Starting phenix.real_space_refine on Sun Mar 17 00:32:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5juy_8178/03_2024/5juy_8178_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5juy_8178/03_2024/5juy_8178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5juy_8178/03_2024/5juy_8178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5juy_8178/03_2024/5juy_8178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5juy_8178/03_2024/5juy_8178_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5juy_8178/03_2024/5juy_8178_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 6 Type Number sf(0) Gaussians Fe 7 7.16 5 P 21 5.49 5 S 499 5.16 5 C 48091 2.51 5 N 13137 2.21 5 O 14303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 41": "OE1" <-> "OE2" Residue "D PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 14": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "J ARG 91": "NH1" <-> "NH2" Residue "K ARG 91": "NH1" <-> "NH2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "M ARG 91": "NH1" <-> "NH2" Residue "N ARG 91": "NH1" <-> "NH2" Residue "O GLU 3": "OE1" <-> "OE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O GLU 33": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O ARG 90": "NH1" <-> "NH2" Residue "P GLU 3": "OE1" <-> "OE2" Residue "P ARG 13": "NH1" <-> "NH2" Residue "P GLU 33": "OE1" <-> "OE2" Residue "P GLU 41": "OE1" <-> "OE2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "Q GLU 3": "OE1" <-> "OE2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q GLU 33": "OE1" <-> "OE2" Residue "Q GLU 41": "OE1" <-> "OE2" Residue "Q ARG 90": "NH1" <-> "NH2" Residue "R GLU 3": "OE1" <-> "OE2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R GLU 33": "OE1" <-> "OE2" Residue "R GLU 41": "OE1" <-> "OE2" Residue "R ARG 90": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 76058 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 9099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1139, 9099 Classifications: {'peptide': 1139} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 1111} Chain breaks: 1 Chain: "B" Number of atoms: 9861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1234, 9861 Classifications: {'peptide': 1234} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 1204} Chain breaks: 2 Chain: "C" Number of atoms: 9099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1139, 9099 Classifications: {'peptide': 1139} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 1111} Chain breaks: 1 Chain: "D" Number of atoms: 9861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1234, 9861 Classifications: {'peptide': 1234} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 1204} Chain breaks: 2 Chain: "E" Number of atoms: 9861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1234, 9861 Classifications: {'peptide': 1234} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 1204} Chain breaks: 2 Chain: "F" Number of atoms: 9099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1139, 9099 Classifications: {'peptide': 1139} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 1111} Chain breaks: 1 Chain: "G" Number of atoms: 9861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1234, 9861 Classifications: {'peptide': 1234} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 1204} Chain breaks: 2 Chain: "H" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 814 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "I" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 814 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 814 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "K" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 814 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 814 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "M" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 814 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "N" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 814 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "O" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "P" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "Q" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "R" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 56 residue: pdb=" N VAL H 11 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL H 11 " occ=0.50 residue: pdb=" N GLN H 12 " occ=0.60 ... (7 atoms not shown) pdb=" NE2 GLN H 12 " occ=0.40 residue: pdb=" N ASN H 52 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN H 52 " occ=0.50 residue: pdb=" N GLU H 61 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU H 61 " occ=0.50 residue: pdb=" N GLU H 62 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU H 62 " occ=0.50 residue: pdb=" N MET H 65 " occ=0.60 ... (6 atoms not shown) pdb=" CE MET H 65 " occ=0.60 residue: pdb=" N THR H 78 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 THR H 78 " occ=0.50 residue: pdb=" N ARG H 91 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG H 91 " occ=0.50 residue: pdb=" N VAL I 11 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL I 11 " occ=0.50 residue: pdb=" N GLN I 12 " occ=0.60 ... (7 atoms not shown) pdb=" NE2 GLN I 12 " occ=0.40 residue: pdb=" N ASN I 52 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN I 52 " occ=0.50 residue: pdb=" N GLU I 61 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU I 61 " occ=0.50 ... (remaining 44 not shown) Time building chain proxies: 28.86, per 1000 atoms: 0.38 Number of scatterers: 76058 At special positions: 0 Unit cell: (310.536, 311.904, 145.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 7 26.01 S 499 16.00 P 21 15.00 O 14303 8.00 N 13137 7.00 C 48091 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 663 " distance=2.03 Simple disulfide: pdb=" SG CYS A 675 " - pdb=" SG CYS A 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A 704 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 761 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 846 " distance=2.03 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 663 " distance=2.03 Simple disulfide: pdb=" SG CYS B 675 " - pdb=" SG CYS B 705 " distance=2.03 Simple disulfide: pdb=" SG CYS B 704 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 761 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 803 " - pdb=" SG CYS B 846 " distance=2.03 Simple disulfide: pdb=" SG CYS C 633 " - pdb=" SG CYS C 663 " distance=2.03 Simple disulfide: pdb=" SG CYS C 675 " - pdb=" SG CYS C 705 " distance=2.03 Simple disulfide: pdb=" SG CYS C 704 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 761 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 803 " - pdb=" SG CYS C 846 " distance=2.03 Simple disulfide: pdb=" SG CYS D 633 " - pdb=" SG CYS D 663 " distance=2.03 Simple disulfide: pdb=" SG CYS D 675 " - pdb=" SG CYS D 705 " distance=2.03 Simple disulfide: pdb=" SG CYS D 704 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D 761 " - pdb=" SG CYS D 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 803 " - pdb=" SG CYS D 846 " distance=2.03 Simple disulfide: pdb=" SG CYS E 633 " - pdb=" SG CYS E 663 " distance=2.03 Simple disulfide: pdb=" SG CYS E 675 " - pdb=" SG CYS E 705 " distance=2.03 Simple disulfide: pdb=" SG CYS E 704 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E 761 " - pdb=" SG CYS E 804 " distance=2.03 