Starting phenix.real_space_refine on Sat May 24 10:25:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y76_33653/05_2025/7y76_33653.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y76_33653/05_2025/7y76_33653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y76_33653/05_2025/7y76_33653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y76_33653/05_2025/7y76_33653.map" model { file = "/net/cci-nas-00/data/ceres_data/7y76_33653/05_2025/7y76_33653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y76_33653/05_2025/7y76_33653.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 S 146 5.16 5 C 16340 2.51 5 N 4006 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25180 Number of models: 1 Model: "" Number of chains: 26 Chain: "B" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4499 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 552} Chain: "A" Number of atoms: 6102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6102 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 35, 'TRANS': 714} Chain: "E" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1578 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4499 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 552} Chain: "C" Number of atoms: 6102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6102 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 35, 'TRANS': 714} Chain: "F" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1578 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "G" 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: "H" 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: "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: "J" 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: "K" 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: "L" 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: "M" 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: 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "B" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 172 Unusual residues: {'3PH': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 172 Unusual residues: {'3PH': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.33, per 1000 atoms: 0.53 Number of scatterers: 25180 At special positions: 0 Unit cell: (159.789, 144.571, 216.313, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 146 16.00 P 6 15.00 O 4680 8.00 N 4006 7.00 C 16340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 358 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.05 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 358 " distance=2.04 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.05 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.04 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.04 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 901 " - " ASN A 322 " " NAG B1001 " - " ASN B 131 " " NAG B1002 " - " ASN B 332 " " NAG C 901 " - " ASN C 322 " " NAG D1001 " - " ASN D 131 " " NAG D1002 " - " ASN D 332 " " NAG G 1 " - " ASN B 357 " " NAG H 1 " - " ASN A 53 " " NAG I 1 " - " ASN A 90 " " NAG J 1 " - " ASN A 103 " " NAG K 1 " - " ASN A 432 " " NAG L 1 " - " ASN A 546 " " NAG M 1 " - " ASN A 690 " " NAG N 1 " - " ASN E 343 " " NAG O 1 " - " ASN D 357 " " NAG P 1 " - " ASN C 53 " " NAG Q 1 " - " ASN C 90 " " NAG R 1 " - " ASN C 103 " " NAG S 1 " - " ASN C 432 " " NAG T 1 " - " ASN C 546 " " NAG U 1 " - " ASN C 690 " " NAG V 1 " - " ASN F 343 " Time building additional restraints: 6.29 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 378 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 374 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 378 " 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5704 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 16 sheets defined 62.1% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.749A pdb=" N TYR B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 55 removed outlier: 3.848A pdb=" N VAL B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 55 through 70 removed outlier: 3.690A pdb=" N LEU B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.578A pdb=" N SER B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 85 through 115 removed outlier: 4.530A pdb=" N VAL B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET B 100 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 removed outlier: 4.000A pdb=" N VAL B 125 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 removed outlier: 3.672A pdb=" N ALA B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 168 through 187 Processing helix chain 'B' and resid 195 through 216 Proline residue: B 203 - end of helix Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.648A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 252 removed outlier: 3.846A pdb=" N TRP B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 263 removed outlier: 3.507A pdb=" N ALA B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 321 removed outlier: 4.001A pdb=" N HIS B 275 " --> pdb=" O ASN B 271 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 340 Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.834A pdb=" N THR B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 388 through 420 removed outlier: 3.774A pdb=" N ALA B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Proline residue: B 417 - end of helix removed outlier: 3.672A pdb=" N ASP B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.803A pdb=" N SER B 426 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS B 427 " --> pdb=" O ILE B 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 423 through 427' Processing helix chain 'B' and resid 429 through 446 removed outlier: 3.644A pdb=" N ILE B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 450 Processing helix chain 'B' and resid 452 through 483 removed outlier: 4.035A pdb=" N TRP B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 498 Processing helix chain 'B' and resid 502 through 509 Processing helix chain 'B' and resid 512 through 528 removed outlier: 3.677A pdb=" N VAL B 518 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 568 removed outlier: 4.450A pdb=" N LEU B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'A' and resid 21 through 53 removed outlier: 3.517A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.674A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.822A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.566A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.668A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.668A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.513A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.768A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.962A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.880A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.647A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.797A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 366 through 383 removed outlier: 3.966A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.292A pdb=" N ALA A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.661A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.549A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.708A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.985A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.635A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.756A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.577A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.761A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 623 through 629 removed outlier: 3.557A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 658 removed outlier: 3.717A pdb=" N MET A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 715 removed outlier: 3.722A pdb=" N SER A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 767 removed outlier: 3.536A pdb=" N VAL A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.757A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.568A pdb=" N ASN E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.748A pdb=" N TYR D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 55 removed outlier: 3.848A pdb=" N VAL D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 55 through 70 removed outlier: 3.691A pdb=" N LEU D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.578A pdb=" N SER D 81 " --> pdb=" O TRP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 85 through 115 removed outlier: 4.530A pdb=" N VAL D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET D 100 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 125 removed outlier: 4.002A pdb=" N VAL D 125 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 142 removed outlier: 3.672A pdb=" N ALA D 142 " --> pdb=" O GLU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 168 through 187 Processing helix chain 'D' and resid 195 through 216 Proline residue: D 203 - end of helix Processing helix chain 'D' and resid 220 through 229 removed outlier: 3.649A pdb=" N LEU D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 252 removed outlier: 3.847A pdb=" N TRP D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 263 removed outlier: 3.507A pdb=" N ALA D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 321 removed outlier: 4.000A pdb=" N HIS D 275 " --> pdb=" O ASN D 271 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D 292 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 321 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 340 Processing helix chain 'D' and resid 344 through 349 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.835A pdb=" N THR D 366 " --> pdb=" O SER D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 388 through 420 removed outlier: 3.774A pdb=" N ALA D 413 " --> pdb=" O GLY D 409 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Proline residue: D 417 - end of helix removed outlier: 3.672A pdb=" N ASP D 420 " --> pdb=" O THR D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 removed outlier: 3.804A pdb=" N SER D 426 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N HIS D 427 " --> pdb=" O ILE D 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 423 through 427' Processing helix chain 'D' and resid 429 through 446 removed outlier: 3.644A pdb=" N ILE D 433 " --> pdb=" O PRO D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 450 Processing helix chain 'D' and resid 452 through 483 removed outlier: 4.035A pdb=" N TRP D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP D 462 " --> pdb=" O ASP D 458 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 498 Processing helix chain 'D' and resid 502 through 509 Processing helix chain 'D' and resid 512 through 528 removed outlier: 3.679A pdb=" N VAL D 518 " --> pdb=" O PRO D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 568 removed outlier: 4.451A pdb=" N LEU D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA D 557 " --> pdb=" O ALA D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 580 Processing helix chain 'C' and resid 21 through 53 removed outlier: 3.517A pdb=" N GLU C 37 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP C 38 " --> pdb=" O HIS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 81 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.675A pdb=" N ILE C 88 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.822A pdb=" N GLN C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 removed outlier: 3.566A pdb=" N ASN C 121 " --> pdb=" O ASN C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.668A pdb=" N ILE C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.668A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 193 removed outlier: 3.513A pdb=" N LEU C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 177 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.768A pdb=" N GLU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 220 through 230 removed outlier: 3.962A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.880A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 293 through 300 removed outlier: 3.647A pdb=" N VAL C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 318 removed outlier: 3.797A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 366 through 383 removed outlier: 3.966A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.291A pdb=" N ALA C 387 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.661A pdb=" N ARG C 393 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 412 removed outlier: 3.550A pdb=" N ALA C 403 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 3.709A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 444 removed outlier: 3.984A pdb=" N ILE C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 448 No H-bonds generated for 'chain 'C' and resid 446 through 448' Processing helix chain 'C' and resid 449 through 466 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.635A pdb=" N ARG C 482 " --> pdb=" O TRP C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 513 through 533 removed outlier: 3.756A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 526 " --> pdb=" O GLN C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 547 through 559 removed outlier: 3.577A pdb=" N GLY C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 574 removed outlier: 3.762A pdb=" N VAL C 573 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 588 through 599 Processing helix chain 'C' and resid 623 through 629 removed outlier: 3.558A pdb=" N ALA C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 658 removed outlier: 3.718A pdb=" N MET C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 715 removed outlier: 3.722A pdb=" N SER C 707 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 767 removed outlier: 3.536A pdb=" N VAL C 745 " --> pdb=" O ILE C 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 403 through 410 removed outlier: 3.757A pdb=" N GLU F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER F 408 " --> pdb=" O ASN F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.567A pdb=" N ASN F 422 " --> pdb=" O ILE F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.098A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.641A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 670 through 676 removed outlier: 4.463A pdb=" N LEU A 675 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER A 680 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS A 619 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.634A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL E 433 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 391 through 392 removed outlier: 3.549A pdb=" N PHE E 392 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AA8, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AB1, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.098A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 347 through 352 removed outlier: 6.641A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 670 through 676 removed outlier: 4.463A pdb=" N LEU C 675 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER C 680 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS C 619 " --> pdb=" O LEU C 725 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.636A pdb=" N VAL F 395 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 433 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS F 378 " --> pdb=" O VAL F 433 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 391 through 392 removed outlier: 3.549A pdb=" N PHE F 392 " --> pdb=" O VAL F 524 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL F 524 " --> pdb=" O PHE F 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 452 through 453 Processing sheet with id=AB7, first strand: chain 'F' and resid 473 through 474 1236 hydrogen bonds defined for protein. 3588 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: 7.24 Time building geometry restraints manager: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7742 1.34 - 1.47: 6946 1.47 - 1.60: 10912 1.60 - 1.72: 6 1.72 - 1.85: 232 Bond restraints: 25838 Sorted by residual: bond pdb=" C31 3PH D1003 " pdb=" O31 3PH D1003 " ideal model delta sigma weight residual 1.325 1.456 -0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C31 3PH B1003 " pdb=" O31 3PH B1003 " ideal model delta sigma weight residual 1.325 1.455 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" C31 3PH D1005 " pdb=" O31 3PH D1005 " ideal model delta sigma weight residual 1.325 1.455 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C21 3PH D1003 " pdb=" O21 3PH D1003 " ideal model delta sigma weight residual 1.328 1.457 -0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C21 3PH B1003 " pdb=" O21 3PH B1003 " ideal model delta sigma weight residual 1.328 1.457 -0.129 2.00e-02 2.50e+03 4.16e+01 ... (remaining 25833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 34475 2.72 - 5.45: 523 5.45 - 8.17: 53 8.17 - 10.89: 16 10.89 - 13.61: 1 Bond angle restraints: 35068 Sorted by residual: angle pdb=" N VAL E 367 " pdb=" CA VAL E 367 " pdb=" C VAL E 367 " ideal model delta sigma weight residual 113.71 107.40 6.31 9.50e-01 1.11e+00 4.41e+01 angle pdb=" N VAL F 367 " pdb=" CA VAL F 367 " pdb=" C VAL F 367 " ideal model delta sigma weight residual 113.71 107.44 6.27 9.50e-01 1.11e+00 4.36e+01 angle pdb=" C LEU A 267 " pdb=" N GLY A 268 " pdb=" CA GLY A 268 " ideal model delta sigma weight residual 123.30 117.60 5.70 1.06e+00 8.90e-01 2.89e+01 angle pdb=" C LEU C 267 " pdb=" N GLY C 268 " pdb=" CA GLY C 268 " ideal model delta sigma weight residual 123.30 117.61 5.69 1.06e+00 8.90e-01 2.88e+01 angle pdb=" N PRO E 373 " pdb=" CA PRO E 373 " pdb=" C PRO E 373 " ideal model delta sigma weight residual 113.47 106.03 7.44 1.43e+00 4.89e-01 2.71e+01 ... (remaining 35063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 13521 17.14 - 34.27: 1613 34.27 - 51.41: 473 51.41 - 68.55: 119 68.55 - 85.68: 26 Dihedral angle restraints: 15752 sinusoidal: 6848 harmonic: 8904 Sorted by residual: dihedral pdb=" CB CYS F 379 " pdb=" SG CYS F 379 " pdb=" SG CYS F 432 " pdb=" CB CYS F 432 " ideal model delta sinusoidal sigma weight residual 93.00 40.25 52.75 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 40.28 52.72 1 1.00e+01 1.00e-02 3.78e+01 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 48.73 44.27 1 1.00e+01 1.00e-02 2.73e+01 ... (remaining 15749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3554 0.085 - 0.169: 318 0.169 - 0.254: 24 0.254 - 0.338: 4 0.338 - 0.423: 2 Chirality restraints: 3902 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 90 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA PHE E 374 " pdb=" N PHE E 374 " pdb=" C PHE E 374 " pdb=" CB PHE E 374 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 3899 not shown) Planarity restraints: 4390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 687 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO A 688 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 688 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 688 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 687 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO C 688 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 688 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 688 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 234 " 0.028 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO C 235 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 235 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 235 " 0.023 5.00e-02 4.00e+02 ... (remaining 4387 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 291 2.58 - 3.16: 22246 3.16 - 3.74: 37992 3.74 - 4.32: 51845 4.32 - 4.90: 86132 Nonbonded interactions: 198506 Sorted by model distance: nonbonded pdb=" OE1 GLU C 402 " pdb="ZN ZN C 902 " model vdw 1.996 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 902 " model vdw 1.996 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 902 " model vdw 2.087 2.230 nonbonded pdb=" OE2 GLU C 402 " pdb="ZN ZN C 902 " model vdw 2.089 2.230 nonbonded pdb=" O ASN E 439 " pdb=" OG SER E 443 " model vdw 2.203 3.040 ... (remaining 198501 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 53.600 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.170 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.010 0.301 25896 Z= 0.443 Angle : 0.868 13.613 35214 Z= 0.448 Chirality : 0.052 0.423 3902 Planarity : 0.004 0.049 4368 Dihedral : 16.482 85.684 10000 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.84 % Favored : 90.83 % Rotamer: Outliers : 5.15 % Allowed : 16.06 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.13), residues: 3030 helix: -1.66 (0.11), residues: 1662 sheet: -1.29 (0.45), residues: 116 loop : -3.15 (0.15), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 459 HIS 0.007 0.001 HIS A 241 PHE 0.019 0.002 PHE B 295 TYR 0.025 0.002 TYR C 183 ARG 0.003 0.000 ARG C 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00823 ( 22) link_NAG-ASN : angle 4.16249 ( 66) link_BETA1-4 : bond 0.00646 ( 16) link_BETA1-4 : angle 2.31834 ( 48) hydrogen bonds : bond 0.15869 ( 1236) hydrogen bonds : angle 6.45196 ( 3588) metal coordination : bond 0.21369 ( 4) SS BOND : bond 0.00851 ( 16) SS BOND : angle 2.00432 ( 32) covalent geometry : bond 0.00954 (25838) covalent geometry : angle 0.84414 (35068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 209 time to evaluate : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 225 MET cc_start: 0.7887 (mtt) cc_final: 0.7587 (mtt) REVERT: A 323 MET cc_start: 0.8921 (mmp) cc_final: 0.8693 (mmp) REVERT: A 736 GLN cc_start: 0.3725 (OUTLIER) cc_final: 0.3177 (tm-30) REVERT: E 357 ARG cc_start: 0.7917 (tmm-80) cc_final: 0.7634 (tmm-80) REVERT: E 471 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7978 (tm-30) REVERT: E 472 ILE cc_start: 0.8965 (mm) cc_final: 0.8743 (mt) REVERT: D 77 TRP cc_start: 0.6830 (m100) cc_final: 0.6123 (m100) REVERT: D 225 MET cc_start: 0.7890 (mtt) cc_final: 0.7592 (mtt) REVERT: C 406 GLU cc_start: 0.8022 (tp30) cc_final: 0.7803 (mm-30) REVERT: C 736 GLN cc_start: 0.3573 (OUTLIER) cc_final: 0.3315 (tt0) REVERT: F 472 ILE cc_start: 0.9021 (mm) cc_final: 0.8805 (mt) outliers start: 136 outliers final: 82 residues processed: 330 average time/residue: 0.3551 time to fit residues: 192.9648 Evaluate side-chains 255 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 171 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 524 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 8.9990 chunk 228 optimal weight: 0.5980 chunk 127 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 176 optimal weight: 0.0980 chunk 274 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN B 243 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 461 ASN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 GLN A 96 GLN A 159 ASN A 210 ASN A 239 HIS A 378 HIS A 472 GLN A 493 HIS A 505 HIS A 599 ASN E 417 ASN E 422 ASN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 ASN D 461 ASN ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 96 GLN C 102 GLN C 159 ASN C 210 ASN C 239 HIS C 378 HIS C 472 GLN C 493 HIS C 505 HIS C 599 ASN F 422 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.124786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.073363 restraints weight = 58559.241| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.83 r_work: 0.2879 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.515 25896 Z= 0.198 Angle : 0.661 12.405 35214 Z= 0.324 Chirality : 0.043 0.293 3902 Planarity : 0.004 0.058 4368 Dihedral : 11.163 77.220 4486 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.01 % Favored : 93.83 % Rotamer: Outliers : 3.30 % Allowed : 17.12 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.15), residues: 3030 helix: -0.08 (0.12), residues: 1694 sheet: -1.16 (0.52), residues: 92 loop : -2.64 (0.16), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 77 HIS 0.005 0.001 HIS A 34 PHE 0.015 0.001 PHE F 371 TYR 0.027 0.001 TYR D 504 ARG 0.005 0.000 ARG B 70 Details of bonding type rmsd link_NAG-ASN : bond 0.00716 ( 22) link_NAG-ASN : angle 3.60791 ( 66) link_BETA1-4 : bond 0.00435 ( 16) link_BETA1-4 : angle 1.92177 ( 48) hydrogen bonds : bond 0.05033 ( 1236) hydrogen bonds : angle 4.50145 ( 3588) metal coordination : bond 0.36266 ( 4) SS BOND : bond 0.00884 ( 16) SS BOND : angle 2.02830 ( 32) covalent geometry : bond 0.00265 (25838) covalent geometry : angle 0.63627 (35068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 199 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 PHE cc_start: 0.6909 (m-80) cc_final: 0.6648 (m-10) REVERT: B 349 SER cc_start: 0.9242 (OUTLIER) cc_final: 0.8989 (p) REVERT: B 446 MET cc_start: 0.7704 (tpp) cc_final: 0.7432 (tpp) REVERT: A 123 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.9046 (mtm) REVERT: E 406 GLU cc_start: 0.8581 (mp0) cc_final: 0.8298 (mp0) REVERT: E 458 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8733 (mmmt) REVERT: E 471 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8082 (tm-30) REVERT: E 472 ILE cc_start: 0.8991 (mm) cc_final: 0.8675 (mt) REVERT: D 100 MET cc_start: 0.8564 (mtt) cc_final: 0.7886 (mpp) REVERT: D 349 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8949 (p) REVERT: D 384 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7569 (t0) REVERT: C 102 GLN cc_start: 0.9207 (pt0) cc_final: 0.8727 (pm20) REVERT: C 123 MET cc_start: 0.9390 (mtp) cc_final: 0.9128 (mtm) REVERT: C 360 MET cc_start: 0.8985 (ptm) cc_final: 0.8758 (ptm) REVERT: F 406 GLU cc_start: 0.8535 (mp0) cc_final: 0.8328 (mp0) REVERT: F 458 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8695 (mmmt) REVERT: F 466 ARG cc_start: 0.8500 (ttt180) cc_final: 0.8300 (tpp80) REVERT: F 472 ILE cc_start: 0.9138 (mm) cc_final: 0.8904 (mt) REVERT: F 488 CYS cc_start: 0.8309 (m) cc_final: 0.8033 (p) outliers start: 87 outliers final: 46 residues processed: 274 average time/residue: 0.3282 time to fit residues: 149.0651 Evaluate side-chains 236 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 384 ASN Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 136 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 147 optimal weight: 0.3980 chunk 272 optimal weight: 0.0980 chunk 107 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 46 optimal weight: 10.0000 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN B 275 HIS ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 ASN A 58 ASN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN C 58 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.125324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.074134 restraints weight = 58554.770| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.84 r_work: 0.2898 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 25896 Z= 0.116 Angle : 0.620 12.401 35214 Z= 0.301 Chirality : 0.042 0.284 3902 Planarity : 0.003 0.044 4368 Dihedral : 9.810 77.302 4409 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.40 % Favored : 93.43 % Rotamer: Outliers : 3.18 % Allowed : 17.80 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3030 helix: 0.49 (0.13), residues: 1690 sheet: -0.81 (0.52), residues: 92 loop : -2.29 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 505 HIS 0.004 0.001 HIS C 378 PHE 0.016 0.001 PHE C 315 TYR 0.022 0.001 TYR B 504 ARG 0.004 0.000 ARG F 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 22) link_NAG-ASN : angle 3.52848 ( 66) link_BETA1-4 : bond 0.00435 ( 16) link_BETA1-4 : angle 1.87745 ( 48) hydrogen bonds : bond 0.04472 ( 1236) hydrogen bonds : angle 4.26991 ( 3588) metal coordination : bond 0.01302 ( 4) SS BOND : bond 0.01179 ( 16) SS BOND : angle 3.21495 ( 32) covalent geometry : bond 0.00243 (25838) covalent geometry : angle 0.59070 (35068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 195 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.8382 (mtt) cc_final: 0.7844 (mpp) REVERT: B 446 MET cc_start: 0.7708 (tpp) cc_final: 0.7408 (tpp) REVERT: B 450 MET cc_start: 0.8570 (tpp) cc_final: 0.8198 (tpp) REVERT: A 428 PHE cc_start: 0.8028 (t80) cc_final: 0.7728 (t80) REVERT: E 406 GLU cc_start: 0.8647 (mp0) cc_final: 0.8352 (mp0) REVERT: E 458 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8802 (mmmt) REVERT: E 471 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8101 (tm-30) REVERT: D 450 MET cc_start: 0.8605 (tpp) cc_final: 0.8224 (tpp) REVERT: C 102 GLN cc_start: 0.9300 (pt0) cc_final: 0.8895 (pm20) REVERT: C 123 MET cc_start: 0.9377 (mtp) cc_final: 0.9095 (mtm) REVERT: F 406 GLU cc_start: 0.8599 (mp0) cc_final: 0.8299 (mp0) REVERT: F 488 CYS cc_start: 0.8287 (m) cc_final: 0.7917 (p) outliers start: 84 outliers final: 43 residues processed: 263 average time/residue: 0.3328 time to fit residues: 146.1448 Evaluate side-chains 221 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 281 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 260 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.124209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.072628 restraints weight = 58227.513| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.88 r_work: 0.2856 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25896 Z= 0.154 Angle : 0.630 12.246 35214 Z= 0.303 Chirality : 0.043 0.271 3902 Planarity : 0.004 0.042 4368 Dihedral : 9.135 76.432 4396 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.67 % Favored : 93.17 % Rotamer: Outliers : 3.41 % Allowed : 18.26 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3030 helix: 0.70 (0.13), residues: 1706 sheet: -0.60 (0.52), residues: 90 loop : -2.08 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 505 HIS 0.006 0.001 HIS C 34 PHE 0.016 0.001 PHE D 489 TYR 0.024 0.001 TYR D 182 ARG 0.008 0.000 ARG E 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00633 ( 22) link_NAG-ASN : angle 3.53330 ( 66) link_BETA1-4 : bond 0.00434 ( 16) link_BETA1-4 : angle 1.83044 ( 48) hydrogen bonds : bond 0.04578 ( 1236) hydrogen bonds : angle 4.18690 ( 3588) metal coordination : bond 0.00490 ( 4) SS BOND : bond 0.00692 ( 16) SS BOND : angle 1.93428 ( 32) covalent geometry : bond 0.00356 (25838) covalent geometry : angle 0.60561 (35068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 195 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.5065 (OUTLIER) cc_final: 0.4426 (m-10) REVERT: B 446 MET cc_start: 0.7668 (tpp) cc_final: 0.7400 (tpp) REVERT: B 450 MET cc_start: 0.8598 (tpp) cc_final: 0.8213 (tpp) REVERT: A 256 ILE cc_start: 0.9685 (OUTLIER) cc_final: 0.9416 (mm) REVERT: A 428 PHE cc_start: 0.8128 (t80) cc_final: 0.7843 (t80) REVERT: A 736 GLN cc_start: 0.3404 (OUTLIER) cc_final: 0.3014 (tm-30) REVERT: E 406 GLU cc_start: 0.8673 (mp0) cc_final: 0.8334 (mp0) REVERT: E 466 ARG cc_start: 0.8314 (tpp80) cc_final: 0.7840 (tpp80) REVERT: E 471 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8038 (tm-30) REVERT: D 83 TYR cc_start: 0.5124 (OUTLIER) cc_final: 0.4569 (m-10) REVERT: D 450 MET cc_start: 0.8651 (tpp) cc_final: 0.8324 (tpp) REVERT: C 102 GLN cc_start: 0.9305 (pt0) cc_final: 0.8836 (pm20) REVERT: C 123 MET cc_start: 0.9441 (mtp) cc_final: 0.9138 (mtm) REVERT: C 256 ILE cc_start: 0.9691 (OUTLIER) cc_final: 0.9435 (mm) REVERT: C 428 PHE cc_start: 0.8012 (t80) cc_final: 0.7532 (t80) REVERT: C 736 GLN cc_start: 0.3064 (OUTLIER) cc_final: 0.2590 (tm-30) REVERT: F 406 GLU cc_start: 0.8702 (mp0) cc_final: 0.8380 (mp0) REVERT: F 466 ARG cc_start: 0.8347 (tpp80) cc_final: 0.7839 (tpp80) REVERT: F 488 CYS cc_start: 0.8292 (m) cc_final: 0.7924 (p) outliers start: 90 outliers final: 52 residues processed: 273 average time/residue: 0.3282 time to fit residues: 149.2050 Evaluate side-chains 235 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 177 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 44 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 345 HIS D 27 ASN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN D 283 ASN D 537 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.123368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.071836 restraints weight = 58605.600| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.76 r_work: 0.2844 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25896 Z= 0.203 Angle : 0.649 12.199 35214 Z= 0.316 Chirality : 0.044 0.268 3902 Planarity : 0.004 0.041 4368 Dihedral : 8.842 74.826 4392 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.77 % Favored : 93.14 % Rotamer: Outliers : 3.22 % Allowed : 19.36 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3030 helix: 0.78 (0.13), residues: 1710 sheet: -0.54 (0.58), residues: 70 loop : -1.98 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 505 HIS 0.006 0.001 HIS C 241 PHE 0.015 0.001 PHE A 315 TYR 0.021 0.001 TYR C 183 ARG 0.006 0.000 ARG F 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00629 ( 22) link_NAG-ASN : angle 3.55749 ( 66) link_BETA1-4 : bond 0.00444 ( 16) link_BETA1-4 : angle 1.87045 ( 48) hydrogen bonds : bond 0.04812 ( 1236) hydrogen bonds : angle 4.21062 ( 3588) metal coordination : bond 0.00636 ( 4) SS BOND : bond 0.00711 ( 16) SS BOND : angle 2.17919 ( 32) covalent geometry : bond 0.00480 (25838) covalent geometry : angle 0.62486 (35068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 186 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.4877 (OUTLIER) cc_final: 0.4297 (m-10) REVERT: B 225 MET cc_start: 0.7932 (mtt) cc_final: 0.7715 (mtm) REVERT: B 446 MET cc_start: 0.7699 (tpp) cc_final: 0.7475 (tpp) REVERT: A 256 ILE cc_start: 0.9674 (OUTLIER) cc_final: 0.9416 (mm) REVERT: A 428 PHE cc_start: 0.8211 (t80) cc_final: 0.7626 (t80) REVERT: E 406 GLU cc_start: 0.8694 (mp0) cc_final: 0.8381 (mp0) REVERT: E 452 ARG cc_start: 0.8629 (mtm110) cc_final: 0.8395 (mtm110) REVERT: E 466 ARG cc_start: 0.8399 (tpp80) cc_final: 0.7918 (tpp80) REVERT: E 471 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8071 (tm-30) REVERT: D 83 TYR cc_start: 0.5380 (OUTLIER) cc_final: 0.4696 (m-10) REVERT: D 450 MET cc_start: 0.8781 (tpp) cc_final: 0.8507 (tpp) REVERT: D 496 MET cc_start: 0.5142 (ptp) cc_final: 0.4515 (ptm) REVERT: C 102 GLN cc_start: 0.9246 (pt0) cc_final: 0.8794 (pm20) REVERT: C 256 ILE cc_start: 0.9679 (OUTLIER) cc_final: 0.9427 (mm) REVERT: C 428 PHE cc_start: 0.8152 (t80) cc_final: 0.7766 (t80) REVERT: C 736 GLN cc_start: 0.3209 (OUTLIER) cc_final: 0.2673 (tm-30) REVERT: F 406 GLU cc_start: 0.8744 (mp0) cc_final: 0.8456 (mp0) REVERT: F 466 ARG cc_start: 0.8369 (tpp80) cc_final: 0.7880 (tpp80) REVERT: F 488 CYS cc_start: 0.8244 (m) cc_final: 0.7941 (p) outliers start: 85 outliers final: 52 residues processed: 259 average time/residue: 0.3178 time to fit residues: 135.2573 Evaluate side-chains 232 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 175 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 282 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 247 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 chunk 245 optimal weight: 0.7980 chunk 276 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN D 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.124672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.073752 restraints weight = 58477.530| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.08 r_work: 0.2852 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 25896 Z= 0.132 Angle : 0.632 12.159 35214 Z= 0.303 Chirality : 0.043 0.281 3902 Planarity : 0.004 0.041 4368 Dihedral : 8.555 73.602 4388 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.50 % Favored : 93.43 % Rotamer: Outliers : 3.18 % Allowed : 19.58 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 3030 helix: 0.88 (0.13), residues: 1714 sheet: -0.36 (0.59), residues: 70 loop : -1.91 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 505 HIS 0.008 0.001 HIS A 345 PHE 0.016 0.001 PHE B 523 TYR 0.015 0.001 TYR A 183 ARG 0.009 0.000 ARG F 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 22) link_NAG-ASN : angle 3.49373 ( 66) link_BETA1-4 : bond 0.00428 ( 16) link_BETA1-4 : angle 1.87294 ( 48) hydrogen bonds : bond 0.04369 ( 1236) hydrogen bonds : angle 4.12165 ( 3588) metal coordination : bond 0.00304 ( 4) SS BOND : bond 0.00967 ( 16) SS BOND : angle 2.87111 ( 32) covalent geometry : bond 0.00298 (25838) covalent geometry : angle 0.60472 (35068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 187 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.4850 (OUTLIER) cc_final: 0.4272 (m-10) REVERT: B 446 MET cc_start: 0.7688 (tpp) cc_final: 0.7359 (tpp) REVERT: B 450 MET cc_start: 0.8475 (tpp) cc_final: 0.8177 (tpp) REVERT: A 102 GLN cc_start: 0.9195 (pt0) cc_final: 0.8728 (pm20) REVERT: A 256 ILE cc_start: 0.9661 (OUTLIER) cc_final: 0.9378 (mm) REVERT: A 428 PHE cc_start: 0.8115 (t80) cc_final: 0.7838 (t80) REVERT: A 736 GLN cc_start: 0.3393 (OUTLIER) cc_final: 0.3023 (tm-30) REVERT: E 406 GLU cc_start: 0.8647 (mp0) cc_final: 0.8316 (mp0) REVERT: E 452 ARG cc_start: 0.8546 (mtm110) cc_final: 0.8298 (mtm110) REVERT: E 466 ARG cc_start: 0.8419 (tpp80) cc_final: 0.7956 (tpp80) REVERT: E 471 GLU cc_start: 0.8276 (tm-30) cc_final: 0.8020 (tm-30) REVERT: D 83 TYR cc_start: 0.5266 (OUTLIER) cc_final: 0.4630 (m-10) REVERT: D 100 MET cc_start: 0.8536 (mtt) cc_final: 0.7868 (mpp) REVERT: D 225 MET cc_start: 0.8205 (mtm) cc_final: 0.7831 (ppp) REVERT: C 102 GLN cc_start: 0.9123 (pt0) cc_final: 0.8754 (pm20) REVERT: C 256 ILE cc_start: 0.9657 (OUTLIER) cc_final: 0.9407 (mm) REVERT: C 428 PHE cc_start: 0.8094 (t80) cc_final: 0.7566 (t80) REVERT: F 346 ARG cc_start: 0.7119 (mmm160) cc_final: 0.6816 (tpt90) REVERT: F 406 GLU cc_start: 0.8629 (mp0) cc_final: 0.8291 (mp0) REVERT: F 466 ARG cc_start: 0.8441 (tpp80) cc_final: 0.8001 (tpp80) outliers start: 84 outliers final: 51 residues processed: 261 average time/residue: 0.3212 time to fit residues: 137.6128 Evaluate side-chains 232 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 176 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 295 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 289 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 43 optimal weight: 0.0770 chunk 236 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 overall best weight: 3.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 243 ASN B 283 ASN B 384 ASN B 537 GLN A 345 HIS ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN C 345 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.123033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.071283 restraints weight = 57843.462| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.76 r_work: 0.2836 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 25896 Z= 0.229 Angle : 0.665 12.102 35214 Z= 0.322 Chirality : 0.045 0.268 3902 Planarity : 0.004 0.050 4368 Dihedral : 8.516 71.987 4386 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.83 % Favored : 93.10 % Rotamer: Outliers : 2.73 % Allowed : 20.19 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 3030 helix: 0.86 (0.13), residues: 1716 sheet: -0.47 (0.59), residues: 70 loop : -1.92 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 77 HIS 0.006 0.001 HIS C 241 PHE 0.014 0.001 PHE A 315 TYR 0.021 0.001 TYR A 183 ARG 0.008 0.000 ARG F 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 22) link_NAG-ASN : angle 3.54874 ( 66) link_BETA1-4 : bond 0.00463 ( 16) link_BETA1-4 : angle 1.88391 ( 48) hydrogen bonds : bond 0.04921 ( 1236) hydrogen bonds : angle 4.16301 ( 3588) metal coordination : bond 0.00781 ( 4) SS BOND : bond 0.00818 ( 16) SS BOND : angle 2.75048 ( 32) covalent geometry : bond 0.00544 (25838) covalent geometry : angle 0.63936 (35068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 182 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.4999 (OUTLIER) cc_final: 0.4330 (m-10) REVERT: B 446 MET cc_start: 0.7706 (tpp) cc_final: 0.7458 (tpp) REVERT: A 256 ILE cc_start: 0.9676 (OUTLIER) cc_final: 0.9442 (mm) REVERT: A 428 PHE cc_start: 0.8268 (t80) cc_final: 0.7488 (t80) REVERT: A 736 GLN cc_start: 0.3453 (OUTLIER) cc_final: 0.3038 (tm-30) REVERT: E 406 GLU cc_start: 0.8696 (mp0) cc_final: 0.8325 (mp0) REVERT: E 452 ARG cc_start: 0.8633 (mtm110) cc_final: 0.8387 (mtm110) REVERT: E 466 ARG cc_start: 0.8426 (tpp80) cc_final: 0.7957 (tpp80) REVERT: E 471 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7985 (tm-30) REVERT: D 83 TYR cc_start: 0.5423 (OUTLIER) cc_final: 0.4766 (m-10) REVERT: D 225 MET cc_start: 0.8271 (mtm) cc_final: 0.7828 (ppp) REVERT: D 450 MET cc_start: 0.8639 (tpp) cc_final: 0.8353 (tpp) REVERT: C 256 ILE cc_start: 0.9677 (OUTLIER) cc_final: 0.9449 (mm) REVERT: C 428 PHE cc_start: 0.8231 (t80) cc_final: 0.7743 (t80) REVERT: C 736 GLN cc_start: 0.3085 (OUTLIER) cc_final: 0.2590 (tm-30) REVERT: F 466 ARG cc_start: 0.8446 (tpp80) cc_final: 0.7985 (tpp80) outliers start: 72 outliers final: 51 residues processed: 245 average time/residue: 0.3288 time to fit residues: 132.7609 Evaluate side-chains 235 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 191 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 290 optimal weight: 0.0980 chunk 123 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN B 537 GLN A 345 HIS ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.124828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.073562 restraints weight = 57761.745| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.77 r_work: 0.2892 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25896 Z= 0.116 Angle : 0.619 12.072 35214 Z= 0.297 Chirality : 0.042 0.283 3902 Planarity : 0.004 0.040 4368 Dihedral : 8.204 70.024 4386 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.30 % Favored : 93.63 % Rotamer: Outliers : 2.65 % Allowed : 20.08 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 3030 helix: 1.00 (0.13), residues: 1720 sheet: 0.08 (0.62), residues: 66 loop : -1.85 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 509 HIS 0.031 0.001 HIS C 345 PHE 0.039 0.001 PHE B 489 TYR 0.014 0.001 TYR D 378 ARG 0.010 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00653 ( 22) link_NAG-ASN : angle 3.43304 ( 66) link_BETA1-4 : bond 0.00451 ( 16) link_BETA1-4 : angle 1.88523 ( 48) hydrogen bonds : bond 0.04149 ( 1236) hydrogen bonds : angle 4.04168 ( 3588) metal coordination : bond 0.00212 ( 4) SS BOND : bond 0.00839 ( 16) SS BOND : angle 2.66155 ( 32) covalent geometry : bond 0.00255 (25838) covalent geometry : angle 0.59231 (35068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 184 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.5008 (OUTLIER) cc_final: 0.4224 (m-10) REVERT: B 446 MET cc_start: 0.7656 (tpp) cc_final: 0.7360 (tpp) REVERT: B 450 MET cc_start: 0.8725 (tpp) cc_final: 0.8384 (tpp) REVERT: A 102 GLN cc_start: 0.9218 (pt0) cc_final: 0.8812 (pm20) REVERT: A 256 ILE cc_start: 0.9677 (OUTLIER) cc_final: 0.9392 (mm) REVERT: A 428 PHE cc_start: 0.8156 (t80) cc_final: 0.7805 (t80) REVERT: A 736 GLN cc_start: 0.3340 (OUTLIER) cc_final: 0.2913 (tm-30) REVERT: E 406 GLU cc_start: 0.8766 (mp0) cc_final: 0.8360 (mp0) REVERT: E 452 ARG cc_start: 0.8659 (mtm110) cc_final: 0.8357 (mtm110) REVERT: D 83 TYR cc_start: 0.5564 (OUTLIER) cc_final: 0.4845 (m-10) REVERT: D 96 PHE cc_start: 0.7250 (t80) cc_final: 0.6918 (t80) REVERT: D 100 MET cc_start: 0.8519 (mtt) cc_final: 0.7950 (mpp) REVERT: D 225 MET cc_start: 0.8241 (mtm) cc_final: 0.7842 (ppp) REVERT: D 450 MET cc_start: 0.8549 (tpp) cc_final: 0.8242 (tpp) REVERT: C 102 GLN cc_start: 0.9221 (pt0) cc_final: 0.8832 (pm20) REVERT: C 256 ILE cc_start: 0.9676 (OUTLIER) cc_final: 0.9395 (mm) REVERT: C 428 PHE cc_start: 0.8106 (t80) cc_final: 0.7683 (t80) REVERT: C 736 GLN cc_start: 0.3100 (OUTLIER) cc_final: 0.2593 (tm-30) outliers start: 70 outliers final: 44 residues processed: 247 average time/residue: 0.3226 time to fit residues: 130.3312 Evaluate side-chains 229 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 179 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 156 optimal weight: 30.0000 chunk 187 optimal weight: 0.8980 chunk 41 optimal weight: 30.0000 chunk 112 optimal weight: 0.0970 chunk 144 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.125214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073777 restraints weight = 58778.124| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.83 r_work: 0.2891 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25896 Z= 0.121 Angle : 0.626 14.043 35214 Z= 0.299 Chirality : 0.042 0.280 3902 Planarity : 0.004 0.052 4368 Dihedral : 8.035 68.278 4384 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.70 % Favored : 93.23 % Rotamer: Outliers : 2.08 % Allowed : 20.38 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 3030 helix: 1.02 (0.13), residues: 1722 sheet: 0.19 (0.56), residues: 82 loop : -1.80 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 509 HIS 0.007 0.001 HIS C 345 PHE 0.014 0.001 PHE C 315 TYR 0.015 0.001 TYR D 378 ARG 0.008 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 22) link_NAG-ASN : angle 3.40566 ( 66) link_BETA1-4 : bond 0.00448 ( 16) link_BETA1-4 : angle 1.83943 ( 48) hydrogen bonds : bond 0.04072 ( 1236) hydrogen bonds : angle 4.02418 ( 3588) metal coordination : bond 0.00248 ( 4) SS BOND : bond 0.00910 ( 16) SS BOND : angle 2.87602 ( 32) covalent geometry : bond 0.00273 (25838) covalent geometry : angle 0.59919 (35068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.5056 (OUTLIER) cc_final: 0.4291 (m-10) REVERT: B 446 MET cc_start: 0.7638 (tpp) cc_final: 0.7295 (tpp) REVERT: B 450 MET cc_start: 0.8611 (tpp) cc_final: 0.8270 (tpp) REVERT: B 508 MET cc_start: 0.7990 (mmm) cc_final: 0.7404 (mmm) REVERT: A 256 ILE cc_start: 0.9659 (OUTLIER) cc_final: 0.9397 (mm) REVERT: A 428 PHE cc_start: 0.8133 (t80) cc_final: 0.7785 (t80) REVERT: A 668 GLU cc_start: 0.9022 (pm20) cc_final: 0.8814 (pm20) REVERT: E 406 GLU cc_start: 0.8730 (mp0) cc_final: 0.8325 (mp0) REVERT: E 452 ARG cc_start: 0.8657 (mtm110) cc_final: 0.8350 (mtm110) REVERT: E 472 ILE cc_start: 0.9005 (mm) cc_final: 0.8768 (mt) REVERT: D 83 TYR cc_start: 0.5620 (OUTLIER) cc_final: 0.4801 (m-10) REVERT: D 96 PHE cc_start: 0.7175 (t80) cc_final: 0.6657 (t80) REVERT: D 100 MET cc_start: 0.8428 (mtt) cc_final: 0.7706 (mpp) REVERT: D 450 MET cc_start: 0.8549 (tpp) cc_final: 0.8233 (tpp) REVERT: D 496 MET cc_start: 0.4883 (ptp) cc_final: 0.4218 (ptm) REVERT: C 102 GLN cc_start: 0.9194 (pt0) cc_final: 0.8804 (pm20) REVERT: C 256 ILE cc_start: 0.9671 (OUTLIER) cc_final: 0.9402 (mm) REVERT: C 428 PHE cc_start: 0.8074 (t80) cc_final: 0.7656 (t80) REVERT: F 340 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8398 (tp30) REVERT: F 466 ARG cc_start: 0.8513 (tpp80) cc_final: 0.8072 (tpp80) outliers start: 55 outliers final: 46 residues processed: 236 average time/residue: 0.3214 time to fit residues: 125.8123 Evaluate side-chains 233 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 151 optimal weight: 30.0000 chunk 113 optimal weight: 3.9990 chunk 263 optimal weight: 0.7980 chunk 173 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 275 optimal weight: 0.5980 chunk 154 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN B 384 ASN A 345 HIS ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.126107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.078986 restraints weight = 57794.255| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.13 r_work: 0.2894 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 25896 Z= 0.104 Angle : 0.611 12.994 35214 Z= 0.290 Chirality : 0.041 0.284 3902 Planarity : 0.003 0.041 4368 Dihedral : 7.728 64.709 4384 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.66 % Rotamer: Outliers : 2.08 % Allowed : 20.42 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 3030 helix: 1.14 (0.13), residues: 1706 sheet: 0.58 (0.64), residues: 62 loop : -1.75 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 509 HIS 0.003 0.001 HIS A 34 PHE 0.033 0.001 PHE B 489 TYR 0.013 0.001 TYR D 378 ARG 0.006 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 22) link_NAG-ASN : angle 3.30146 ( 66) link_BETA1-4 : bond 0.00489 ( 16) link_BETA1-4 : angle 1.82322 ( 48) hydrogen bonds : bond 0.03671 ( 1236) hydrogen bonds : angle 3.96052 ( 3588) metal coordination : bond 0.00118 ( 4) SS BOND : bond 0.00846 ( 16) SS BOND : angle 3.24864 ( 32) covalent geometry : bond 0.00220 (25838) covalent geometry : angle 0.58275 (35068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.4949 (OUTLIER) cc_final: 0.4257 (m-10) REVERT: B 385 MET cc_start: 0.8049 (mmm) cc_final: 0.7775 (mtm) REVERT: B 446 MET cc_start: 0.7594 (tpp) cc_final: 0.7249 (tpp) REVERT: B 450 MET cc_start: 0.8701 (tpp) cc_final: 0.8327 (tpp) REVERT: B 508 MET cc_start: 0.8049 (mmm) cc_final: 0.7482 (mmm) REVERT: A 256 ILE cc_start: 0.9649 (OUTLIER) cc_final: 0.9344 (mm) REVERT: A 428 PHE cc_start: 0.7892 (t80) cc_final: 0.7536 (t80) REVERT: A 736 GLN cc_start: 0.3182 (OUTLIER) cc_final: 0.2825 (tm-30) REVERT: E 406 GLU cc_start: 0.8700 (mp0) cc_final: 0.8261 (mp0) REVERT: E 409 GLN cc_start: 0.9057 (mt0) cc_final: 0.8798 (mt0) REVERT: E 452 ARG cc_start: 0.8526 (mtm110) cc_final: 0.8239 (mtm110) REVERT: E 466 ARG cc_start: 0.8522 (tpp80) cc_final: 0.8060 (tpp80) REVERT: D 96 PHE cc_start: 0.7108 (t80) cc_final: 0.6618 (t80) REVERT: D 100 MET cc_start: 0.8439 (mtt) cc_final: 0.7719 (mpp) REVERT: D 344 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7297 (p90) REVERT: D 450 MET cc_start: 0.8540 (tpp) cc_final: 0.8232 (tpp) REVERT: C 102 GLN cc_start: 0.9084 (pt0) cc_final: 0.8656 (pm20) REVERT: C 256 ILE cc_start: 0.9647 (OUTLIER) cc_final: 0.9364 (mm) REVERT: C 428 PHE cc_start: 0.7877 (t80) cc_final: 0.7443 (t80) REVERT: C 736 GLN cc_start: 0.3011 (OUTLIER) cc_final: 0.2614 (tm-30) REVERT: F 346 ARG cc_start: 0.7312 (mmm160) cc_final: 0.7007 (tpt90) REVERT: F 466 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8074 (tpp80) outliers start: 55 outliers final: 39 residues processed: 243 average time/residue: 0.3312 time to fit residues: 133.6531 Evaluate side-chains 231 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 22 optimal weight: 10.0000 chunk 251 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 249 optimal weight: 0.0060 chunk 8 optimal weight: 6.9990 chunk 111 optimal weight: 0.0030 chunk 10 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 228 optimal weight: 0.6980 overall best weight: 0.9208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN A 345 HIS ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 HIS ** F 409 GLN ** 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 = 0.4077 r_free = 0.4077 target = 0.126054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.079233 restraints weight = 57939.187| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.01 r_work: 0.2893 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.181 25896 Z= 0.189 Angle : 0.750 59.144 35214 Z= 0.402 Chirality : 0.044 0.950 3902 Planarity : 0.004 0.067 4368 Dihedral : 7.722 64.685 4380 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.30 % Favored : 93.60 % Rotamer: Outliers : 2.05 % Allowed : 20.72 % Favored : 77.23 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 3030 helix: 1.13 (0.13), residues: 1706 sheet: 0.58 (0.64), residues: 62 loop : -1.74 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP B 505 HIS 0.004 0.001 HIS C 34 PHE 0.023 0.001 PHE B 489 TYR 0.031 0.001 TYR B 504 ARG 0.006 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 22) link_NAG-ASN : angle 3.30247 ( 66) link_BETA1-4 : bond 0.00418 ( 16) link_BETA1-4 : angle 1.83171 ( 48) hydrogen bonds : bond 0.03768 ( 1236) hydrogen bonds : angle 3.97487 ( 3588) metal coordination : bond 0.00126 ( 4) SS BOND : bond 0.01339 ( 16) SS BOND : angle 4.31851 ( 32) covalent geometry : bond 0.00347 (25838) covalent geometry : angle 0.72253 (35068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18379.57 seconds wall clock time: 316 minutes 36.60 seconds (18996.60 seconds total)