Starting phenix.real_space_refine (version: dev) on Mon Feb 27 04:49:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sby_24992/02_2023/7sby_24992_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sby_24992/02_2023/7sby_24992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sby_24992/02_2023/7sby_24992.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sby_24992/02_2023/7sby_24992.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sby_24992/02_2023/7sby_24992_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sby_24992/02_2023/7sby_24992_updated.pdb" } resolution = 3.0 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= 0.009 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 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 PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 942": "OE1" <-> "OE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1207": "OE1" <-> "OE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 779": "OE1" <-> "OE2" Residue "B GLU 811": "OE1" <-> "OE2" Residue "B GLU 1124": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29314 Number of models: 1 Model: "" Number of chains: 23 Chain: "H" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 610 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'TRANS': 121} Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'UNK:plan-1': 122} Unresolved non-hydrogen planarities: 122 Chain: "L" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 500 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 100} Unresolved non-hydrogen planarities: 100 Chain: "J" Number of atoms: 9114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1171, 9114 Classifications: {'peptide': 1171} Link IDs: {'PTRANS': 52, 'TRANS': 1118} Chain breaks: 7 Chain: "A" Number of atoms: 9147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9147 Classifications: {'peptide': 1176} Link IDs: {'PTRANS': 51, 'TRANS': 1124} Chain breaks: 5 Chain: "B" Number of atoms: 9097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9097 Classifications: {'peptide': 1169} Link IDs: {'PTRANS': 50, 'TRANS': 1118} Chain breaks: 7 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: 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 dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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: 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: "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: 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 dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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: "J" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Unusual residues: {'8Z9': 2, 'NAG': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 144 Unusual residues: {'8Z9': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.57, per 1000 atoms: 0.53 Number of scatterers: 29314 At special positions: 0 Unit cell: (152.44, 148.32, 181.28, 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 189 16.00 O 5740 8.00 N 4767 7.00 C 18618 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=2.02 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=2.07 Simple disulfide: pdb=" SG CYS J 386 " - pdb=" SG CYS J 439 " distance=2.03 Simple disulfide: pdb=" SG CYS J 398 " - pdb=" SG CYS J 614 " distance=2.09 Simple disulfide: pdb=" SG CYS J 491 " - pdb=" SG CYS J 561 " distance=2.16 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=2.03 Simple disulfide: pdb=" SG CYS J 591 " - pdb=" SG CYS J 597 " distance=2.05 Simple disulfide: pdb=" SG CYS J 630 " - pdb=" SG CYS J 683 " distance=2.07 Simple disulfide: pdb=" SG CYS J 708 " - pdb=" SG CYS J 732 " distance=2.09 Simple disulfide: pdb=" SG CYS J 747 " - pdb=" SG CYS J 756 " distance=2.01 Simple disulfide: pdb=" SG CYS J 825 " - pdb=" SG CYS J 847 " distance=2.11 Simple disulfide: pdb=" SG CYS J 830 " - pdb=" SG CYS J 836 " distance=2.03 Simple disulfide: pdb=" SG CYS J 937 " - pdb=" SG CYS J 948 " distance=2.11 Simple disulfide: pdb=" SG CYS J1125 " - pdb=" SG CYS J1136 " distance=2.01 Simple disulfide: pdb=" SG CYS J1175 " - pdb=" SG CYS J1220 " distance=2.04 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 201 " distance=2.05 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 260 " distance=2.04 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 308 " distance=2.01 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.04 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.04 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.13 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=2.04 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.04 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.05 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 732 " distance=2.06 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 847 " distance=2.08 Simple disulfide: pdb=" SG CYS A 830 " - pdb=" SG CYS A 836 " distance=2.06 Simple disulfide: pdb=" SG CYS A 937 " - pdb=" SG CYS A 948 " distance=2.08 Simple disulfide: pdb=" SG CYS A1125 " - pdb=" SG CYS A1136 " distance=2.03 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1220 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 260 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 308 " distance=2.03 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=2.07 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.13 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=2.05 Simple disulfide: pdb=" SG CYS B 747 " - pdb=" SG CYS B 756 " distance=2.02 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 847 " distance=2.10 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 937 " - pdb=" SG CYS B 948 " distance=2.09 Simple disulfide: pdb=" SG CYS B1125 " - pdb=" SG CYS B1136 " distance=2.02 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1220 " distance=2.03 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 D 2 " - " BMA D 3 " " 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1401 " - " ASN A 449 " " NAG A1402 " - " ASN A 675 " " NAG A1403 " - " ASN A 648 " " NAG A1404 " - " ASN A 695 " " NAG A1405 " - " ASN A 787 " " NAG A1406 " - " ASN A1223 " " NAG B1401 " - " ASN B 936 " " NAG B1402 " - " ASN B 63 " " NAG B1403 " - " ASN B 212 " " NAG B1404 " - " ASN B 449 " " NAG B1405 " - " ASN B 648 " " NAG B1406 " - " ASN B 713 " " NAG B1407 " - " ASN B 787 " " NAG B1408 " - " ASN B1193 " " NAG B1409 " - " ASN B1223 " " NAG C 1 " - " ASN J 371 " " NAG D 1 " - " ASN J 206 " " NAG E 1 " - " ASN J 675 " " NAG F 1 " - " ASN A 206 " " NAG G 1 " - " ASN A 371 " " NAG I 1 " - " ASN A 713 " " NAG J1401 " - " ASN J 137 " " NAG J1402 " - " ASN J 212 " " NAG J1403 " - " ASN J 449 " " NAG J1404 " - " ASN J 713 " " NAG J1405 " - " ASN J 738 " " NAG J1406 " - " ASN J 787 " " NAG J1407 " - " ASN J 936 " " NAG J1408 " - " ASN J1193 " " NAG J1409 " - " ASN J 695 " " NAG J1410 " - " ASN J 648 " " NAG K 1 " - " ASN A 738 " " NAG M 1 " - " ASN A1193 " " NAG N 1 " - " ASN A 936 " " NAG O 1 " - " ASN A 137 " " NAG P 1 " - " ASN B 738 " " NAG Q 1 " - " ASN B 137 " " NAG R 1 " - " ASN B 206 " " NAG S 1 " - " ASN B 371 " " NAG T 1 " - " ASN B 675 " Time building additional restraints: 11.92 Conformation dependent library (CDL) restraints added in 4.1 seconds 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7010 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 57 sheets defined 23.2% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 90 through 92 No H-bonds generated for 'chain 'H' and resid 90 through 92' Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'J' and resid 92 through 95 Processing helix chain 'J' and resid 182 through 184 No H-bonds generated for 'chain 'J' and resid 182 through 184' 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 377 removed outlier: 4.862A pdb=" N SER J 377 " --> pdb=" O SER J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 393 No H-bonds generated for 'chain 'J' and resid 391 through 393' Processing helix chain 'J' and resid 414 through 417 Processing helix chain 'J' and resid 425 through 428 No H-bonds generated for 'chain 'J' and resid 425 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: 3.937A 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 539 through 541 No H-bonds generated for 'chain 'J' and resid 539 through 541' 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 711 No H-bonds generated for 'chain 'J' and resid 708 through 711' Processing helix chain 'J' and resid 825 through 829 Processing helix chain 'J' and resid 834 through 873 removed outlier: 3.692A pdb=" N VAL J 841 " --> pdb=" O LYS J 837 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLU J 842 " --> pdb=" O SER J 838 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR J 843 " --> pdb=" O GLN J 839 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER J 845 " --> pdb=" O VAL J 841 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N PHE J 846 " --> pdb=" O GLU J 842 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N CYS J 847 " --> pdb=" O TYR J 843 " (cutoff:3.500A) Processing helix chain 'J' and resid 880 through 883 Processing helix chain 'J' and resid 914 through 921 Processing helix chain 'J' and resid 927 through 936 removed outlier: 3.878A pdb=" N ASN J 936 " --> pdb=" O ALA J 932 " (cutoff:3.500A) Processing helix chain 'J' and resid 946 through 953 removed outlier: 3.562A pdb=" N LYS J 953 " --> pdb=" O VAL J 949 " (cutoff:3.500A) Processing helix chain 'J' and resid 964 through 979 removed outlier: 3.560A pdb=" N THR J 975 " --> pdb=" O THR J 971 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER J 978 " --> pdb=" O ALA J 974 " (cutoff:3.500A) Processing helix chain 'J' and resid 991 through 1002 removed outlier: 3.862A pdb=" N LEU J1002 " --> pdb=" O ARG J 998 " (cutoff:3.500A) Processing helix chain 'J' and resid 1006 through 1011 removed outlier: 4.225A pdb=" N GLN J1011 " --> pdb=" O ASP J1007 " (cutoff:3.500A) Processing helix chain 'J' and resid 1013 through 1030 Processing helix chain 'J' and resid 1036 through 1060 removed outlier: 3.698A pdb=" N GLN J1057 " --> pdb=" O ASN J1053 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN J1058 " --> pdb=" O ASN J1054 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU J1059 " --> pdb=" O LEU J1055 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER J1060 " --> pdb=" O LEU J1056 " (cutoff:3.500A) Processing helix chain 'J' and resid 1070 through 1076 Processing helix chain 'J' and resid 1079 through 1124 removed outlier: 4.748A pdb=" N ALA J1084 " --> pdb=" O PRO J1080 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR J1109 " --> pdb=" O LEU J1105 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU J1110 " --> pdb=" O SER J1106 " (cutoff:3.500A) 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 372 through 378 removed outlier: 4.963A 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 463 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 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 713 Processing helix chain 'A' and resid 825 through 829 Processing helix chain 'A' and resid 834 through 873 removed outlier: 3.904A pdb=" N GLN A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLU A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N SER A 845 " --> pdb=" O VAL A 841 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE A 846 " --> pdb=" O GLU A 842 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS A 847 " --> pdb=" O TYR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 884 No H-bonds generated for 'chain 'A' and resid 882 through 884' Processing helix chain 'A' and resid 914 through 921 Processing helix chain 'A' and resid 927 through 936 removed outlier: 3.874A pdb=" N ASN A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 952 Processing helix chain 'A' and resid 964 through 978 removed outlier: 4.029A pdb=" N SER A 978 " --> pdb=" O ALA A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 986 No H-bonds generated for 'chain 'A' and resid 984 through 986' Processing helix chain 'A' and resid 991 through 1002 removed outlier: 3.826A pdb=" N LEU A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1011 Processing helix chain 'A' and resid 1013 through 1029 Processing helix chain 'A' and resid 1036 through 1060 removed outlier: 4.052A pdb=" N ALA A1047 " --> pdb=" O ALA A1043 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A1048 " --> pdb=" O VAL A1044 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU A1050 " --> pdb=" O ASN A1046 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER A1060 " --> pdb=" O LEU A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1076 Processing helix chain 'A' and resid 1079 through 1124 removed outlier: 4.812A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN A1103 " --> pdb=" O ALA A1099 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A1109 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 3.726A 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 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' 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 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 378 removed outlier: 4.248A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 378 " --> pdb=" O SER B 374 " (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 425 through 428 No H-bonds generated for 'chain 'B' and resid 425 through 428' 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 459 through 463 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 713 Processing helix chain 'B' and resid 825 through 829 Processing helix chain 'B' and resid 834 through 872 removed outlier: 4.330A pdb=" N GLN B 839 " --> pdb=" O ALA B 835 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 841 " --> pdb=" O LYS B 837 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLU B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR B 843 " --> pdb=" O GLN B 839 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER B 845 " --> pdb=" O VAL B 841 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE B 846 " --> pdb=" O GLU B 842 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N CYS B 847 " --> pdb=" O TYR B 843 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 848 " --> pdb=" O GLY B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 883 Processing helix chain 'B' and resid 914 through 921 Processing helix chain 'B' and resid 927 through 936 removed outlier: 4.009A 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: 4.276A pdb=" N SER B 978 " --> pdb=" O ALA B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 998 Processing helix chain 'B' and resid 1006 through 1011 removed outlier: 4.900A pdb=" N GLN B1011 " --> pdb=" O ASP B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1030 Processing helix chain 'B' and resid 1036 through 1060 removed outlier: 4.083A pdb=" N ALA B1047 " --> pdb=" O ALA B1043 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN B1048 " --> pdb=" O VAL B1044 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLU B1050 " --> pdb=" O ASN B1046 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN B1053 " --> pdb=" O ALA B1049 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B1058 " --> pdb=" O ASN B1054 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU B1059 " --> pdb=" O LEU B1055 " (cutoff:3.500A) removed outlier: 4.480A 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 1099 removed outlier: 3.879A pdb=" N ALA B1084 " --> pdb=" O PRO B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1101 through 1124 removed outlier: 3.687A pdb=" N THR B1109 " --> pdb=" O LEU B1105 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B1110 " --> pdb=" O SER B1106 " (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 sheet with id= A, first strand: chain 'H' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'H' and resid 118 through 120 removed outlier: 5.782A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= D, first strand: chain 'L' and resid 84 through 88 removed outlier: 3.760A pdb=" N UNK L 84 " --> pdb=" O UNK L 38 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N UNK L 37 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N UNK L 46 " --> pdb=" O UNK L 37 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'J' and resid 29 through 31 Processing sheet with id= F, first strand: chain 'J' and resid 42 through 44 Processing sheet with id= G, first strand: chain 'J' and resid 64 through 73 removed outlier: 3.799A pdb=" N ASN J 294 " --> pdb=" O ALA J 285 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 272 through 276 removed outlier: 5.534A pdb=" N PHE J 231 " --> pdb=" O PHE J 240 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE J 240 " --> pdb=" O PHE J 231 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'J' and resid 114 through 118 Processing sheet with id= J, first strand: chain 'J' and resid 252 through 255 removed outlier: 3.675A pdb=" N GLY J 161 " --> pdb=" O TYR J 209 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 177 through 179 No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'J' and resid 318 through 321 Processing sheet with id= M, first strand: chain 'J' and resid 332 through 335 removed outlier: 8.018A pdb=" N VAL J 333 " --> pdb=" O CYS J 630 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN J 632 " --> pdb=" O VAL J 333 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ARG J 335 " --> pdb=" O ASN J 632 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP J 634 " --> pdb=" O ARG J 335 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR J 677 " --> pdb=" O VAL J 647 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TYR J 667 " --> pdb=" O ILE J 680 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU J 659 " --> pdb=" O TYR J 667 " (cutoff:3.500A) Processing sheet with id= N, 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= N Processing sheet with id= O, first strand: chain 'J' and resid 361 through 365 removed outlier: 3.612A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN J 444 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA J 381 " --> pdb=" O ASN J 444 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 484 through 488 Processing sheet with id= Q, first strand: chain 'J' and resid 755 through 759 Processing sheet with id= R, first strand: chain 'J' and resid 797 through 802 Processing sheet with id= S, first strand: chain 'J' and resid 805 through 815 Processing sheet with id= T, first strand: chain 'J' and resid 820 through 823 removed outlier: 4.212A pdb=" N LYS J 820 " --> pdb=" O LEU J 958 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 1225 through 1227 Processing sheet with id= V, first strand: chain 'J' and resid 1187 through 1192 Processing sheet with id= W, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= X, first strand: chain 'A' and resid 65 through 73 removed outlier: 3.560A pdb=" N ASN A 294 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 272 through 276 removed outlier: 5.553A pdb=" N PHE A 231 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N PHE A 240 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 116 through 118 Processing sheet with id= AA, first strand: chain 'A' and resid 252 through 255 removed outlier: 3.880A pdb=" N GLY A 161 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 177 through 179 No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'A' and resid 318 through 321 Processing sheet with id= AD, first strand: chain 'A' and resid 331 through 335 removed outlier: 4.036A pdb=" N ALA A 331 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR A 677 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.127A pdb=" N SER A 451 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'A' and resid 361 through 366 removed outlier: 6.590A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 484 through 488 Processing sheet with id= AH, first strand: chain 'A' and resid 755 through 759 Processing sheet with id= AI, first strand: chain 'A' and resid 805 through 815 Processing sheet with id= AJ, first strand: chain 'A' and resid 820 through 823 removed outlier: 4.161A pdb=" N LYS A 820 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'A' and resid 1225 through 1227 Processing sheet with id= AL, first strand: chain 'A' and resid 1187 through 1192 Processing sheet with id= AM, first strand: chain 'A' and resid 797 through 804 removed outlier: 6.564A pdb=" N LYS A1164 " --> pdb=" O SER A 803 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 29 through 31 Processing sheet with id= AO, first strand: chain 'B' and resid 42 through 44 Processing sheet with id= AP, first strand: chain 'B' and resid 64 through 72 removed outlier: 3.607A pdb=" N ASN B 294 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'B' and resid 272 through 276 removed outlier: 5.498A pdb=" N PHE B 231 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N PHE B 240 " --> pdb=" O PHE B 231 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'B' and resid 114 through 118 Processing sheet with id= AS, first strand: chain 'B' and resid 252 through 256 removed outlier: 4.232A pdb=" N ALA B 128 " --> pdb=" O MET B 256 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 161 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'B' and resid 177 through 179 No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'B' and resid 318 through 321 Processing sheet with id= AV, first strand: chain 'B' and resid 332 through 335 removed outlier: 8.062A pdb=" N VAL B 333 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASN B 632 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ARG B 335 " --> pdb=" O ASN B 632 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP B 634 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.001A pdb=" N SER B 451 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.670A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'B' and resid 484 through 488 Processing sheet with id= AZ, first strand: chain 'B' and resid 773 through 777 removed outlier: 6.404A pdb=" N VAL B 757 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N THR B 750 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'B' and resid 797 through 802 Processing sheet with id= BB, first strand: chain 'B' and resid 805 through 815 Processing sheet with id= BC, first strand: chain 'B' and resid 820 through 823 removed outlier: 4.162A pdb=" N LYS B 820 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'B' and resid 1225 through 1227 Processing sheet with id= BE, first strand: chain 'B' and resid 1187 through 1192 986 hydrogen bonds defined for protein. 2745 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: 14.63 Time building geometry restraints manager: 12.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 8615 1.33 - 1.48: 9653 1.48 - 1.63: 11427 1.63 - 1.78: 86 1.78 - 1.93: 160 Bond restraints: 29941 Sorted by residual: bond pdb=" CB TYR J 725 " pdb=" CG TYR J 725 " ideal model delta sigma weight residual 1.512 1.373 0.139 2.20e-02 2.07e+03 3.98e+01 bond pdb=" C3 NAG K 2 " pdb=" C4 NAG K 2 " ideal model delta sigma weight residual 1.523 1.585 -0.062 1.00e-02 1.00e+04 3.88e+01 bond pdb=" C5 NAG J1402 " pdb=" O5 NAG J1402 " ideal model delta sigma weight residual 1.435 1.502 -0.067 1.10e-02 8.26e+03 3.76e+01 bond pdb=" C3 NAG S 2 " pdb=" C4 NAG S 2 " ideal model delta sigma weight residual 1.523 1.583 -0.060 1.00e-02 1.00e+04 3.55e+01 bond pdb=" C3 NAG B1409 " pdb=" C4 NAG B1409 " ideal model delta sigma weight residual 1.523 1.582 -0.059 1.00e-02 1.00e+04 3.50e+01 ... (remaining 29936 not shown) Histogram of bond angle deviations from ideal: 79.77 - 97.14: 4 97.14 - 114.52: 17397 114.52 - 131.89: 23331 131.89 - 149.26: 36 149.26 - 166.63: 4 Bond angle restraints: 40772 Sorted by residual: angle pdb=" C8 NAG B1404 " pdb=" C7 NAG B1404 " pdb=" N2 NAG B1404 " ideal model delta sigma weight residual 116.06 166.63 -50.57 9.90e-01 1.02e+00 2.61e+03 angle pdb=" N2 NAG B1404 " pdb=" C7 NAG B1404 " pdb=" O7 NAG B1404 " ideal model delta sigma weight residual 122.06 79.77 42.29 1.01e+00 9.88e-01 1.77e+03 angle pdb=" C8 NAG B1404 " pdb=" C7 NAG B1404 " pdb=" O7 NAG B1404 " ideal model delta sigma weight residual 122.09 86.86 35.23 9.70e-01 1.06e+00 1.32e+03 angle pdb=" C2 NAG T 1 " pdb=" N2 NAG T 1 " pdb=" C7 NAG T 1 " ideal model delta sigma weight residual 123.12 162.02 -38.90 1.28e+00 6.08e-01 9.19e+02 angle pdb=" C2 NAG M 2 " pdb=" N2 NAG M 2 " pdb=" C7 NAG M 2 " ideal model delta sigma weight residual 123.12 160.97 -37.85 1.28e+00 6.08e-01 8.70e+02 ... (remaining 40767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.09: 17454 29.09 - 58.17: 222 58.17 - 87.26: 47 87.26 - 116.34: 3 116.34 - 145.43: 2 Dihedral angle restraints: 17728 sinusoidal: 6797 harmonic: 10931 Sorted by residual: dihedral pdb=" CB CYS A 535 " pdb=" SG CYS A 535 " pdb=" SG CYS A 548 " pdb=" CB CYS A 548 " ideal model delta sinusoidal sigma weight residual -86.00 -161.16 75.16 1 1.00e+01 1.00e-02 7.14e+01 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 93.00 132.93 -39.93 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 368 " pdb=" CB CYS A 368 " ideal model delta sinusoidal sigma weight residual 93.00 53.32 39.68 1 1.00e+01 1.00e-02 2.21e+01 ... (remaining 17725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 3458 0.109 - 0.217: 1052 0.217 - 0.326: 176 0.326 - 0.434: 78 0.434 - 0.543: 38 Chirality restraints: 4802 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.31e+02 chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.24e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.97e+01 ... (remaining 4799 not shown) Planarity restraints: 5235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN J 212 " -0.069 2.00e-02 2.50e+03 7.34e-02 6.74e+01 pdb=" CG ASN J 212 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN J 212 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN J 212 " 0.115 2.00e-02 2.50e+03 pdb=" C1 NAG J1402 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 675 " 0.057 2.00e-02 2.50e+03 6.06e-02 4.59e+01 pdb=" CG ASN B 675 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN B 675 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 675 " -0.095 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 713 " -0.054 2.00e-02 2.50e+03 5.74e-02 4.12e+01 pdb=" CG ASN J 713 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN J 713 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN J 713 " 0.090 2.00e-02 2.50e+03 pdb=" C1 NAG J1404 " -0.070 2.00e-02 2.50e+03 ... (remaining 5232 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6019 2.77 - 3.30: 26364 3.30 - 3.84: 47558 3.84 - 4.37: 60367 4.37 - 4.90: 98521 Nonbonded interactions: 238829 Sorted by model distance: nonbonded pdb=" N TRP A 94 " pdb=" O TRP A 94 " model vdw 2.238 2.496 nonbonded pdb=" N TRP B 94 " pdb=" O TRP B 94 " model vdw 2.285 2.496 nonbonded pdb=" N ASN A1046 " pdb=" O ASN A1046 " model vdw 2.298 2.496 nonbonded pdb=" N ASN B1046 " pdb=" O ASN B1046 " model vdw 2.323 2.496 nonbonded pdb=" N VAL B 136 " pdb=" O VAL B 136 " model vdw 2.367 2.496 ... (remaining 238824 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 23 or resid 28 through 194 or resid 199 through \ 474 or resid 478 through 760 or resid 771 through 901 or resid 911 through 1232 \ or resid 1401 through 1406)) selection = (chain 'B' and (resid 15 through 23 or resid 28 through 194 or resid 199 through \ 760 or resid 771 through 901 or resid 911 through 1232 or resid 1402 through 14 \ 07)) selection = (chain 'J' and (resid 15 through 23 or resid 28 through 32 or resid 39 through 4 \ 74 or resid 478 through 760 or resid 771 through 901 or resid 911 through 1232 o \ r resid 1402 through 1407)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'D' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 189 5.16 5 C 18618 2.51 5 N 4767 2.21 5 O 5740 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.130 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: 11.180 Check model and map are aligned: 0.390 Process input model: 76.490 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.240 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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 : 0.021 0.139 29941 Z= 1.372 Angle : 1.777 50.570 40772 Z= 1.258 Chirality : 0.118 0.543 4802 Planarity : 0.008 0.034 5195 Dihedral : 10.381 145.426 10529 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.09 % 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: 0.12 (0.13), residues: 3472 helix: -1.04 (0.15), residues: 811 sheet: 0.90 (0.17), residues: 785 loop : 0.40 (0.14), residues: 1876 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 582 time to evaluate : 3.413 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 585 average time/residue: 1.2220 time to fit residues: 861.1882 Evaluate side-chains 270 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 3.372 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 4.7902 ------------------------------------------------------------------------------- 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: 0.9990 chunk 281 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 291 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 337 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 171 ASN J 187 HIS J 388 ASN J 581 GLN J 598 ASN J1058 GLN A 31 ASN A 63 ASN A 186 ASN A 252 HIS A 380 GLN A 619 GLN A 663 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 GLN A 965 ASN A1028 GLN A1035 ASN A1213 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS B 252 HIS B 421 ASN B 469 ASN B 579 GLN B 784 ASN B1000 ASN B1011 GLN B1053 ASN B1098 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 29941 Z= 0.186 Angle : 0.599 9.120 40772 Z= 0.336 Chirality : 0.046 0.541 4802 Planarity : 0.004 0.049 5195 Dihedral : 7.051 135.399 4404 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 2.68 % 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: 0.56 (0.14), residues: 3472 helix: 0.70 (0.19), residues: 784 sheet: 0.80 (0.17), residues: 810 loop : 0.15 (0.14), residues: 1878 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 334 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 28 residues processed: 378 average time/residue: 1.2619 time to fit residues: 581.3346 Evaluate side-chains 279 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 251 time to evaluate : 3.460 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 17 residues processed: 11 average time/residue: 0.5921 time to fit residues: 13.7917 ------------------------------------------------------------------------------- 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: 9.9990 chunk 104 optimal weight: 2.9990 chunk 281 optimal weight: 7.9990 chunk 230 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 338 optimal weight: 9.9990 chunk 365 optimal weight: 5.9990 chunk 301 optimal weight: 7.9990 chunk 335 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 271 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 HIS J 388 ASN J 444 ASN J 777 ASN J1053 ASN J1057 GLN J1061 ASN J1223 ASN ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 ASN A 63 ASN A 150 ASN A 219 HIS A 497 ASN A 532 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN B 380 GLN B1213 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.072 29941 Z= 0.566 Angle : 0.794 11.775 40772 Z= 0.428 Chirality : 0.055 0.424 4802 Planarity : 0.006 0.074 5195 Dihedral : 7.294 113.412 4404 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 4.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % 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: -0.20 (0.13), residues: 3472 helix: 0.46 (0.18), residues: 793 sheet: 0.37 (0.17), residues: 811 loop : -0.56 (0.13), residues: 1868 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 256 time to evaluate : 3.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 72 residues processed: 359 average time/residue: 1.2008 time to fit residues: 529.6312 Evaluate side-chains 310 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 238 time to evaluate : 3.541 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 54 residues processed: 18 average time/residue: 0.4813 time to fit residues: 17.5835 ------------------------------------------------------------------------------- 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: 0.9990 chunk 254 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 chunk 339 optimal weight: 9.9990 chunk 359 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 321 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 581 GLN J1053 ASN J1103 GLN A 150 ASN A 482 ASN A 483 HIS A 532 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN B 482 ASN B 849 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 29941 Z= 0.213 Angle : 0.565 11.578 40772 Z= 0.308 Chirality : 0.045 0.389 4802 Planarity : 0.004 0.061 5195 Dihedral : 6.508 97.730 4404 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 3.99 % 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: 0.06 (0.14), residues: 3472 helix: 1.00 (0.19), residues: 794 sheet: 0.52 (0.17), residues: 821 loop : -0.58 (0.14), residues: 1857 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 256 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 71 residues processed: 342 average time/residue: 1.1523 time to fit residues: 485.3541 Evaluate side-chains 297 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 226 time to evaluate : 3.319 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 56 residues processed: 15 average time/residue: 0.7061 time to fit residues: 18.6594 ------------------------------------------------------------------------------- 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: 2.9990 chunk 204 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 267 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 306 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 322 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 581 GLN J1071 GLN ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN A 482 ASN A 532 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN B 532 HIS B 724 ASN B 777 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 29941 Z= 0.306 Angle : 0.605 9.653 40772 Z= 0.327 Chirality : 0.047 0.375 4802 Planarity : 0.005 0.064 5195 Dihedral : 6.444 93.812 4404 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 3.43 % 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: -0.10 (0.14), residues: 3472 helix: 0.99 (0.19), residues: 802 sheet: 0.46 (0.17), residues: 807 loop : -0.76 (0.13), residues: 1863 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 246 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 81 residues processed: 326 average time/residue: 1.1815 time to fit residues: 477.4395 Evaluate side-chains 308 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 227 time to evaluate : 3.212 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 65 residues processed: 17 average time/residue: 0.6768 time to fit residues: 20.3676 ------------------------------------------------------------------------------- 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: 7.9990 chunk 323 optimal weight: 8.9990 chunk 71 optimal weight: 0.0270 chunk 211 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 359 optimal weight: 5.9990 chunk 298 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 overall best weight: 1.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 581 GLN A 150 ASN A 482 ASN A 532 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 ASN B 724 ASN B1011 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 29941 Z= 0.202 Angle : 0.536 9.077 40772 Z= 0.293 Chirality : 0.044 0.363 4802 Planarity : 0.005 0.086 5195 Dihedral : 6.145 85.703 4404 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 3.60 % 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: 3472 helix: 1.20 (0.19), residues: 798 sheet: 0.50 (0.17), residues: 805 loop : -0.73 (0.13), residues: 1869 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 243 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 76 residues processed: 326 average time/residue: 1.1100 time to fit residues: 458.0935 Evaluate side-chains 303 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 227 time to evaluate : 3.223 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 64 residues processed: 12 average time/residue: 0.7607 time to fit residues: 17.3941 ------------------------------------------------------------------------------- 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: 4.9990 chunk 40 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 262 optimal weight: 0.0050 chunk 203 optimal weight: 0.9980 chunk 302 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 chunk 358 optimal weight: 10.0000 chunk 224 optimal weight: 0.0060 chunk 218 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 overall best weight: 1.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN A 482 ASN A 532 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 ASN B 724 ASN B 839 GLN B1011 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 29941 Z= 0.168 Angle : 0.511 8.879 40772 Z= 0.279 Chirality : 0.043 0.403 4802 Planarity : 0.004 0.076 5195 Dihedral : 5.938 80.818 4404 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.14), residues: 3472 helix: 1.32 (0.19), residues: 798 sheet: 0.48 (0.17), residues: 810 loop : -0.71 (0.14), residues: 1864 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 247 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 73 residues processed: 324 average time/residue: 1.1494 time to fit residues: 460.8719 Evaluate side-chains 299 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 226 time to evaluate : 4.165 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 64 residues processed: 9 average time/residue: 0.7047 time to fit residues: 13.2568 ------------------------------------------------------------------------------- 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: 7.9990 chunk 143 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 227 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 177 optimal weight: 0.0970 chunk 33 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 overall best weight: 4.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1071 GLN A 150 ASN A 482 ASN A 532 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 ASN A1061 ASN B 724 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 29941 Z= 0.427 Angle : 0.667 9.755 40772 Z= 0.359 Chirality : 0.049 0.423 4802 Planarity : 0.005 0.079 5195 Dihedral : 6.499 92.345 4404 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 3.50 % 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: -0.26 (0.14), residues: 3472 helix: 0.99 (0.19), residues: 799 sheet: 0.40 (0.17), residues: 798 loop : -0.95 (0.13), residues: 1875 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 229 time to evaluate : 3.373 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: symmetry clash outliers start: 107 outliers final: 78 residues processed: 313 average time/residue: 1.1485 time to fit residues: 446.4470 Evaluate side-chains 299 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 221 time to evaluate : 3.467 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 68 residues processed: 10 average time/residue: 0.8163 time to fit residues: 15.4213 ------------------------------------------------------------------------------- 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: 1.9990 chunk 343 optimal weight: 7.9990 chunk 313 optimal weight: 5.9990 chunk 334 optimal weight: 0.9980 chunk 201 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 301 optimal weight: 0.8980 chunk 316 optimal weight: 2.9990 chunk 332 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN A 482 ASN A 532 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 ASN B 724 ASN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 29941 Z= 0.156 Angle : 0.510 8.936 40772 Z= 0.280 Chirality : 0.043 0.388 4802 Planarity : 0.004 0.073 5195 Dihedral : 5.943 79.038 4404 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3472 helix: 1.33 (0.20), residues: 794 sheet: 0.46 (0.17), residues: 797 loop : -0.84 (0.13), residues: 1881 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 234 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 70 residues processed: 311 average time/residue: 1.1233 time to fit residues: 433.6270 Evaluate side-chains 292 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 222 time to evaluate : 3.095 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 65 residues processed: 6 average time/residue: 0.5431 time to fit residues: 8.9481 ------------------------------------------------------------------------------- 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: 6.9990 chunk 353 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 167 optimal weight: 0.6980 chunk 245 optimal weight: 0.7980 chunk 370 optimal weight: 5.9990 chunk 341 optimal weight: 8.9990 chunk 295 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 227 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 444 ASN ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN A 532 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 ASN B 724 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 29941 Z= 0.278 Angle : 0.575 9.247 40772 Z= 0.312 Chirality : 0.045 0.393 4802 Planarity : 0.005 0.073 5195 Dihedral : 6.109 82.024 4404 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 2.78 % 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: -0.11 (0.14), residues: 3472 helix: 1.26 (0.19), residues: 793 sheet: 0.45 (0.17), residues: 791 loop : -0.90 (0.13), residues: 1888 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 224 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 71 residues processed: 296 average time/residue: 1.1439 time to fit residues: 423.1224 Evaluate side-chains 291 residues out of total 3059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 220 time to evaluate : 3.259 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 65 residues processed: 6 average time/residue: 0.8805 time to fit residues: 11.7330 ------------------------------------------------------------------------------- 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: 1.9990 chunk 314 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 272 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 295 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 chunk 303 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN A 532 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 ASN A1061 ASN B 724 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.112897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.090556 restraints weight = 38138.545| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.83 r_work: 0.2820 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 29941 Z= 0.159 Angle : 0.505 8.877 40772 Z= 0.277 Chirality : 0.043 0.376 4802 Planarity : 0.004 0.069 5195 Dihedral : 5.779 73.165 4404 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 2.42 % 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: -0.00 (0.14), residues: 3472 helix: 1.41 (0.20), residues: 792 sheet: 0.46 (0.17), residues: 808 loop : -0.84 (0.13), residues: 1872 =============================================================================== Job complete usr+sys time: 8606.75 seconds wall clock time: 156 minutes 1.88 seconds (9361.88 seconds total)