Simple disulfide: pdb=" SG CYS E 803 " - pdb=" SG CYS E 846 " distance=2.03 Simple disulfide: pdb=" SG CYS F 633 " - pdb=" SG CYS F 663 " distance=2.03 Simple disulfide: pdb=" SG CYS F 675 " - pdb=" SG CYS F 705 " distance=2.03 Simple disulfide: pdb=" SG CYS F 704 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F 761 " - pdb=" SG CYS F 804 " distance=2.03 Simple disulfide: pdb=" SG CYS F 803 " - pdb=" SG CYS F 846 " distance=2.03 Simple disulfide: pdb=" SG CYS G 633 " - pdb=" SG CYS G 663 " distance=2.03 Simple disulfide: pdb=" SG CYS G 675 " - pdb=" SG CYS G 705 " distance=2.03 Simple disulfide: pdb=" SG CYS G 704 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G 761 " - pdb=" SG CYS G 804 " distance=2.03 Simple disulfide: pdb=" SG CYS G 803 " - pdb=" SG CYS G 846 " 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 Time building additional restraints: 22.79 Conformation dependent library (CDL) restraints added in 10.5 seconds 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 291 helices and 119 sheets defined 28.7% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 16.31 Creating SS restraints... Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 130 through 142 removed outlier: 3.609A pdb=" N ALA A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 192 through 206 Processing helix chain 'A' and resid 220 through 233 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.915A pdb=" N ALA A 253 " --> pdb=" O TRP A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 299 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.670A pdb=" N ILE A 313 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 314 " --> pdb=" O HIS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 333 removed outlier: 4.020A pdb=" N ARG A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.690A pdb=" N MET A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 removed outlier: 3.769A pdb=" N TYR A 383 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 385 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 388 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 404 Processing helix chain 'A' and resid 408 through 420 removed outlier: 3.965A pdb=" N ILE A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 448 Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 480 through 493 removed outlier: 5.169A pdb=" N ALA A 488 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR A 489 " --> pdb=" O ASN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'A' and resid 519 through 531 removed outlier: 5.373A pdb=" N HIS A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 553 removed outlier: 3.873A pdb=" N ALA A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 540 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 549 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.696A pdb=" N CYS A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 586 Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing helix chain 'A' and resid 911 through 914 No H-bonds generated for 'chain 'A' and resid 911 through 914' Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 22 through 24 No H-bonds generated for 'chain 'B' and resid 22 through 24' Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 37 through 44 Processing helix chain 'B' and resid 49 through 62 removed outlier: 4.004A pdb=" N LYS B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 81 through 90 removed outlier: 4.651A pdb=" N ASP B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 130 through 142 removed outlier: 3.608A pdb=" N ALA B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 192 through 206 Processing helix chain 'B' and resid 220 through 233 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.915A pdb=" N ALA B 253 " --> pdb=" O TRP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 299 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 308 through 317 removed outlier: 3.671A pdb=" N ILE B 313 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 314 " --> pdb=" O HIS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 333 removed outlier: 4.020A pdb=" N ARG B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 344 Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.691A pdb=" N MET B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 3.769A pdb=" N TYR B 383 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 385 " --> pdb=" O TYR B 382 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 388 " --> pdb=" O ASP B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 404 Processing helix chain 'B' and resid 408 through 420 removed outlier: 3.965A pdb=" N ILE B 414 " --> pdb=" O GLU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 448 Processing helix chain 'B' and resid 453 through 467 Processing helix chain 'B' and resid 480 through 493 removed outlier: 5.169A pdb=" N ALA B 488 " --> pdb=" O TYR B 484 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR B 489 " --> pdb=" O ASN B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 504 Processing helix chain 'B' and resid 507 through 516 Processing helix chain 'B' and resid 519 through 531 removed outlier: 5.372A pdb=" N HIS B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 553 removed outlier: 3.873A pdb=" N ALA B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 540 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 549 " --> pdb=" O GLN B 545 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS B 553 " --> pdb=" O SER B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 569 removed outlier: 3.696A pdb=" N CYS B 569 " --> pdb=" O GLN B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 586 Processing helix chain 'B' and resid 599 through 601 No H-bonds generated for 'chain 'B' and resid 599 through 601' Processing helix chain 'B' and resid 911 through 914 No H-bonds generated for 'chain 'B' and resid 911 through 914' Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 130 through 142 removed outlier: 3.609A pdb=" N ALA C 135 " --> pdb=" O LYS C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 167 through 169 No H-bonds generated for 'chain 'C' and resid 167 through 169' Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 192 through 206 Processing helix chain 'C' and resid 220 through 233 Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.915A pdb=" N ALA C 253 " --> pdb=" O TRP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 299 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 308 through 317 removed outlier: 3.669A pdb=" N ILE C 313 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE C 314 " --> pdb=" O HIS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 removed outlier: 4.019A pdb=" N ARG C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 344 Processing helix chain 'C' and resid 364 through 373 removed outlier: 3.690A pdb=" N MET C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 388 removed outlier: 3.768A pdb=" N TYR C 383 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP C 385 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C 388 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 404 Processing helix chain 'C' and resid 408 through 420 removed outlier: 3.965A pdb=" N ILE C 414 " --> pdb=" O GLU C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 448 Processing helix chain 'C' and resid 453 through 467 Processing helix chain 'C' and resid 480 through 493 removed outlier: 5.169A pdb=" N ALA C 488 " --> pdb=" O TYR C 484 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR C 489 " --> pdb=" O ASN C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 507 through 516 Processing helix chain 'C' and resid 519 through 531 removed outlier: 5.373A pdb=" N HIS C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 553 removed outlier: 3.873A pdb=" N ALA C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 540 " --> pdb=" O LYS C 536 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 549 " --> pdb=" O GLN C 545 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N HIS C 553 " --> pdb=" O SER C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 569 removed outlier: 3.696A pdb=" N CYS C 569 " --> pdb=" O GLN C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 586 Processing helix chain 'C' and resid 599 through 601 No H-bonds generated for 'chain 'C' and resid 599 through 601' Processing helix chain 'C' and resid 911 through 914 No H-bonds generated for 'chain 'C' and resid 911 through 914' Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 13 through 19 Processing helix chain 'D' and resid 22 through 24 No H-bonds generated for 'chain 'D' and resid 22 through 24' Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 37 through 44 Processing helix chain 'D' and resid 49 through 62 removed outlier: 4.000A pdb=" N LYS D 62 " --> pdb=" O LYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 81 through 90 removed outlier: 4.650A pdb=" N ASP D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLY D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.608A pdb=" N ALA D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 192 through 206 Processing helix chain 'D' and resid 220 through 233 Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.915A pdb=" N ALA D 253 " --> pdb=" O TRP D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 299 Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 308 through 317 removed outlier: 3.669A pdb=" N ILE D 313 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE D 314 " --> pdb=" O HIS D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 333 removed outlier: 4.020A pdb=" N ARG D 332 " --> pdb=" O GLY D 328 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 344 Processing helix chain 'D' and resid 364 through 373 removed outlier: 3.691A pdb=" N MET D 368 " --> pdb=" O LEU D 364 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 388 removed outlier: 3.769A pdb=" N TYR D 383 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP D 385 " --> pdb=" O TYR D 382 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D 388 " --> pdb=" O ASP D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 404 Processing helix chain 'D' and resid 408 through 420 removed outlier: 3.965A pdb=" N ILE D 414 " --> pdb=" O GLU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 448 Processing helix chain 'D' and resid 453 through 467 Processing helix chain 'D' and resid 480 through 493 removed outlier: 5.169A pdb=" N ALA D 488 " --> pdb=" O TYR D 484 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR D 489 " --> pdb=" O ASN D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 504 Processing helix chain 'D' and resid 507 through 516 Processing helix chain 'D' and resid 519 through 531 removed outlier: 5.373A pdb=" N HIS D 531 " --> pdb=" O VAL D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 553 removed outlier: 3.873A pdb=" N ALA D 539 " --> pdb=" O GLU D 535 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL D 540 " --> pdb=" O LYS D 536 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 549 " --> pdb=" O GLN D 545 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS D 553 " --> pdb=" O SER D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 569 removed outlier: 3.696A pdb=" N CYS D 569 " --> pdb=" O GLN D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 586 Processing helix chain 'D' and resid 599 through 601 No H-bonds generated for 'chain 'D' and resid 599 through 601' Processing helix chain 'D' and resid 911 through 914 No H-bonds generated for 'chain 'D' and resid 911 through 914' Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 13 through 19 Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 26 through 31 Processing helix chain 'E' and resid 37 through 44 Processing helix chain 'E' and resid 49 through 62 removed outlier: 4.001A pdb=" N LYS E 62 " --> pdb=" O LYS E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 81 through 90 removed outlier: 4.650A pdb=" N ASP E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY E 90 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.608A pdb=" N ALA E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 171 through 177 Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 220 through 233 Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.915A pdb=" N ALA E 253 " --> pdb=" O TRP E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 299 Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 308 through 317 removed outlier: 3.670A pdb=" N ILE E 313 " --> pdb=" O ALA E 310 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE E 314 " --> pdb=" O HIS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 333 removed outlier: 4.020A pdb=" N ARG E 332 " --> pdb=" O GLY E 328 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 344 Processing helix chain 'E' and resid 364 through 373 removed outlier: 3.690A pdb=" N MET E 368 " --> pdb=" O LEU E 364 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU E 373 " --> pdb=" O SER E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 388 removed outlier: 3.770A pdb=" N TYR E 383 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP E 385 " --> pdb=" O TYR E 382 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 388 " --> pdb=" O ASP E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 404 Processing helix chain 'E' and resid 408 through 420 removed outlier: 3.965A pdb=" N ILE E 414 " --> pdb=" O GLU E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 448 Processing helix chain 'E' and resid 453 through 467 Processing helix chain 'E' and resid 480 through 493 removed outlier: 5.169A pdb=" N ALA E 488 " --> pdb=" O TYR E 484 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR E 489 " --> pdb=" O ASN E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 504 Processing helix chain 'E' and resid 507 through 516 Processing helix chain 'E' and resid 519 through 531 removed outlier: 5.373A pdb=" N HIS E 531 " --> pdb=" O VAL E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 553 removed outlier: 3.874A pdb=" N ALA E 539 " --> pdb=" O GLU E 535 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 540 " --> pdb=" O LYS E 536 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER E 549 " --> pdb=" O GLN E 545 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS E 553 " --> pdb=" O SER E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 569 removed outlier: 3.696A pdb=" N CYS E 569 " --> pdb=" O GLN E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 586 Processing helix chain 'E' and resid 599 through 601 No H-bonds generated for 'chain 'E' and resid 599 through 601' Processing helix chain 'E' and resid 911 through 914 No H-bonds generated for 'chain 'E' and resid 911 through 914' Processing helix chain 'F' and resid 108 through 113 Processing helix chain 'F' and resid 130 through 142 removed outlier: 3.609A pdb=" N ALA F 135 " --> pdb=" O LYS F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 165 Processing helix chain 'F' and resid 167 through 169 No H-bonds generated for 'chain 'F' and resid 167 through 169' Processing helix chain 'F' and resid 171 through 177 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 220 through 233 Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.915A pdb=" N ALA F 253 " --> pdb=" O TRP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 299 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 308 through 317 removed outlier: 3.669A pdb=" N ILE F 313 " --> pdb=" O ALA F 310 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE F 314 " --> pdb=" O HIS F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 333 removed outlier: 4.020A pdb=" N ARG F 332 " --> pdb=" O GLY F 328 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP F 333 " --> pdb=" O ALA F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 344 Processing helix chain 'F' and resid 364 through 373 removed outlier: 3.691A pdb=" N MET F 368 " --> pdb=" O LEU F 364 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU F 373 " --> pdb=" O SER F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 388 removed outlier: 3.769A pdb=" N TYR F 383 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP F 385 " --> pdb=" O TYR F 382 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE F 388 " --> pdb=" O ASP F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 404 Processing helix chain 'F' and resid 408 through 420 removed outlier: 3.965A pdb=" N ILE F 414 " --> pdb=" O GLU F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 448 Processing helix chain 'F' and resid 453 through 467 Processing helix chain 'F' and resid 480 through 493 removed outlier: 5.169A pdb=" N ALA F 488 " --> pdb=" O TYR F 484 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYR F 489 " --> pdb=" O ASN F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 504 Processing helix chain 'F' and resid 507 through 516 Processing helix chain 'F' and resid 519 through 531 removed outlier: 5.373A pdb=" N HIS F 531 " --> pdb=" O VAL F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 553 removed outlier: 3.874A pdb=" N ALA F 539 " --> pdb=" O GLU F 535 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL F 540 " --> pdb=" O LYS F 536 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER F 549 " --> pdb=" O GLN F 545 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS F 553 " --> pdb=" O SER F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 569 removed outlier: 3.695A pdb=" N CYS F 569 " --> pdb=" O GLN F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 586 Processing helix chain 'F' and resid 599 through 601 No H-bonds generated for 'chain 'F' and resid 599 through 601' Processing helix chain 'F' and resid 911 through 914 No H-bonds generated for 'chain 'F' and resid 911 through 914' Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 13 through 19 Processing helix chain 'G' and resid 22 through 24 No H-bonds generated for 'chain 'G' and resid 22 through 24' Processing helix chain 'G' and resid 26 through 31 Processing helix chain 'G' and resid 37 through 44 Processing helix chain 'G' and resid 49 through 62 removed outlier: 4.004A pdb=" N LYS G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 81 through 90 removed outlier: 4.652A pdb=" N ASP G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY G 90 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 113 Processing helix chain 'G' and resid 130 through 142 removed outlier: 3.609A pdb=" N ALA G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 165 Processing helix chain 'G' and resid 167 through 169 No H-bonds generated for 'chain 'G' and resid 167 through 169' Processing helix chain 'G' and resid 171 through 177 Processing helix chain 'G' and resid 192 through 206 Processing helix chain 'G' and resid 220 through 233 Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.914A pdb=" N ALA G 253 " --> pdb=" O TRP G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 299 Processing helix chain 'G' and resid 303 through 305 No H-bonds generated for 'chain 'G' and resid 303 through 305' Processing helix chain 'G' and resid 308 through 317 removed outlier: 3.670A pdb=" N ILE G 313 " --> pdb=" O ALA G 310 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE G 314 " --> pdb=" O HIS G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 333 removed outlier: 4.020A pdb=" N ARG G 332 " --> pdb=" O GLY G 328 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP G 333 " --> pdb=" O ALA G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 344 Processing helix chain 'G' and resid 364 through 373 removed outlier: 3.690A pdb=" N MET G 368 " --> pdb=" O LEU G 364 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU G 373 " --> pdb=" O SER G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 388 removed outlier: 3.769A pdb=" N TYR G 383 " --> pdb=" O LYS G 380 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP G 385 " --> pdb=" O TYR G 382 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE G 388 " --> pdb=" O ASP G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 404 Processing helix chain 'G' and resid 408 through 420 removed outlier: 3.965A pdb=" N ILE G 414 " --> pdb=" O GLU G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 448 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 480 through 493 removed outlier: 5.169A pdb=" N ALA G 488 " --> pdb=" O TYR G 484 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR G 489 " --> pdb=" O ASN G 485 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 504 Processing helix chain 'G' and resid 507 through 516 Processing helix chain 'G' and resid 519 through 531 removed outlier: 5.373A pdb=" N HIS G 531 " --> pdb=" O VAL G 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 535 through 553 removed outlier: 3.874A pdb=" N ALA G 539 " --> pdb=" O GLU G 535 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL G 540 " --> pdb=" O LYS G 536 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER G 549 " --> pdb=" O GLN G 545 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS G 553 " --> pdb=" O SER G 549 " (cutoff:3.500A) Processing helix chain 'G' and resid 563 through 569 removed outlier: 3.696A pdb=" N CYS G 569 " --> pdb=" O GLN G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 575 through 586 Processing helix chain 'G' and resid 599 through 601 No H-bonds generated for 'chain 'G' and resid 599 through 601' Processing helix chain 'G' and resid 911 through 914 No H-bonds generated for 'chain 'G' and resid 911 through 914' Processing helix chain 'H' and resid 3 through 13 Processing helix chain 'H' and resid 50 through 53 No H-bonds generated for 'chain 'H' and resid 50 through 53' Processing helix chain 'H' and resid 61 through 67 Processing helix chain 'H' and resid 71 through 74 No H-bonds generated for 'chain 'H' and resid 71 through 74' Processing helix chain 'H' and resid 88 through 101 Processing helix chain 'I' and resid 3 through 13 Processing helix chain 'I' and resid 50 through 53 No H-bonds generated for 'chain 'I' and resid 50 through 53' Processing helix chain 'I' and resid 61 through 67 Processing helix chain 'I' and resid 71 through 74 No H-bonds generated for 'chain 'I' and resid 71 through 74' Processing helix chain 'I' and resid 88 through 101 Processing helix chain 'J' and resid 3 through 13 Processing helix chain 'J' and resid 50 through 53 No H-bonds generated for 'chain 'J' and resid 50 through 53' Processing helix chain 'J' and resid 61 through 67 Processing helix chain 'J' and resid 71 through 74 No H-bonds generated for 'chain 'J' and resid 71 through 74' Processing helix chain 'J' and resid 88 through 101 Processing helix chain 'K' and resid 3 through 13 Processing helix chain 'K' and resid 50 through 53 No H-bonds generated for 'chain 'K' and resid 50 through 53' Processing helix chain 'K' and resid 61 through 67 Processing helix chain 'K' and resid 71 through 74 No H-bonds generated for 'chain 'K' and resid 71 through 74' Processing helix chain 'K' and resid 88 through 101 Processing helix chain 'L' and resid 3 through 13 Processing helix chain 'L' and resid 50 through 53 No H-bonds generated for 'chain 'L' and resid 50 through 53' Processing helix chain 'L' and resid 61 through 67 Processing helix chain 'L' and resid 71 through 74 No H-bonds generated for 'chain 'L' and resid 71 through 74' Processing helix chain 'L' and resid 88 through 101 Processing helix chain 'M' and resid 3 through 13 Processing helix chain 'M' and resid 50 through 53 No H-bonds generated for 'chain 'M' and resid 50 through 53' Processing helix chain 'M' and resid 61 through 67 Processing helix chain 'M' and resid 71 through 74 No H-bonds generated for 'chain 'M' and resid 71 through 74' Processing helix chain 'M' and resid 88 through 101 Processing helix chain 'N' and resid 3 through 13 Processing helix chain 'N' and resid 50 through 53 No H-bonds generated for 'chain 'N' and resid 50 through 53' Processing helix chain 'N' and resid 61 through 67 Processing helix chain 'N' and resid 71 through 74 No H-bonds generated for 'chain 'N' and resid 71 through 74' Processing helix chain 'N' and resid 88 through 101 Processing helix chain 'O' and resid 3 through 11 Processing helix chain 'O' and resid 13 through 19 Processing helix chain 'O' and resid 26 through 31 Processing helix chain 'O' and resid 37 through 44 Processing helix chain 'O' and resid 51 through 64 removed outlier: 3.720A pdb=" N GLU O 63 " --> pdb=" O ILE O 59 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR O 64 " --> pdb=" O ILE O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 80 Processing helix chain 'O' and resid 83 through 93 removed outlier: 3.757A pdb=" N ASN O 92 " --> pdb=" O PHE O 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 11 Processing helix chain 'P' and resid 13 through 19 Processing helix chain 'P' and resid 26 through 31 Processing helix chain 'P' and resid 37 through 44 Processing helix chain 'P' and resid 51 through 64 removed outlier: 3.721A pdb=" N GLU P 63 " --> pdb=" O ILE P 59 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR P 64 " --> pdb=" O ILE P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 80 Processing helix chain 'P' and resid 83 through 93 removed outlier: 3.753A pdb=" N ASN P 92 " --> pdb=" O PHE P 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 11 Processing helix chain 'Q' and resid 13 through 19 Processing helix chain 'Q' and resid 26 through 31 Processing helix chain 'Q' and resid 37 through 44 Processing helix chain 'Q' and resid 51 through 64 removed outlier: 3.722A pdb=" N GLU Q 63 " --> pdb=" O ILE Q 59 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR Q 64 " --> pdb=" O ILE Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 80 Processing helix chain 'Q' and resid 83 through 93 removed outlier: 3.753A pdb=" N ASN Q 92 " --> pdb=" O PHE Q 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 11 Processing helix chain 'R' and resid 13 through 19 Processing helix chain 'R' and resid 26 through 31 Processing helix chain 'R' and resid 37 through 44 Processing helix chain 'R' and resid 51 through 64 removed outlier: 3.719A pdb=" N GLU R 63 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR R 64 " --> pdb=" O ILE R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 80 Processing helix chain 'R' and resid 83 through 93 removed outlier: 3.757A pdb=" N ASN R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 148 through 153 removed outlier: 6.936A pdb=" N LEU A 240 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR A 263 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU A 242 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 425 through 428 Processing sheet with id= C, first strand: chain 'A' and resid 609 through 611 removed outlier: 4.401A pdb=" N SER A 896 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 629 through 632 removed outlier: 6.323A pdb=" N LYS A 643 " --> pdb=" O LYS A 649 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS A 649 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 682 through 685 removed outlier: 3.690A pdb=" N CYS A 675 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS A 662 " --> pdb=" O CYS A 675 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 715 through 719 removed outlier: 6.025A pdb=" N ASP A 729 " --> pdb=" O CYS A 735 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N CYS A 735 " --> pdb=" O ASP A 729 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 748 through 751 removed outlier: 6.022A pdb=" N ASP A 771 " --> pdb=" O GLU A 777 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU A 777 " --> pdb=" O ASP A 771 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 804 through 806 Processing sheet with id= I, first strand: chain 'A' and resid 845 through 848 removed outlier: 3.874A pdb=" N VAL A 864 " --> pdb=" O CYS A 878 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASN A 868 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LYS A 874 " --> pdb=" O ASN A 868 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 926 through 931 Processing sheet with id= K, first strand: chain 'A' and resid 966 through 969 removed outlier: 4.503A pdb=" N ILE A 985 " --> pdb=" O ARG A 999 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG A 999 " --> pdb=" O ILE A 985 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1009 through 1011 Processing sheet with id= M, first strand: chain 'A' and resid 1049 through 1052 Processing sheet with id= N, first strand: chain 'A' and resid 1101 through 1104 removed outlier: 3.939A pdb=" N THR A1103 " --> pdb=" O LYS A1110 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS A1110 " --> pdb=" O THR A1103 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 1132 through 1135 Processing sheet with id= P, first strand: chain 'A' and resid 1191 through 1195 Processing sheet with id= Q, first strand: chain 'A' and resid 1232 through 1235 Processing sheet with id= R, first strand: chain 'B' and resid 148 through 153 removed outlier: 6.935A pdb=" N LEU B 240 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR B 263 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU B 242 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 425 through 428 Processing sheet with id= T, first strand: chain 'B' and resid 609 through 611 removed outlier: 4.402A pdb=" N SER B 896 " --> pdb=" O SER B 891 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 629 through 632 removed outlier: 6.323A pdb=" N LYS B 643 " --> pdb=" O LYS B 649 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS B 649 " --> pdb=" O LYS B 643 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 682 through 685 removed outlier: 3.690A pdb=" N CYS B 675 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS B 662 " --> pdb=" O CYS B 675 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 715 through 719 removed outlier: 6.025A pdb=" N ASP B 729 " --> pdb=" O CYS B 735 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N CYS B 735 " --> pdb=" O ASP B 729 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.022A pdb=" N ASP B 771 " --> pdb=" O GLU B 777 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU B 777 " --> pdb=" O ASP B 771 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 804 through 806 Processing sheet with id= Z, first strand: chain 'B' and resid 845 through 848 removed outlier: 3.874A pdb=" N VAL B 864 " --> pdb=" O CYS B 878 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASN B 868 " --> pdb=" O LYS B 874 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LYS B 874 " --> pdb=" O ASN B 868 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 926 through 931 Processing sheet with id= AB, first strand: chain 'B' and resid 966 through 969 removed outlier: 4.503A pdb=" N ILE B 985 " --> pdb=" O ARG B 999 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG B 999 " --> pdb=" O ILE B 985 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 1009 through 1011 Processing sheet with id= AD, first strand: chain 'B' and resid 1049 through 1052 Processing sheet with id= AE, first strand: chain 'B' and resid 1101 through 1104 removed outlier: 3.939A pdb=" N THR B1103 " --> pdb=" O LYS B1110 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS B1110 " --> pdb=" O THR B1103 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 1132 through 1135 Processing sheet with id= AG, first strand: chain 'B' and resid 1191 through 1195 Processing sheet with id= AH, first strand: chain 'B' and resid 1232 through 1235 Processing sheet with id= AI, first strand: chain 'C' and resid 148 through 153 removed outlier: 6.936A pdb=" N LEU C 240 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR C 263 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU C 242 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 425 through 428 Processing sheet with id= AK, first strand: chain 'C' and resid 609 through 611 removed outlier: 4.401A pdb=" N SER C 896 " --> pdb=" O SER C 891 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 629 through 632 removed outlier: 6.323A pdb=" N LYS C 643 " --> pdb=" O LYS C 649 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS C 649 " --> pdb=" O LYS C 643 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 682 through 685 removed outlier: 3.690A pdb=" N CYS C 675 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS C 662 " --> pdb=" O CYS C 675 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 715 through 719 removed outlier: 6.025A pdb=" N ASP C 729 " --> pdb=" O CYS C 735 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N CYS C 735 " --> pdb=" O ASP C 729 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 748 through 751 removed outlier: 6.022A pdb=" N ASP C 771 " --> pdb=" O GLU C 777 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU C 777 " --> pdb=" O ASP C 771 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'C' and resid 804 through 806 Processing sheet with id= AQ, first strand: chain 'C' and resid 845 through 848 removed outlier: 3.874A pdb=" N VAL C 864 " --> pdb=" O CYS C 878 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASN C 868 " --> pdb=" O LYS C 874 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LYS C 874 " --> pdb=" O ASN C 868 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'C' and resid 926 through 931 Processing sheet with id= AS, first strand: chain 'C' and resid 966 through 969 removed outlier: 4.503A pdb=" N ILE C 985 " --> pdb=" O ARG C 999 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG C 999 " --> pdb=" O ILE C 985 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'C' and resid 1009 through 1011 Processing sheet with id= AU, first strand: chain 'C' and resid 1049 through 1052 Processing sheet with id= AV, first strand: chain 'C' and resid 1101 through 1104 removed outlier: 3.939A pdb=" N THR C1103 " --> pdb=" O LYS C1110 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS C1110 " --> pdb=" O THR C1103 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'C' and resid 1132 through 1135 Processing sheet with id= AX, first strand: chain 'C' and resid 1191 through 1195 Processing sheet with id= AY, first strand: chain 'C' and resid 1232 through 1235 Processing sheet with id= AZ, first strand: chain 'D' and resid 148 through 153 removed outlier: 6.936A pdb=" N LEU D 240 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR D 263 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU D 242 " --> pdb=" O THR D 263 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'D' and resid 425 through 428 Processing sheet with id= BB, first strand: chain 'D' and resid 609 through 611 removed outlier: 4.401A pdb=" N SER D 896 " --> pdb=" O SER D 891 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'D' and resid 629 through 632 removed outlier: 6.323A pdb=" N LYS D 643 " --> pdb=" O LYS D 649 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS D 649 " --> pdb=" O LYS D 643 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'D' and resid 682 through 685 removed outlier: 3.689A pdb=" N CYS D 675 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS D 662 " --> pdb=" O CYS D 675 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'D' and resid 715 through 719 removed outlier: 6.024A pdb=" N ASP D 729 " --> pdb=" O CYS D 735 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N CYS D 735 " --> pdb=" O ASP D 729 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'D' and resid 748 through 751 removed outlier: 6.023A pdb=" N ASP D 771 " --> pdb=" O GLU D 777 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU D 777 " --> pdb=" O ASP D 771 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'D' and resid 804 through 806 Processing sheet with id= BH, first strand: chain 'D' and resid 845 through 848 removed outlier: 3.874A pdb=" N VAL D 864 " --> pdb=" O CYS D 878 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASN D 868 " --> pdb=" O LYS D 874 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LYS D 874 " --> pdb=" O ASN D 868 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'D' and resid 926 through 931 Processing sheet with id= BJ, first strand: chain 'D' and resid 966 through 969 removed outlier: 4.503A pdb=" N ILE D 985 " --> pdb=" O ARG D 999 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG D 999 " --> pdb=" O ILE D 985 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'D' and resid 1009 through 1011 Processing sheet with id= BL, first strand: chain 'D' and resid 1049 through 1052 Processing sheet with id= BM, first strand: chain 'D' and resid 1101 through 1104 removed outlier: 3.939A pdb=" N THR D1103 " --> pdb=" O LYS D1110 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LYS D1110 " --> pdb=" O THR D1103 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'D' and resid 1132 through 1135 Processing sheet with id= BO, first strand: chain 'D' and resid 1191 through 1195 Processing sheet with id= BP, first strand: chain 'D' and resid 1232 through 1235 Processing sheet with id= BQ, first strand: chain 'E' and resid 148 through 153 removed outlier: 6.936A pdb=" N LEU E 240 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR E 263 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU E 242 " --> pdb=" O THR E 263 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'E' and resid 425 through 428 Processing sheet with id= BS, first strand: chain 'E' and resid 609 through 611 removed outlier: 4.401A pdb=" N SER E 896 " --> pdb=" O SER E 891 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'E' and resid 629 through 632 removed outlier: 6.322A pdb=" N LYS E 643 " --> pdb=" O LYS E 649 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS E 649 " --> pdb=" O LYS E 643 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'E' and resid 682 through 685 removed outlier: 3.689A pdb=" N CYS E 675 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS E 662 " --> pdb=" O CYS E 675 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'E' and resid 715 through 719 removed outlier: 6.025A pdb=" N ASP E 729 " --> pdb=" O CYS E 735 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N CYS E 735 " --> pdb=" O ASP E 729 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'E' and resid 748 through 751 removed outlier: 6.022A pdb=" N ASP E 771 " --> pdb=" O GLU E 777 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU E 777 " --> pdb=" O ASP E 771 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'E' and resid 804 through 806 Processing sheet with id= BY, first strand: chain 'E' and resid 845 through 848 removed outlier: 3.874A pdb=" N VAL E 864 " --> pdb=" O CYS E 878 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASN E 868 " --> pdb=" O LYS E 874 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LYS E 874 " --> pdb=" O ASN E 868 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'E' and resid 926 through 931 Processing sheet with id= CA, first strand: chain 'E' and resid 966 through 969 removed outlier: 4.503A pdb=" N ILE E 985 " --> pdb=" O ARG E 999 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG E 999 " --> pdb=" O ILE E 985 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'E' and resid 1009 through 1011 Processing sheet with id= CC, first strand: chain 'E' and resid 1049 through 1052 Processing sheet with id= CD, first strand: chain 'E' and resid 1101 through 1104 removed outlier: 3.940A pdb=" N THR E1103 " --> pdb=" O LYS E1110 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS E1110 " --> pdb=" O THR E1103 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'E' and resid 1132 through 1135 Processing sheet with id= CF, first strand: chain 'E' and resid 1191 through 1195 Processing sheet with id= CG, first strand: chain 'E' and resid 1232 through 1235 Processing sheet with id= CH, first strand: chain 'F' and resid 148 through 153 removed outlier: 6.935A pdb=" N LEU F 240 " --> pdb=" O LEU F 261 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR F 263 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU F 242 " --> pdb=" O THR F 263 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'F' and resid 425 through 428 Processing sheet with id= CJ, first strand: chain 'F' and resid 609 through 611 removed outlier: 4.401A pdb=" N SER F 896 " --> pdb=" O SER F 891 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'F' and resid 629 through 632 removed outlier: 6.323A pdb=" N LYS F 643 " --> pdb=" O LYS F 649 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS F 649 " --> pdb=" O LYS F 643 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'F' and resid 682 through 685 removed outlier: 3.690A pdb=" N CYS F 675 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS F 662 " --> pdb=" O CYS F 675 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'F' and resid 715 through 719 removed outlier: 6.025A pdb=" N ASP F 729 " --> pdb=" O CYS F 735 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N CYS F 735 " --> pdb=" O ASP F 729 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'F' and resid 748 through 751 removed outlier: 6.022A pdb=" N ASP F 771 " --> pdb=" O GLU F 777 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU F 777 " --> pdb=" O ASP F 771 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'F' and resid 804 through 806 Processing sheet with id= CP, first strand: chain 'F' and resid 845 through 848 removed outlier: 3.874A pdb=" N VAL F 864 " --> pdb=" O CYS F 878 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASN F 868 " --> pdb=" O LYS F 874 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LYS F 874 " --> pdb=" O ASN F 868 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'F' and resid 926 through 931 Processing sheet with id= CR, first strand: chain 'F' and resid 966 through 969 removed outlier: 4.503A pdb=" N ILE F 985 " --> pdb=" O ARG F 999 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG F 999 " --> pdb=" O ILE F 985 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'F' and resid 1009 through 1011 Processing sheet with id= CT, first strand: chain 'F' and resid 1049 through 1052 Processing sheet with id= CU, first strand: chain 'F' and resid 1101 through 1104 removed outlier: 3.940A pdb=" N THR F1103 " --> pdb=" O LYS F1110 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS F1110 " --> pdb=" O THR F1103 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'F' and resid 1132 through 1135 Processing sheet with id= CW, first strand: chain 'F' and resid 1191 through 1195 Processing sheet with id= CX, first strand: chain 'F' and resid 1232 through 1235 Processing sheet with id= CY, first strand: chain 'G' and resid 148 through 153 removed outlier: 6.935A pdb=" N LEU G 240 " --> pdb=" O LEU G 261 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR G 263 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU G 242 " --> pdb=" O THR G 263 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'G' and resid 425 through 428 Processing sheet with id= DA, first strand: chain 'G' and resid 609 through 611 removed outlier: 4.402A pdb=" N SER G 896 " --> pdb=" O SER G 891 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'G' and resid 629 through 632 removed outlier: 6.324A pdb=" N LYS G 643 " --> pdb=" O LYS G 649 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS G 649 " --> pdb=" O LYS G 643 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'G' and resid 682 through 685 removed outlier: 3.690A pdb=" N CYS G 675 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS G 662 " --> pdb=" O CYS G 675 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'G' and resid 715 through 719 removed outlier: 6.024A pdb=" N ASP G 729 " --> pdb=" O CYS G 735 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N CYS G 735 " --> pdb=" O ASP G 729 " (cutoff:3.500A) Processing sheet with id= DE, first strand: chain 'G' and resid 748 through 751 removed outlier: 6.023A pdb=" N ASP G 771 " --> pdb=" O GLU G 777 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU G 777 " --> pdb=" O ASP G 771 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'G' and resid 804 through 806 Processing sheet with id= DG, first strand: chain 'G' and resid 845 through 848 removed outlier: 3.875A pdb=" N VAL G 864 " --> pdb=" O CYS G 878 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASN G 868 " --> pdb=" O LYS G 874 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LYS G 874 " --> pdb=" O ASN G 868 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'G' and resid 926 through 931 Processing sheet with id= DI, first strand: chain 'G' and resid 966 through 969 removed outlier: 4.503A pdb=" N ILE G 985 " --> pdb=" O ARG G 999 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG G 999 " --> pdb=" O ILE G 985 " (cutoff:3.500A) Processing sheet with id= DJ, first strand: chain 'G' and resid 1009 through 1011 Processing sheet with id= DK, first strand: chain 'G' and resid 1049 through 1052 Processing sheet with id= DL, first strand: chain 'G' and resid 1101 through 1104 removed outlier: 3.940A pdb=" N THR G1103 " --> pdb=" O LYS G1110 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS G1110 " --> pdb=" O THR G1103 " (cutoff:3.500A) Processing sheet with id= DM, first strand: chain 'G' and resid 1132 through 1135 Processing sheet with id= DN, first strand: chain 'G' and resid 1191 through 1195 Processing sheet with id= DO, first strand: chain 'G' and resid 1232 through 1235 2451 hydrogen bonds defined for protein. 6681 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: 35.39 Time building geometry restraints manager: 25.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 25998 1.37 - 1.54: 50187 1.54 - 1.71: 772 1.71 - 1.89: 692 1.89 - 2.06: 28 Bond restraints: 77677 Sorted by residual: bond pdb=" C2' DTP D1301 " pdb=" C3' DTP D1301 " ideal model delta sigma weight residual 1.523 1.210 0.313 1.00e-02 1.00e+04 9.77e+02 bond pdb=" C2' DTP G1301 " pdb=" C3' DTP G1301 " ideal model delta sigma weight residual 1.523 1.211 0.312 1.00e-02 1.00e+04 9.75e+02 bond pdb=" C2' DTP F1301 " pdb=" C3' DTP F1301 " ideal model delta sigma weight residual 1.523 1.211 0.312 1.00e-02 1.00e+04 9.75e+02 bond pdb=" C2' DTP A1301 " pdb=" C3' DTP A1301 " ideal model delta sigma weight residual 1.523 1.211 0.312 1.00e-02 1.00e+04 9.73e+02 bond pdb=" C2' DTP E1301 " pdb=" C3' DTP E1301 " ideal model delta sigma weight residual 1.523 1.211 0.312 1.00e-02 1.00e+04 9.72e+02 ... (remaining 77672 not shown) Histogram of bond angle deviations from ideal: 86.16 - 103.08: 500 103.08 - 120.00: 67797 120.00 - 136.93: 36757 136.93 - 153.85: 0 153.85 - 170.77: 14 Bond angle restraints: 105068 Sorted by residual: angle pdb=" PB DTP B1301 " pdb=" O3B DTP B1301 " pdb=" PG DTP B1301 " ideal model delta sigma weight residual 139.87 117.05 22.82 1.00e+00 1.00e+00 5.21e+02 angle pdb=" PB DTP E1301 " pdb=" O3B DTP E1301 " pdb=" PG DTP E1301 " ideal model delta sigma weight residual 139.87 117.07 22.80 1.00e+00 1.00e+00 5.20e+02 angle pdb=" PB DTP C1301 " pdb=" O3B DTP C1301 " pdb=" PG DTP C1301 " ideal model delta sigma weight residual 139.87 117.10 22.77 1.00e+00 1.00e+00 5.19e+02 angle pdb=" PB DTP A1301 " pdb=" O3B DTP A1301 " pdb=" PG DTP A1301 " ideal model delta sigma weight residual 139.87 117.10 22.77 1.00e+00 1.00e+00 5.19e+02 angle pdb=" PB DTP F1301 " pdb=" O3B DTP F1301 " pdb=" PG DTP F1301 " ideal model delta sigma weight residual 139.87 117.11 22.76 1.00e+00 1.00e+00 5.18e+02 ... (remaining 105063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.50: 45892 32.50 - 64.99: 658 64.99 - 97.49: 118 97.49 - 129.99: 0 129.99 - 162.48: 7 Dihedral angle restraints: 46675 sinusoidal: 19180 harmonic: 27495 Sorted by residual: dihedral pdb=" CB CYS G 704 " pdb=" SG CYS G 704 " pdb=" SG CYS G 749 " pdb=" CB CYS G 749 " ideal model delta sinusoidal sigma weight residual -86.00 -176.18 90.18 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS B 704 " pdb=" SG CYS B 704 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual -86.00 -176.16 90.16 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS A 704 " pdb=" SG CYS A 704 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -176.16 90.16 1 1.00e+01 1.00e-02 9.63e+01 ... (remaining 46672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 9420 0.062 - 0.125: 1830 0.125 - 0.187: 265 0.187 - 0.250: 54 0.250 - 0.312: 28 Chirality restraints: 11597 Sorted by residual: chirality pdb=" C3' DTP D1301 " pdb=" C2' DTP D1301 " pdb=" C4' DTP D1301 " pdb=" O3' DTP D1301 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C3' DTP F1301 " pdb=" C2' DTP F1301 " pdb=" C4' DTP F1301 " pdb=" O3' DTP F1301 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C3' DTP C1301 " pdb=" C2' DTP C1301 " pdb=" C4' DTP C1301 " pdb=" O3' DTP C1301 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 11594 not shown) Planarity restraints: 13339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 168 " -0.024 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C VAL B 168 " 0.076 2.00e-02 2.50e+03 pdb=" O VAL B 168 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG B 169 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 168 " -0.024 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C VAL C 168 " 0.076 2.00e-02 2.50e+03 pdb=" O VAL C 168 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG C 169 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 168 " -0.024 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C VAL A 168 " 0.076 2.00e-02 2.50e+03 pdb=" O VAL A 168 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG A 169 " -0.023 2.00e-02 2.50e+03 ... (remaining 13336 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 34 2.14 - 2.83: 22433 2.83 - 3.52: 103329 3.52 - 4.21: 171175 4.21 - 4.90: 292247 Nonbonded interactions: 589218 Sorted by model distance: nonbonded pdb=" OE2 GLU D 316 " pdb=" NE2 GLN D 346 " model vdw 1.447 2.520 nonbonded pdb=" OE2 GLU B 316 " pdb=" NE2 GLN B 346 " model vdw 1.447 2.520 nonbonded pdb=" OE2 GLU F 316 " pdb=" NE2 GLN F 346 " model vdw 1.447 2.520 nonbonded pdb=" OE2 GLU G 316 " pdb=" NE2 GLN G 346 " model vdw 1.447 2.520 nonbonded pdb=" OE2 GLU A 316 " pdb=" NE2 GLN A 346 " model vdw 1.447 2.520 ... (remaining 589213 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' selection = (chain 'B' and (resid 105 through 1248 or resid 1301)) selection = chain 'C' selection = (chain 'D' and (resid 105 through 1248 or resid 1301)) selection = (chain 'E' and (resid 105 through 1248 or resid 1301)) selection = chain 'F' selection = (chain 'G' and (resid 105 through 1248 or resid 1301)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 0.070 Extract box with map and model: 9.600 Check model and map are aligned: 0.840 Set scattering table: 0.510 Process input model: 162.040 Find NCS groups from input model: 4.830 Set up NCS constraints: 0.550 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: 0.020 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 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 : 0.009 0.313 77677 Z= 0.601 Angle : 1.230 22.815 105068 Z= 0.849 Chirality : 0.053 0.312 11597 Planarity : 0.004 0.066 13339 Dihedral : 11.010 162.482 28740 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.59 % Favored : 92.96 % Rotamer: Outliers : 0.71 % