Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 04:36:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbv_24989/04_2023/7sbv_24989_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbv_24989/04_2023/7sbv_24989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbv_24989/04_2023/7sbv_24989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbv_24989/04_2023/7sbv_24989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbv_24989/04_2023/7sbv_24989_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbv_24989/04_2023/7sbv_24989_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 188 5.16 5 C 18624 2.51 5 N 4776 2.21 5 O 5751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 223": "OE1" <-> "OE2" Residue "J TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "A PHE 1020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 29339 Number of models: 1 Model: "" Number of chains: 24 Chain: "J" Number of atoms: 9145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9145 Classifications: {'peptide': 1176} Link IDs: {'PTRANS': 51, 'TRANS': 1124} Chain breaks: 5 Chain: "A" Number of atoms: 9115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 9115 Classifications: {'peptide': 1172} Link IDs: {'PTRANS': 53, 'TRANS': 1118} Chain breaks: 7 Chain: "B" Number of atoms: 9199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9199 Classifications: {'peptide': 1183} Link IDs: {'PTRANS': 53, 'TRANS': 1129} Chain breaks: 6 Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 480 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'TRANS': 95} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'UNK:plan-1': 96} Unresolved non-hydrogen planarities: 96 Chain: "C" 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 chiralities: 2 Chain: "D" 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 chiralities: 2 Chain: "E" 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 chiralities: 2 Chain: "F" 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 chiralities: 2 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 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 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 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 chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 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 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 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 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 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 chiralities: 2 Chain: "J" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 148 Unusual residues: {'8Z9': 2, 'NAG': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 102 Unusual residues: {'8Z9': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 15.13, per 1000 atoms: 0.52 Number of scatterers: 29339 At special positions: 0 Unit cell: (150.38, 149.35, 193.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 188 16.00 O 5751 8.00 N 4776 7.00 C 18624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 168 " - pdb=" SG CYS J 201 " distance=2.02 Simple disulfide: pdb=" SG CYS J 180 " - pdb=" SG CYS J 260 " distance=2.03 Simple disulfide: pdb=" SG CYS J 298 " - pdb=" SG CYS J 308 " distance=2.03 Simple disulfide: pdb=" SG CYS J 343 " - pdb=" SG CYS J 368 " distance=2.05 Simple disulfide: pdb=" SG CYS J 386 " - pdb=" SG CYS J 439 " distance=2.02 Simple disulfide: pdb=" SG CYS J 398 " - pdb=" SG CYS J 614 " distance=2.03 Simple disulfide: pdb=" SG CYS J 491 " - pdb=" SG CYS J 561 " distance=2.03 Simple disulfide: pdb=" SG CYS J 499 " - pdb=" SG CYS J 522 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS J 576 " distance=2.02 Simple disulfide: pdb=" SG CYS J 535 " - pdb=" SG CYS J 548 " distance=2.03 Simple disulfide: pdb=" SG CYS J 571 " - pdb=" SG CYS J 578 " distance=2.18 Simple disulfide: pdb=" SG CYS J 591 " - pdb=" SG CYS J 597 " distance=2.04 Simple disulfide: pdb=" SG CYS J 630 " - pdb=" SG CYS J 683 " distance=2.05 Simple disulfide: pdb=" SG CYS J 708 " - pdb=" SG CYS J 732 " distance=2.04 Simple disulfide: pdb=" SG CYS J 747 " - pdb=" SG CYS J 756 " distance=2.02 Simple disulfide: pdb=" SG CYS J 825 " - pdb=" SG CYS J 847 " distance=2.06 Simple disulfide: pdb=" SG CYS J 830 " - pdb=" SG CYS J 836 " distance=2.07 Simple disulfide: pdb=" SG CYS J 937 " - pdb=" SG CYS J 948 " distance=2.07 Simple disulfide: pdb=" SG CYS J1125 " - pdb=" SG CYS J1136 " distance=2.02 Simple disulfide: pdb=" SG CYS J1175 " - pdb=" SG CYS J1220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 173 " distance=2.04 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 201 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 260 " distance=2.02 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 308 " distance=2.02 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.07 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.05 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.08 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 732 " distance=2.04 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 756 " distance=2.02 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 847 " distance=2.06 Simple disulfide: pdb=" SG CYS A 830 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 937 " - pdb=" SG CYS A 948 " distance=2.04 Simple disulfide: pdb=" SG CYS A1125 " - pdb=" SG CYS A1136 " distance=2.03 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 260 " distance=2.02 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 308 " distance=2.04 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.04 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 614 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 576 " distance=2.02 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 597 " distance=2.04 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.07 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 732 " distance=2.04 Simple disulfide: pdb=" SG CYS B 747 " - pdb=" SG CYS B 756 " distance=2.01 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 847 " distance=2.11 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 836 " distance=2.02 Simple disulfide: pdb=" SG CYS B 937 " - pdb=" SG CYS B 948 " distance=2.08 Simple disulfide: pdb=" SG CYS B1125 " - pdb=" SG CYS B1136 " distance=2.02 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1220 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " 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-ASN " NAG A1401 " - " ASN A 212 " " NAG A1402 " - " ASN A 449 " " NAG A1403 " - " ASN A 713 " " NAG A1404 " - " ASN A 787 " " NAG A1405 " - " ASN A 936 " " NAG A1406 " - " ASN A 675 " " NAG A1407 " - " ASN A 695 " " NAG A1408 " - " ASN A 648 " " NAG B1401 " - " ASN B 212 " " NAG B1402 " - " ASN B 449 " " NAG B1403 " - " ASN B 787 " " NAG B1404 " - " ASN B 936 " " NAG B1405 " - " ASN B 675 " " NAG B1406 " - " ASN B 648 " " NAG C 1 " - " ASN J 137 " " NAG D 1 " - " ASN J 738 " " NAG E 1 " - " ASN J1193 " " NAG F 1 " - " ASN J 206 " " NAG G 1 " - " ASN A 137 " " NAG I 1 " - " ASN A 371 " " NAG J1401 " - " ASN J 212 " " NAG J1402 " - " ASN J 371 " " NAG J1403 " - " ASN J 449 " " NAG J1404 " - " ASN J 713 " " NAG J1405 " - " ASN J 787 " " NAG J1406 " - " ASN J 936 " " NAG J1407 " - " ASN J 675 " " NAG J1408 " - " ASN J 695 " " NAG J1409 " - " ASN J 648 " " NAG K 1 " - " ASN A 738 " " NAG M 1 " - " ASN A1193 " " NAG N 1 " - " ASN A 206 " " NAG O 1 " - " ASN B 137 " " NAG P 1 " - " ASN B 371 " " NAG Q 1 " - " ASN B 713 " " NAG R 1 " - " ASN B 738 " " NAG S 1 " - " ASN B1193 " " NAG T 1 " - " ASN B 206 " " NAG U 1 " - " ASN B 695 " Time building additional restraints: 13.08 Conformation dependent library (CDL) restraints added in 4.5 seconds 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7014 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 55 sheets defined 22.7% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.99 Creating SS restraints... Processing helix chain 'J' and resid 92 through 95 Processing helix chain 'J' and resid 264 through 266 No H-bonds generated for 'chain 'J' and resid 264 through 266' Processing helix chain 'J' and resid 302 through 309 Processing helix chain 'J' and resid 345 through 349 Processing helix chain 'J' and resid 357 through 359 No H-bonds generated for 'chain 'J' and resid 357 through 359' Processing helix chain 'J' and resid 372 through 378 removed outlier: 5.061A pdb=" N SER J 377 " --> pdb=" O SER J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 417 Processing helix chain 'J' and resid 424 through 428 Processing helix chain 'J' and resid 447 through 449 No H-bonds generated for 'chain 'J' and resid 447 through 449' Processing helix chain 'J' and resid 459 through 464 removed outlier: 3.866A pdb=" N PHE J 464 " --> pdb=" O TRP J 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 468 through 471 No H-bonds generated for 'chain 'J' and resid 468 through 471' Processing helix chain 'J' and resid 475 through 477 No H-bonds generated for 'chain 'J' and resid 475 through 477' Processing helix chain 'J' and resid 568 through 570 No H-bonds generated for 'chain 'J' and resid 568 through 570' Processing helix chain 'J' and resid 580 through 582 No H-bonds generated for 'chain 'J' and resid 580 through 582' Processing helix chain 'J' and resid 708 through 713 removed outlier: 3.590A pdb=" N ASN J 713 " --> pdb=" O ASN J 709 " (cutoff:3.500A) Processing helix chain 'J' and resid 825 through 829 Processing helix chain 'J' and resid 834 through 873 removed outlier: 4.381A pdb=" N GLN J 839 " --> pdb=" O ALA J 835 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLU J 842 " --> pdb=" O SER J 838 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR J 843 " --> pdb=" O GLN J 839 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER J 845 " --> pdb=" O VAL J 841 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N PHE J 846 " --> pdb=" O GLU J 842 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N CYS J 847 " --> pdb=" O TYR J 843 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP J 848 " --> pdb=" O GLY J 844 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN J 849 " --> pdb=" O SER J 845 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE J 853 " --> pdb=" O ASN J 849 " (cutoff:3.500A) Processing helix chain 'J' and resid 880 through 883 Processing helix chain 'J' and resid 914 through 920 removed outlier: 3.908A pdb=" N LEU J 919 " --> pdb=" O ILE J 915 " (cutoff:3.500A) Processing helix chain 'J' and resid 927 through 932 removed outlier: 3.615A pdb=" N ALA J 932 " --> pdb=" O VAL J 928 " (cutoff:3.500A) Processing helix chain 'J' and resid 934 through 936 No H-bonds generated for 'chain 'J' and resid 934 through 936' Processing helix chain 'J' and resid 946 through 953 Processing helix chain 'J' and resid 964 through 976 removed outlier: 3.761A pdb=" N THR J 975 " --> pdb=" O THR J 971 " (cutoff:3.500A) Processing helix chain 'J' and resid 993 through 995 No H-bonds generated for 'chain 'J' and resid 993 through 995' Processing helix chain 'J' and resid 997 through 1002 removed outlier: 4.148A pdb=" N LEU J1002 " --> pdb=" O ARG J 998 " (cutoff:3.500A) Processing helix chain 'J' and resid 1006 through 1026 removed outlier: 3.987A pdb=" N GLN J1011 " --> pdb=" O ASP J1007 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN J1013 " --> pdb=" O LEU J1009 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS J1014 " --> pdb=" O SER J1010 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU J1015 " --> pdb=" O GLN J1011 " (cutoff:3.500A) Processing helix chain 'J' and resid 1036 through 1053 removed outlier: 4.046A pdb=" N LEU J1052 " --> pdb=" O ASN J1048 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN J1053 " --> pdb=" O ALA J1049 " (cutoff:3.500A) Processing helix chain 'J' and resid 1057 through 1060 Processing helix chain 'J' and resid 1070 through 1076 Processing helix chain 'J' and resid 1079 through 1124 removed outlier: 4.852A pdb=" N ALA J1084 " --> pdb=" O PRO J1080 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG J1088 " --> pdb=" O ALA J1084 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU J1089 " --> pdb=" O GLN J1085 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG J1093 " --> pdb=" O LEU J1089 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ALA J1096 " --> pdb=" O GLY J1092 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN J1103 " --> pdb=" O ALA J1099 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR J1109 " --> pdb=" O LEU J1105 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU J1110 " --> pdb=" O SER J1106 " (cutoff:3.500A) Processing helix chain 'J' and resid 1211 through 1213 No H-bonds generated for 'chain 'J' and resid 1211 through 1213' Processing helix chain 'A' and resid 92 through 95 removed outlier: 3.822A pdb=" N PHE A 95 " --> pdb=" O THR A 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 95' Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 372 through 378 removed outlier: 5.115A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 425 through 428 No H-bonds generated for 'chain 'A' and resid 425 through 428' Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.789A pdb=" N PHE A 464 " --> pdb=" O TRP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 471 No H-bonds generated for 'chain 'A' and resid 468 through 471' Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 708 through 711 No H-bonds generated for 'chain 'A' and resid 708 through 711' Processing helix chain 'A' and resid 825 through 829 Processing helix chain 'A' and resid 834 through 873 removed outlier: 3.525A pdb=" N VAL A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N SER A 845 " --> pdb=" O VAL A 841 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE A 846 " --> pdb=" O GLU A 842 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N CYS A 847 " --> pdb=" O TYR A 843 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP A 848 " --> pdb=" O GLY A 844 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU A 866 " --> pdb=" O ASP A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 883 Processing helix chain 'A' and resid 914 through 921 Processing helix chain 'A' and resid 927 through 932 Processing helix chain 'A' and resid 946 through 953 Processing helix chain 'A' and resid 964 through 978 removed outlier: 3.650A pdb=" N ALA A 977 " --> pdb=" O ALA A 973 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER A 978 " --> pdb=" O ALA A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1002 removed outlier: 3.715A pdb=" N LEU A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1016 removed outlier: 4.020A pdb=" N GLN A1011 " --> pdb=" O ASP A1007 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS A1014 " --> pdb=" O SER A1010 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A1016 " --> pdb=" O ASN A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1030 Processing helix chain 'A' and resid 1036 through 1059 removed outlier: 3.548A pdb=" N VAL A1044 " --> pdb=" O LYS A1040 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A1045 " --> pdb=" O ILE A1041 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA A1047 " --> pdb=" O ALA A1043 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A1048 " --> pdb=" O VAL A1044 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU A1050 " --> pdb=" O ASN A1046 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLN A1058 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1076 Processing helix chain 'A' and resid 1079 through 1123 removed outlier: 4.825A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A1109 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A1110 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1213 No H-bonds generated for 'chain 'A' and resid 1211 through 1213' Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 345 through 349 removed outlier: 3.878A pdb=" N LEU B 349 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 372 through 377 removed outlier: 5.297A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 414 through 417 Processing helix chain 'B' and resid 424 through 427 No H-bonds generated for 'chain 'B' and resid 424 through 427' Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 462 through 464 No H-bonds generated for 'chain 'B' and resid 462 through 464' Processing helix chain 'B' and resid 468 through 471 No H-bonds generated for 'chain 'B' and resid 468 through 471' Processing helix chain 'B' and resid 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 580 through 582 No H-bonds generated for 'chain 'B' and resid 580 through 582' Processing helix chain 'B' and resid 708 through 711 No H-bonds generated for 'chain 'B' and resid 708 through 711' Processing helix chain 'B' and resid 825 through 829 Processing helix chain 'B' and resid 834 through 839 Processing helix chain 'B' and resid 844 through 873 removed outlier: 4.148A pdb=" N GLN B 867 " --> pdb=" O THR B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 883 Processing helix chain 'B' and resid 890 through 892 No H-bonds generated for 'chain 'B' and resid 890 through 892' Processing helix chain 'B' and resid 914 through 921 Processing helix chain 'B' and resid 927 through 936 removed outlier: 4.051A pdb=" N ASN B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 953 Processing helix chain 'B' and resid 964 through 978 removed outlier: 3.782A pdb=" N LEU B 972 " --> pdb=" O SER B 968 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER B 978 " --> pdb=" O ALA B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1002 removed outlier: 3.842A pdb=" N ARG B 998 " --> pdb=" O ASN B 994 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B1002 " --> pdb=" O ARG B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1008 No H-bonds generated for 'chain 'B' and resid 1006 through 1008' Processing helix chain 'B' and resid 1010 through 1030 removed outlier: 4.102A pdb=" N GLN B1013 " --> pdb=" O SER B1010 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS B1014 " --> pdb=" O GLN B1011 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B1016 " --> pdb=" O GLN B1013 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B1017 " --> pdb=" O LYS B1014 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU B1029 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1039 Processing helix chain 'B' and resid 1041 through 1060 removed outlier: 3.631A pdb=" N GLN B1058 " --> pdb=" O ASN B1054 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU B1059 " --> pdb=" O LEU B1055 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER B1060 " --> pdb=" O LEU B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1076 Processing helix chain 'B' and resid 1079 through 1125 removed outlier: 3.607A pdb=" N ARG B1088 " --> pdb=" O ALA B1084 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN B1103 " --> pdb=" O ALA B1099 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B1109 " --> pdb=" O LEU B1105 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1213 No H-bonds generated for 'chain 'B' and resid 1211 through 1213' Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'L' and resid 54 through 56 No H-bonds generated for 'chain 'L' and resid 54 through 56' Processing sheet with id= A, first strand: chain 'J' and resid 29 through 31 Processing sheet with id= B, first strand: chain 'J' and resid 65 through 73 removed outlier: 3.534A pdb=" N ASN J 294 " --> pdb=" O ALA J 285 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'J' and resid 272 through 276 removed outlier: 3.511A pdb=" N PHE J 242 " --> pdb=" O ALA J 229 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'J' and resid 114 through 118 Processing sheet with id= E, first strand: chain 'J' and resid 252 through 255 removed outlier: 3.792A pdb=" N GLY J 161 " --> pdb=" O TYR J 209 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'J' and resid 318 through 321 Processing sheet with id= G, first strand: chain 'J' and resid 331 through 335 removed outlier: 4.009A pdb=" N ALA J 331 " --> pdb=" O CYS J 630 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR J 677 " --> pdb=" O VAL J 647 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TYR J 667 " --> pdb=" O ILE J 680 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU J 659 " --> pdb=" O TYR J 667 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 353 through 355 removed outlier: 6.182A pdb=" N SER J 451 " --> pdb=" O VAL J 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'J' and resid 361 through 365 removed outlier: 3.641A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 484 through 488 Processing sheet with id= K, first strand: chain 'J' and resid 491 through 494 removed outlier: 4.443A pdb=" N CYS J 491 " --> pdb=" O SER J 553 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 773 through 777 removed outlier: 6.108A pdb=" N VAL J 757 " --> pdb=" O THR J 750 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N THR J 750 " --> pdb=" O VAL J 757 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'J' and resid 797 through 802 Processing sheet with id= N, first strand: chain 'J' and resid 805 through 808 Processing sheet with id= O, first strand: chain 'J' and resid 811 through 815 removed outlier: 3.502A pdb=" N ILE J1143 " --> pdb=" O PHE J1158 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 820 through 823 removed outlier: 4.117A pdb=" N LYS J 820 " --> pdb=" O LEU J 958 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 1182 through 1184 Processing sheet with id= R, first strand: chain 'J' and resid 1187 through 1192 Processing sheet with id= S, first strand: chain 'A' and resid 29 through 31 Processing sheet with id= T, first strand: chain 'A' and resid 65 through 73 removed outlier: 3.794A pdb=" N ASN A 294 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 272 through 276 removed outlier: 5.466A pdb=" N PHE A 231 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE A 240 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 114 through 118 Processing sheet with id= W, first strand: chain 'A' and resid 252 through 255 removed outlier: 3.646A pdb=" N GLY A 161 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 318 through 321 Processing sheet with id= Y, first strand: chain 'A' and resid 331 through 335 removed outlier: 3.704A pdb=" N ALA A 331 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR A 677 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.175A pdb=" N SER A 451 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'A' and resid 361 through 366 removed outlier: 4.008A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 484 through 488 Processing sheet with id= AC, first strand: chain 'A' and resid 492 through 494 Processing sheet with id= AD, first strand: chain 'A' and resid 755 through 759 Processing sheet with id= AE, first strand: chain 'A' and resid 797 through 802 Processing sheet with id= AF, first strand: chain 'A' and resid 805 through 815 Processing sheet with id= AG, first strand: chain 'A' and resid 820 through 823 removed outlier: 4.227A pdb=" N LYS A 820 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 958 " --> pdb=" O LYS A 820 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 1174 through 1176 Processing sheet with id= AI, first strand: chain 'A' and resid 1187 through 1192 Processing sheet with id= AJ, first strand: chain 'B' and resid 29 through 31 Processing sheet with id= AK, first strand: chain 'B' and resid 64 through 73 removed outlier: 3.782A pdb=" N ASN B 294 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'B' and resid 272 through 276 removed outlier: 5.526A pdb=" N PHE B 231 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHE B 240 " --> pdb=" O PHE B 231 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 114 through 118 Processing sheet with id= AN, first strand: chain 'B' and resid 252 through 255 Processing sheet with id= AO, first strand: chain 'B' and resid 318 through 321 Processing sheet with id= AP, first strand: chain 'B' and resid 324 through 326 Processing sheet with id= AQ, first strand: chain 'B' and resid 332 through 335 removed outlier: 8.034A pdb=" N VAL B 333 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN B 632 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ARG B 335 " --> pdb=" O ASN B 632 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP B 634 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 680 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.075A pdb=" N SER B 451 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.605A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'B' and resid 484 through 488 Processing sheet with id= AU, first strand: chain 'B' and resid 773 through 777 removed outlier: 6.388A pdb=" N VAL B 757 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N THR B 750 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'B' and resid 797 through 802 Processing sheet with id= AW, first strand: chain 'B' and resid 805 through 815 Processing sheet with id= AX, first strand: chain 'B' and resid 820 through 823 removed outlier: 4.349A pdb=" N LYS B 820 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'B' and resid 1225 through 1227 Processing sheet with id= AZ, first strand: chain 'B' and resid 1187 through 1192 removed outlier: 4.462A pdb=" N GLY B1200 " --> pdb=" O TYR B1205 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N TYR B1205 " --> pdb=" O GLY B1200 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'H' and resid 5 through 8 removed outlier: 3.504A pdb=" N UNK H 21 " --> pdb=" O UNK H 8 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'H' and resid 50 through 53 removed outlier: 4.340A pdb=" N UNK H 50 " --> pdb=" O UNK H 37 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'L' and resid 31 through 36 909 hydrogen bonds defined for protein. 2478 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: 12.67 Time building geometry restraints manager: 13.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 8642 1.33 - 1.48: 9474 1.48 - 1.62: 11602 1.62 - 1.77: 79 1.77 - 1.91: 174 Bond restraints: 29971 Sorted by residual: bond pdb=" CB HIS J1157 " pdb=" CG HIS J1157 " ideal model delta sigma weight residual 1.497 1.388 0.109 1.40e-02 5.10e+03 6.11e+01 bond pdb=" CB HIS A 193 " pdb=" CG HIS A 193 " ideal model delta sigma weight residual 1.497 1.399 0.098 1.40e-02 5.10e+03 4.94e+01 bond pdb=" CB ILE A 33 " pdb=" CG1 ILE A 33 " ideal model delta sigma weight residual 1.530 1.666 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" CB HIS B 219 " pdb=" CG HIS B 219 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.19e+01 bond pdb=" CB HIS J 483 " pdb=" CG HIS J 483 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.14e+01 ... (remaining 29966 not shown) Histogram of bond angle deviations from ideal: 94.24 - 102.26: 187 102.26 - 110.27: 8540 110.27 - 118.28: 14526 118.28 - 126.29: 17260 126.29 - 134.30: 302 Bond angle restraints: 40815 Sorted by residual: angle pdb=" N PHE J 240 " pdb=" CA PHE J 240 " pdb=" C PHE J 240 " ideal model delta sigma weight residual 111.33 124.77 -13.44 1.21e+00 6.83e-01 1.23e+02 angle pdb=" C PRO A 959 " pdb=" N PRO A 960 " pdb=" CA PRO A 960 " ideal model delta sigma weight residual 120.03 129.12 -9.09 9.90e-01 1.02e+00 8.43e+01 angle pdb=" N GLY J1092 " pdb=" CA GLY J1092 " pdb=" C GLY J1092 " ideal model delta sigma weight residual 112.66 98.17 14.49 1.62e+00 3.81e-01 8.00e+01 angle pdb=" C PRO B 959 " pdb=" N PRO B 960 " pdb=" CA PRO B 960 " ideal model delta sigma weight residual 120.03 128.73 -8.70 9.90e-01 1.02e+00 7.71e+01 angle pdb=" C ALA J1227 " pdb=" N PRO J1228 " pdb=" CA PRO J1228 " ideal model delta sigma weight residual 119.56 128.49 -8.93 1.02e+00 9.61e-01 7.66e+01 ... (remaining 40810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.39: 17056 25.39 - 50.78: 274 50.78 - 76.16: 63 76.16 - 101.55: 16 101.55 - 126.94: 2 Dihedral angle restraints: 17411 sinusoidal: 6473 harmonic: 10938 Sorted by residual: dihedral pdb=" CB CYS J 535 " pdb=" SG CYS J 535 " pdb=" SG CYS J 548 " pdb=" CB CYS J 548 " ideal model delta sinusoidal sigma weight residual -86.00 -165.87 79.87 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS J 491 " pdb=" SG CYS J 491 " pdb=" SG CYS J 561 " pdb=" CB CYS J 561 " ideal model delta sinusoidal sigma weight residual -86.00 -129.87 43.87 1 1.00e+01 1.00e-02 2.68e+01 dihedral pdb=" CB CYS B 491 " pdb=" SG CYS B 491 " pdb=" SG CYS B 561 " pdb=" CB CYS B 561 " ideal model delta sinusoidal sigma weight residual -86.00 -126.46 40.46 1 1.00e+01 1.00e-02 2.30e+01 ... (remaining 17408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 3349 0.102 - 0.204: 1055 0.204 - 0.306: 249 0.306 - 0.408: 87 0.408 - 0.510: 56 Chirality restraints: 4796 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.22e+02 ... (remaining 4793 not shown) Planarity restraints: 5247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 137 " 0.064 2.00e-02 2.50e+03 6.74e-02 5.68e+01 pdb=" CG ASN A 137 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 137 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 137 " -0.106 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 695 " 0.062 2.00e-02 2.50e+03 6.50e-02 5.28e+01 pdb=" CG ASN J 695 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN J 695 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN J 695 " -0.102 2.00e-02 2.50e+03 pdb=" C1 NAG J1408 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 695 " -0.059 2.00e-02 2.50e+03 6.18e-02 4.78e+01 pdb=" CG ASN A 695 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 695 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 695 " 0.097 2.00e-02 2.50e+03 pdb=" C1 NAG A1407 " -0.074 2.00e-02 2.50e+03 ... (remaining 5244 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7884 2.80 - 3.33: 26869 3.33 - 3.85: 47998 3.85 - 4.38: 59998 4.38 - 4.90: 96328 Nonbonded interactions: 239077 Sorted by model distance: nonbonded pdb=" N ASN A1046 " pdb=" O ASN A1046 " model vdw 2.276 2.496 nonbonded pdb=" N LEU J1055 " pdb=" O LEU J1055 " model vdw 2.304 2.496 nonbonded pdb=" N GLY J1092 " pdb=" O GLY J1092 " model vdw 2.305 2.496 nonbonded pdb=" O ASN J 787 " pdb=" OD1 ASP J 788 " model vdw 2.310 3.040 nonbonded pdb=" N ALA A 933 " pdb=" O ALA A 933 " model vdw 2.390 2.496 ... (remaining 239072 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 32 or resid 39 through 900 or resid 910 through \ 1232 or resid 1402 through 1406)) selection = (chain 'B' and (resid 15 through 22 or resid 28 through 32 or resid 39 through 1 \ 51 or resid 160 through 195 or resid 199 through 505 or resid 517 through 760 or \ resid 771 through 900 or resid 910 through 1232 or resid 1402 through 1406)) selection = (chain 'J' and (resid 15 through 22 or resid 28 through 195 or resid 199 through \ 505 or resid 517 through 770 or resid 772 through 1232 or resid 1401 through 14 \ 05)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 1.690 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: 0.030 Extract box with map and model: 11.330 Check model and map are aligned: 0.460 Set scattering table: 0.250 Process input model: 75.850 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.270 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 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 : 0.023 0.151 29971 Z= 1.462 Angle : 1.763 14.492 40815 Z= 1.178 Chirality : 0.121 0.510 4796 Planarity : 0.009 0.044 5208 Dihedral : 10.194 126.940 10208 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 3489 helix: -1.77 (0.15), residues: 791 sheet: 1.07 (0.17), residues: 755 loop : 0.21 (0.14), residues: 1943 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 311 time to evaluate : 3.697 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 317 average time/residue: 0.4245 time to fit residues: 214.7040 Evaluate side-chains 147 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 142 time to evaluate : 3.498 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2963 time to fit residues: 7.3282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 337 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 426 GLN J 483 HIS J 839 GLN J1061 ASN A 31 ASN A 177 HIS A 252 HIS A 418 GLN A 839 GLN A 849 ASN A 996 GLN ** A1054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 ASN A1213 ASN B 177 HIS B 219 HIS B 426 GLN B 593 GLN ** B 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 29971 Z= 0.193 Angle : 0.618 12.200 40815 Z= 0.334 Chirality : 0.044 0.216 4796 Planarity : 0.004 0.055 5208 Dihedral : 6.980 117.713 4058 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3489 helix: -0.21 (0.19), residues: 780 sheet: 0.78 (0.17), residues: 758 loop : -0.03 (0.14), residues: 1951 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 194 average time/residue: 0.4081 time to fit residues: 133.6692 Evaluate side-chains 135 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 4.063 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2830 time to fit residues: 13.0653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 281 optimal weight: 0.6980 chunk 230 optimal weight: 4.9990 chunk 93 optimal weight: 0.0010 chunk 338 optimal weight: 4.9990 chunk 365 optimal weight: 20.0000 chunk 301 optimal weight: 5.9990 chunk 335 optimal weight: 7.9990 chunk 115 optimal weight: 0.0670 chunk 271 optimal weight: 4.9990 overall best weight: 1.2926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 252 HIS ** J 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1058 GLN J1071 GLN ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN A 849 ASN A 996 GLN B 252 HIS B1138 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 29971 Z= 0.195 Angle : 0.536 9.376 40815 Z= 0.288 Chirality : 0.043 0.302 4796 Planarity : 0.004 0.044 5208 Dihedral : 6.087 99.342 4058 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3489 helix: 0.29 (0.20), residues: 780 sheet: 0.84 (0.18), residues: 748 loop : -0.20 (0.14), residues: 1961 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 147 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 168 average time/residue: 0.3836 time to fit residues: 109.2945 Evaluate side-chains 137 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 3.349 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2595 time to fit residues: 13.5856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 339 optimal weight: 3.9990 chunk 359 optimal weight: 40.0000 chunk 177 optimal weight: 0.5980 chunk 321 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 193 HIS ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A 777 ASN B 777 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.092 29971 Z= 0.320 Angle : 0.576 10.014 40815 Z= 0.306 Chirality : 0.045 0.224 4796 Planarity : 0.004 0.049 5208 Dihedral : 5.965 81.080 4058 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3489 helix: 0.40 (0.20), residues: 786 sheet: 0.73 (0.18), residues: 734 loop : -0.38 (0.14), residues: 1969 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 3.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 18 residues processed: 142 average time/residue: 0.4049 time to fit residues: 97.1210 Evaluate side-chains 133 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 3.416 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.3362 time to fit residues: 15.0368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 267 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 306 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 322 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 160 GLN J1103 GLN ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 29971 Z= 0.185 Angle : 0.501 9.152 40815 Z= 0.267 Chirality : 0.042 0.223 4796 Planarity : 0.004 0.048 5208 Dihedral : 5.613 77.412 4058 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3489 helix: 0.61 (0.20), residues: 786 sheet: 0.82 (0.18), residues: 741 loop : -0.40 (0.14), residues: 1962 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 3.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 137 average time/residue: 0.4178 time to fit residues: 96.8506 Evaluate side-chains 124 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 3.401 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.2749 time to fit residues: 9.5322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 4.9990 chunk 323 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 359 optimal weight: 40.0000 chunk 298 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 598 ASN J 663 ASN J 777 ASN J1157 HIS ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN A 721 GLN B1057 GLN B1091 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.073 29971 Z= 0.572 Angle : 0.686 10.842 40815 Z= 0.359 Chirality : 0.049 0.254 4796 Planarity : 0.005 0.062 5208 Dihedral : 6.292 76.789 4058 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3489 helix: 0.44 (0.20), residues: 778 sheet: 0.57 (0.18), residues: 737 loop : -0.72 (0.13), residues: 1974 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 135 average time/residue: 0.4097 time to fit residues: 93.6323 Evaluate side-chains 131 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 3.199 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3007 time to fit residues: 14.4954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 205 optimal weight: 0.5980 chunk 262 optimal weight: 0.9990 chunk 203 optimal weight: 0.7980 chunk 302 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 358 optimal weight: 20.0000 chunk 224 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 160 GLN J 598 ASN ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.090 29971 Z= 0.142 Angle : 0.503 9.011 40815 Z= 0.268 Chirality : 0.042 0.232 4796 Planarity : 0.004 0.051 5208 Dihedral : 5.638 77.512 4058 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3489 helix: 0.75 (0.20), residues: 774 sheet: 0.77 (0.18), residues: 729 loop : -0.62 (0.14), residues: 1986 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 3.677 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 131 average time/residue: 0.4161 time to fit residues: 92.0142 Evaluate side-chains 118 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 3.218 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2970 time to fit residues: 6.8933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 69 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 HIS A 187 HIS A1057 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 29971 Z= 0.420 Angle : 0.603 10.158 40815 Z= 0.317 Chirality : 0.046 0.258 4796 Planarity : 0.004 0.055 5208 Dihedral : 5.939 78.768 4058 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3489 helix: 0.72 (0.20), residues: 770 sheet: 0.67 (0.18), residues: 728 loop : -0.77 (0.13), residues: 1991 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 3.352 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 123 average time/residue: 0.4505 time to fit residues: 93.4950 Evaluate side-chains 121 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 3.443 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3311 time to fit residues: 9.1985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 0.7980 chunk 343 optimal weight: 3.9990 chunk 313 optimal weight: 4.9990 chunk 334 optimal weight: 0.8980 chunk 201 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 262 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 301 optimal weight: 0.8980 chunk 316 optimal weight: 0.7980 chunk 332 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 160 GLN A 606 HIS ** A1054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 29971 Z= 0.130 Angle : 0.492 10.379 40815 Z= 0.263 Chirality : 0.041 0.227 4796 Planarity : 0.004 0.051 5208 Dihedral : 5.410 83.621 4058 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3489 helix: 0.90 (0.20), residues: 778 sheet: 0.75 (0.18), residues: 721 loop : -0.66 (0.14), residues: 1990 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 3.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 130 average time/residue: 0.4076 time to fit residues: 90.3387 Evaluate side-chains 115 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 3.408 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2628 time to fit residues: 5.4957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.7980 chunk 353 optimal weight: 40.0000 chunk 215 optimal weight: 0.8980 chunk 167 optimal weight: 6.9990 chunk 245 optimal weight: 3.9990 chunk 370 optimal weight: 30.0000 chunk 341 optimal weight: 0.9980 chunk 295 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 160 GLN J 193 HIS ** A1054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 29971 Z= 0.201 Angle : 0.500 9.462 40815 Z= 0.266 Chirality : 0.042 0.231 4796 Planarity : 0.004 0.062 5208 Dihedral : 5.388 86.408 4058 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3489 helix: 0.99 (0.20), residues: 779 sheet: 0.79 (0.18), residues: 714 loop : -0.65 (0.14), residues: 1996 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 3.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 119 average time/residue: 0.4306 time to fit residues: 88.0011 Evaluate side-chains 122 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 3.631 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.3011 time to fit residues: 10.2794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 10.0000 chunk 314 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 272 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 295 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 303 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 186 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.071008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.053645 restraints weight = 67194.553| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.67 r_work: 0.2526 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2395 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 29971 Z= 0.368 Angle : 0.577 9.918 40815 Z= 0.304 Chirality : 0.045 0.259 4796 Planarity : 0.004 0.066 5208 Dihedral : 5.763 88.984 4058 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3489 helix: 0.84 (0.20), residues: 777 sheet: 0.72 (0.18), residues: 719 loop : -0.78 (0.14), residues: 1993 =============================================================================== Job complete usr+sys time: 4842.17 seconds wall clock time: 89 minutes 56.17 seconds (5396.17 seconds total)