 0.172 Angle : 0.582 14.776 28714 Z= 0.297 Chirality : 0.045 0.275 3351 Planarity : 0.005 0.051 3675 Dihedral : 4.001 38.197 2972 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.84 % Allowed : 17.85 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.38 (0.16), residues: 2582 helix: -0.05 (0.32), residues: 263 sheet: 1.23 (0.17), residues: 957 loop : -0.38 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 451 TYR 0.016 0.001 TYR F 515 PHE 0.021 0.002 PHE K 516 TRP 0.021 0.001 TRP E 418 HIS 0.007 0.001 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.17 (20920) covalent geometry : angle 0.56107 / 0.29 (28614) SS BOND : bond 0.00473 / 0.36 ( 38) SS BOND : angle 1.49416 / 1.08 ( 76) hydrogen bonds : bond 0.03865 / 2.54 ( 648) hydrogen bonds : angle 5.47469 / 3.80 ( 2019) link_BETA1-4 : bond 0.00871 / 0.46 ( 1) link_BETA1-4 : angle 1.37768 / 0.72 ( 3) link_NAG-ASN : bond 0.00443 / 0.23 ( 7) link_NAG-ASN : angle 5.04926 / 3.51 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 172 time to evaluate : 0.822 Fit side-chains REVERT: N 154 LYS cc_start: 0.6586 (tttm) cc_final: 0.6093 (mmtm) REVERT: N 178 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.6072 (tt0) REVERT: B 441 ILE cc_start: 0.6525 (OUTLIER) cc_final: 0.6319 (pp) REVERT: B 489 MET cc_start: 0.8108 (mtp) cc_final: 0.7708 (mtt) REVERT: L 549 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: K 359 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5994 (mm) REVERT: K 489 MET cc_start: 0.8812 (mtm) cc_final: 0.8556 (mtp) REVERT: H 495 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7691 (mp) REVERT: G 418 TRP cc_start: 0.7723 (t-100) cc_final: 0.6552 (t-100) REVERT: E 350 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7697 (pt) REVERT: F 527 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: F 568 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6483 (tmm) REVERT: A 545 ASN cc_start: 0.7332 (t0) cc_final: 0.6773 (t0) outliers start: 66 outliers final: 46 residues processed: 224 average time/residue: 0.1507 time to fit residues: 51.1228 Evaluate side-chains 218 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 516 PHE Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 552 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 568 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 450 HIS Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 83 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 163 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 465 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN K 487 GLN ** H 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS F 487 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.192955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.126240 restraints weight = 25087.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.117280 restraints weight = 23200.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119510 restraints weight = 21130.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120036 restraints weight = 16766.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120614 restraints weight = 15160.851| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20966 Z= 0.184 Angle : 0.594 14.259 28714 Z= 0.303 Chirality : 0.046 0.258 3351 Planarity : 0.005 0.048 3675 Dihedral : 4.131 42.348 2972 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.53 % Allowed : 18.19 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.36 (0.16), residues: 2582 helix: -0.13 (0.32), residues: 265 sheet: 1.24 (0.17), residues: 963 loop : -0.41 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 451 TYR 0.017 0.001 TYR F 515 PHE 0.023 0.002 PHE K 516 TRP 0.015 0.001 TRP E 418 HIS 0.013 0.001 HIS E 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.18 (20920) covalent geometry : angle 0.57465 / 0.30 (28614) SS BOND : bond 0.00526 / 0.34 ( 38) SS BOND : angle 1.58059 / 1.19 ( 76) hydrogen bonds : bond 0.03885 / 2.56 ( 648) hydrogen bonds : angle 5.39291 / 3.75 ( 2019) link_BETA1-4 : bond 0.00705 / 0.37 ( 1) link_BETA1-4 : angle 1.33159 / 0.70 ( 3) link_NAG-ASN : bond 0.00491 / 0.25 ( 7) link_NAG-ASN : angle 4.73422 / 3.29 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 169 time to evaluate : 0.813 Fit side-chains REVERT: N 154 LYS cc_start: 0.6808 (tttm) cc_final: 0.6125 (mmtm) REVERT: N 178 GLN cc_start: 0.6266 (OUTLIER) cc_final: 0.5924 (tt0) REVERT: N 193 LYS cc_start: 0.3647 (mmpt) cc_final: 0.3337 (pttt) REVERT: B 423 ARG cc_start: 0.8375 (mtm110) cc_final: 0.7621 (mtm110) REVERT: B 489 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7729 (mtt) REVERT: B 506 MET cc_start: 0.6403 (mtt) cc_final: 0.6051 (mtm) REVERT: C 525 GLU cc_start: 0.7243 (mm-30) cc_final: 0.7027 (tp30) REVERT: D 499 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8412 (tptm) REVERT: L 549 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7022 (tt0) REVERT: K 364 LYS cc_start: 0.6732 (ptpp) cc_final: 0.6115 (ptpp) REVERT: K 516 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8738 (p90) REVERT: H 415 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7637 (tm-30) REVERT: H 423 ARG cc_start: 0.8632 (mtt180) cc_final: 0.7530 (ptm-80) REVERT: H 483 ASP cc_start: 0.7765 (t0) cc_final: 0.7515 (t0) REVERT: H 495 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7683 (mp) REVERT: G 418 TRP cc_start: 0.7735 (t-100) cc_final: 0.6589 (t-100) REVERT: E 350 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7812 (pt) REVERT: E 568 MET cc_start: 0.7007 (tpp) cc_final: 0.5994 (mtt) REVERT: F 527 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: A 545 ASN cc_start: 0.7492 (t0) cc_final: 0.6897 (t0) REVERT: J 23 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6565 (tpp-160) REVERT: J 105 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6240 (mtm110) outliers start: 82 outliers final: 49 residues processed: 235 average time/residue: 0.1603 time to fit residues: 57.0797 Evaluate side-chains 227 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 168 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 516 PHE Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 552 VAL Chi-restraints excluded: chain K residue 560 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 105 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 247 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 103 optimal weight: 0.0770 chunk 109 optimal weight: 0.8980 chunk 241 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 59 optimal weight: 0.0170 chunk 157 optimal weight: 9.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN F 487 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.196463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127929 restraints weight = 24733.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120182 restraints weight = 23136.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121644 restraints weight = 21407.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122076 restraints weight = 17683.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.122237 restraints weight = 16341.815| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20966 Z= 0.108 Angle : 0.533 13.805 28714 Z= 0.270 Chirality : 0.044 0.258 3351 Planarity : 0.004 0.044 3675 Dihedral : 3.873 42.195 2972 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.71 % Allowed : 18.88 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.54 (0.16), residues: 2582 helix: -0.14 (0.31), residues: 267 sheet: 1.40 (0.17), residues: 963 loop : -0.28 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 190 TYR 0.015 0.001 TYR J 101 PHE 0.021 0.001 PHE H 424 TRP 0.014 0.001 TRP N 202 HIS 0.004 0.001 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (20920) covalent geometry : angle 0.51480 / 0.27 (28614) SS BOND : bond 0.00418 / 0.29 ( 38) SS BOND : angle 1.42617 / 1.04 ( 76) hydrogen bonds : bond 0.03092 / 2.03 ( 648) hydrogen bonds : angle 5.05324 / 3.51 ( 2019) link_BETA1-4 : bond 0.00466 / 0.25 ( 1) link_BETA1-4 : angle 1.38180 / 0.72 ( 3) link_NAG-ASN : bond 0.00539 / 0.27 ( 7) link_NAG-ASN : angle 4.36638 / 2.98 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 174 time to evaluate : 0.784 Fit side-chains REVERT: N 154 LYS cc_start: 0.6832 (tttm) cc_final: 0.6126 (mmtm) REVERT: N 178 GLN cc_start: 0.6244 (OUTLIER) cc_final: 0.5942 (tt0) REVERT: N 193 LYS cc_start: 0.3940 (mmpt) cc_final: 0.3447 (pttt) REVERT: N 276 LYS cc_start: 0.7576 (mtpt) cc_final: 0.7186 (tttt) REVERT: B 423 ARG cc_start: 0.8389 (mtm110) cc_final: 0.7665 (mtm110) REVERT: B 489 MET cc_start: 0.7995 (mtp) cc_final: 0.7584 (mtt) REVERT: B 506 MET cc_start: 0.6365 (mtt) cc_final: 0.6016 (mtm) REVERT: C 462 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7728 (pt0) REVERT: L 549 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6850 (tt0) REVERT: K 364 LYS cc_start: 0.6714 (ptpp) cc_final: 0.6150 (ptpp) REVERT: H 415 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: H 483 ASP cc_start: 0.7738 (t0) cc_final: 0.7461 (t0) REVERT: G 418 TRP cc_start: 0.7708 (t-100) cc_final: 0.6529 (t-100) REVERT: E 350 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7748 (pt) REVERT: E 467 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7194 (mmp80) REVERT: E 568 MET cc_start: 0.6986 (tpp) cc_final: 0.6046 (mtt) REVERT: F 525 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7241 (tm-30) REVERT: F 527 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: F 568 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6321 (tmm) REVERT: A 545 ASN cc_start: 0.7418 (t0) cc_final: 0.6868 (t0) REVERT: J 105 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.6193 (mtm110) outliers start: 63 outliers final: 39 residues processed: 223 average time/residue: 0.1607 time to fit residues: 54.8772 Evaluate side-chains 211 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 281 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 552 VAL Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 105 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 146 optimal weight: 0.5980 chunk 210 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 59 optimal weight: 0.0870 chunk 34 optimal weight: 0.5980 chunk 184 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 187 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 510 GLN F 487 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.195893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.128489 restraints weight = 24726.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125025 restraints weight = 28238.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.127031 restraints weight = 23121.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127381 restraints weight = 17327.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127610 restraints weight = 16797.006| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20966 Z= 0.119 Angle : 0.530 13.655 28714 Z= 0.269 Chirality : 0.044 0.255 3351 Planarity : 0.004 0.044 3675 Dihedral : 3.837 38.613 2972 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.92 % Allowed : 18.71 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.60 (0.17), residues: 2582 helix: -0.07 (0.32), residues: 265 sheet: 1.50 (0.17), residues: 949 loop : -0.28 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 467 TYR 0.013 0.001 TYR N 160 PHE 0.016 0.001 PHE L 485 TRP 0.033 0.001 TRP E 418 HIS 0.005 0.001 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (20920) covalent geometry : angle 0.51450 / 0.26 (28614) SS BOND : bond 0.00417 / 0.30 ( 38) SS BOND : angle 1.27347 / 0.91 ( 76) hydrogen bonds : bond 0.03124 / 2.05 ( 648) hydrogen bonds : angle 4.96787 / 3.46 ( 2019) link_BETA1-4 : bond 0.00686 / 0.36 ( 1) link_BETA1-4 : angle 1.26397 / 0.66 ( 3) link_NAG-ASN : bond 0.00545 / 0.27 ( 7) link_NAG-ASN : angle 4.21212 / 2.87 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 172 time to evaluate : 0.845 Fit side-chains REVERT: N 154 LYS cc_start: 0.6715 (tttm) cc_final: 0.6166 (mmtm) REVERT: N 178 GLN cc_start: 0.6366 (OUTLIER) cc_final: 0.6134 (tt0) REVERT: N 193 LYS cc_start: 0.4011 (mmpt) cc_final: 0.3393 (pttt) REVERT: N 276 LYS cc_start: 0.7657 (mtpt) cc_final: 0.7335 (tttt) REVERT: B 489 MET cc_start: 0.7918 (mtp) cc_final: 0.7531 (mtt) REVERT: B 506 MET cc_start: 0.6401 (mtt) cc_final: 0.6064 (mtm) REVERT: C 462 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7707 (pt0) REVERT: L 549 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6803 (tt0) REVERT: K 364 LYS cc_start: 0.7024 (ptpp) cc_final: 0.6489 (ptpp) REVERT: H 415 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: H 495 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7607 (mp) REVERT: G 418 TRP cc_start: 0.7775 (t-100) cc_final: 0.6713 (t-100) REVERT: E 350 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7545 (pt) REVERT: E 445 LYS cc_start: 0.6211 (mppt) cc_final: 0.5975 (mmtm) REVERT: E 467 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7229 (mmp80) REVERT: E 568 MET cc_start: 0.6945 (tpp) cc_final: 0.5996 (mtt) REVERT: F 525 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7199 (tm-30) REVERT: F 527 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: F 568 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6350 (tmm) REVERT: A 545 ASN cc_start: 0.7441 (t0) cc_final: 0.6852 (t0) REVERT: J 23 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6598 (tpp-160) REVERT: J 70 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6362 (pttp) REVERT: J 105 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6186 (mtm110) outliers start: 68 outliers final: 45 residues processed: 225 average time/residue: 0.1626 time to fit residues: 55.1615 Evaluate side-chains 227 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 281 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 568 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain J residue 105 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 87 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 223 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 250 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS ** H 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.194554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.127277 restraints weight = 24884.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122582 restraints weight = 30119.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124823 restraints weight = 24707.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125252 restraints weight = 18241.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125443 restraints weight = 17621.299| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20966 Z= 0.145 Angle : 0.551 13.554 28714 Z= 0.281 Chirality : 0.045 0.257 3351 Planarity : 0.004 0.045 3675 Dihedral : 3.952 31.763 2972 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.80 % Allowed : 19.05 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.52 (0.17), residues: 2582 helix: -0.16 (0.31), residues: 271 sheet: 1.42 (0.17), residues: 963 loop : -0.33 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 TYR 0.015 0.001 TYR N 160 PHE 0.017 0.002 PHE K 516 TRP 0.021 0.001 TRP E 418 HIS 0.006 0.001 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (20920) covalent geometry : angle 0.53605 / 0.28 (28614) SS BOND : bond 0.00448 / 0.32 ( 38) SS BOND : angle 1.33510 / 0.95 ( 76) hydrogen bonds : bond 0.03367 / 2.20 ( 648) hydrogen bonds : angle 5.02001 / 3.50 ( 2019) link_BETA1-4 : bond 0.00579 / 0.30 ( 1) link_BETA1-4 : angle 1.14395 / 0.59 ( 3) link_NAG-ASN : bond 0.00566 / 0.29 ( 7) link_NAG-ASN : angle 4.15535 / 2.83 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 181 time to evaluate : 0.783 Fit side-chains REVERT: N 154 LYS cc_start: 0.6732 (tttm) cc_final: 0.5803 (mttp) REVERT: N 178 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.6186 (tt0) REVERT: N 193 LYS cc_start: 0.4317 (mmpt) cc_final: 0.3661 (pttt) REVERT: B 489 MET cc_start: 0.8000 (mtp) cc_final: 0.7620 (mtt) REVERT: B 506 MET cc_start: 0.6504 (mtt) cc_final: 0.6168 (mtm) REVERT: C 462 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7729 (pt0) REVERT: D 499 LYS cc_start: 0.8627 (mmmt) cc_final: 0.8143 (tptm) REVERT: L 549 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6947 (tt0) REVERT: K 364 LYS cc_start: 0.7192 (ptpp) cc_final: 0.6660 (ptpp) REVERT: H 415 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: H 495 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7660 (mp) REVERT: G 418 TRP cc_start: 0.7794 (t-100) cc_final: 0.6719 (t-100) REVERT: E 350 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7617 (pt) REVERT: E 467 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7243 (mmp80) REVERT: E 568 MET cc_start: 0.6979 (tpp) cc_final: 0.6000 (mtt) REVERT: F 525 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7159 (tm-30) REVERT: F 527 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: F 568 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6411 (tmm) REVERT: A 545 ASN cc_start: 0.7456 (t0) cc_final: 0.6927 (t0) REVERT: J 23 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6535 (tpp-160) REVERT: J 70 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6495 (pttp) REVERT: J 105 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6199 (mtm110) outliers start: 65 outliers final: 47 residues processed: 231 average time/residue: 0.1607 time to fit residues: 55.4201 Evaluate side-chains 234 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 176 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 568 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain J residue 105 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 81 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 238 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 119 optimal weight: 0.0270 chunk 85 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 37 optimal weight: 0.0000 overall best weight: 0.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 333 HIS ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN ** H 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 = 0.4270 r_free = 0.4270 target = 0.195486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126930 restraints weight = 24799.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122283 restraints weight = 26585.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124599 restraints weight = 21676.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125130 restraints weight = 16351.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125345 restraints weight = 15614.006| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20966 Z= 0.117 Angle : 0.529 13.373 28714 Z= 0.269 Chirality : 0.044 0.252 3351 Planarity : 0.004 0.044 3675 Dihedral : 3.830 28.462 2972 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.80 % Allowed : 18.97 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.62 (0.17), residues: 2582 helix: -0.11 (0.32), residues: 267 sheet: 1.48 (0.17), residues: 963 loop : -0.26 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 TYR 0.013 0.001 TYR N 160 PHE 0.016 0.001 PHE L 485 TRP 0.021 0.001 TRP E 418 HIS 0.005 0.001 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (20920) covalent geometry : angle 0.51499 / 0.27 (28614) SS BOND : bond 0.00452 / 0.31 ( 38) SS BOND : angle 1.20373 / 0.88 ( 76) hydrogen bonds : bond 0.03032 / 1.99 ( 648) hydrogen bonds : angle 4.84916 / 3.38 ( 2019) link_BETA1-4 : bond 0.00602 / 0.32 ( 1) link_BETA1-4 : angle 1.12194 / 0.58 ( 3) link_NAG-ASN : bond 0.00573 / 0.29 ( 7) link_NAG-ASN : angle 4.00249 / 2.71 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 174 time to evaluate : 0.841 Fit side-chains REVERT: N 154 LYS cc_start: 0.6711 (tttm) cc_final: 0.5798 (mttp) REVERT: N 178 GLN cc_start: 0.6317 (OUTLIER) cc_final: 0.5917 (tt0) REVERT: N 193 LYS cc_start: 0.4357 (mmpt) cc_final: 0.3631 (pttt) REVERT: B 489 MET cc_start: 0.7963 (mtp) cc_final: 0.7580 (mtt) REVERT: B 506 MET cc_start: 0.6428 (mtt) cc_final: 0.6109 (mtm) REVERT: C 462 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7706 (pt0) REVERT: D 499 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8126 (tptm) REVERT: L 549 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6811 (tt0) REVERT: K 364 LYS cc_start: 0.7073 (ptpp) cc_final: 0.6563 (ptpp) REVERT: K 489 MET cc_start: 0.8629 (mtm) cc_final: 0.8330 (mtp) REVERT: H 415 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: H 424 PHE cc_start: 0.7140 (m-80) cc_final: 0.6937 (m-10) REVERT: H 495 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7633 (mp) REVERT: G 418 TRP cc_start: 0.7785 (t-100) cc_final: 0.6731 (t-100) REVERT: E 350 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7615 (pt) REVERT: E 467 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7231 (mmp80) REVERT: E 568 MET cc_start: 0.6973 (tpp) cc_final: 0.5993 (mtt) REVERT: F 525 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7147 (tm-30) REVERT: F 527 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: F 568 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6409 (tmm) REVERT: A 545 ASN cc_start: 0.7431 (t0) cc_final: 0.6885 (t0) REVERT: J 23 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6523 (tpp-160) REVERT: J 70 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6408 (pttp) REVERT: J 105 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6216 (mtm110) outliers start: 65 outliers final: 48 residues processed: 224 average time/residue: 0.1605 time to fit residues: 53.9951 Evaluate side-chains 229 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 419 ASN Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 506 MET Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 568 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain J residue 105 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 54 optimal weight: 0.9980 chunk 132 optimal weight: 0.0040 chunk 176 optimal weight: 0.9980 chunk 238 optimal weight: 0.8980 chunk 235 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 197 optimal weight: 0.5980 chunk 227 optimal weight: 20.0000 chunk 59 optimal weight: 0.0040 chunk 163 optimal weight: 0.6980 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN ** H 419 ASN ** 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 = 0.4279 r_free = 0.4279 target = 0.196442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127751 restraints weight = 25021.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124326 restraints weight = 28419.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126366 restraints weight = 24505.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126545 restraints weight = 17788.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.126804 restraints weight = 15969.567| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20966 Z= 0.103 Angle : 0.512 13.196 28714 Z= 0.260 Chirality : 0.043 0.253 3351 Planarity : 0.004 0.045 3675 Dihedral : 3.731 24.085 2972 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.71 % Allowed : 18.88 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.69 (0.17), residues: 2582 helix: -0.06 (0.32), residues: 267 sheet: 1.56 (0.17), residues: 957 loop : -0.22 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 TYR 0.012 0.001 TYR N 160 PHE 0.014 0.001 PHE H 354 TRP 0.020 0.001 TRP E 418 HIS 0.010 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.10 (20920) covalent geometry : angle 0.49910 / 0.26 (28614) SS BOND : bond 0.00368 / 0.26 ( 38) SS BOND : angle 1.07550 / 0.77 ( 76) hydrogen bonds : bond 0.02848 / 1.87 ( 648) hydrogen bonds : angle 4.71287 / 3.28 ( 2019) link_BETA1-4 : bond 0.00580 / 0.31 ( 1) link_BETA1-4 : angle 1.10514 / 0.57 ( 3) link_NAG-ASN : bond 0.00597 / 0.30 ( 7) link_NAG-ASN : angle 3.90041 / 2.62 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 174 time to evaluate : 0.845 Fit side-chains REVERT: N 154 LYS cc_start: 0.6705 (tttm) cc_final: 0.5806 (mttp) REVERT: N 178 GLN cc_start: 0.6286 (OUTLIER) cc_final: 0.5607 (tt0) REVERT: N 193 LYS cc_start: 0.4272 (mmpt) cc_final: 0.3470 (pttt) REVERT: B 489 MET cc_start: 0.8022 (mtp) cc_final: 0.7639 (mtt) REVERT: B 506 MET cc_start: 0.6283 (mtt) cc_final: 0.5975 (mtm) REVERT: C 462 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7728 (pt0) REVERT: C 483 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7846 (p0) REVERT: D 499 LYS cc_start: 0.8554 (mmmt) cc_final: 0.8142 (tptm) REVERT: L 549 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6805 (tt0) REVERT: K 364 LYS cc_start: 0.7024 (ptpp) cc_final: 0.6541 (ptpp) REVERT: K 489 MET cc_start: 0.8623 (mtm) cc_final: 0.8364 (mtp) REVERT: H 384 ARG cc_start: 0.6507 (mpp80) cc_final: 0.5887 (mpp80) REVERT: H 415 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: H 495 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7541 (mp) REVERT: G 418 TRP cc_start: 0.7758 (t-100) cc_final: 0.6728 (t-100) REVERT: E 350 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7568 (pt) REVERT: E 467 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7186 (mmp80) REVERT: E 568 MET cc_start: 0.6945 (tpp) cc_final: 0.5980 (mtt) REVERT: F 525 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7058 (tm-30) REVERT: F 527 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: F 568 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6495 (tmm) REVERT: A 545 ASN cc_start: 0.7426 (t0) cc_final: 0.6873 (t0) REVERT: J 23 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6513 (tpp-160) REVERT: J 70 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6359 (pttp) REVERT: J 105 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.6224 (mtm110) outliers start: 63 outliers final: 44 residues processed: 221 average time/residue: 0.1703 time to fit residues: 56.3258 Evaluate side-chains 226 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 281 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 506 MET Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 568 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain J residue 105 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 158 optimal weight: 5.9990 chunk 231 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 237 optimal weight: 0.5980 chunk 243 optimal weight: 0.9980 chunk 79 optimal weight: 0.3980 chunk 156 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 225 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN ** H 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.195956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127901 restraints weight = 24775.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125383 restraints weight = 29005.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.127243 restraints weight = 22864.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127663 restraints weight = 17316.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127779 restraints weight = 17074.845| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20966 Z= 0.106 Angle : 0.514 13.157 28714 Z= 0.261 Chirality : 0.043 0.252 3351 Planarity : 0.004 0.045 3675 Dihedral : 3.710 25.314 2972 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.67 % Allowed : 19.10 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.71 (0.17), residues: 2582 helix: -0.05 (0.32), residues: 268 sheet: 1.57 (0.17), residues: 957 loop : -0.20 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 TYR 0.010 0.001 TYR N 160 PHE 0.014 0.001 PHE L 485 TRP 0.019 0.001 TRP E 418 HIS 0.011 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (20920) covalent geometry : angle 0.50113 / 0.26 (28614) SS BOND : bond 0.00378 / 0.27 ( 38) SS BOND : angle 1.05891 / 0.76 ( 76) hydrogen bonds : bond 0.02853 / 1.87 ( 648) hydrogen bonds : angle 4.66908 / 3.26 ( 2019) link_BETA1-4 : bond 0.00607 / 0.32 ( 1) link_BETA1-4 : angle 1.07380 / 0.56 ( 3) link_NAG-ASN : bond 0.00598 / 0.30 ( 7) link_NAG-ASN : angle 3.87226 / 2.60 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3720.31 seconds wall clock time: 65 minutes 11.04 seconds (3911.04 seconds total)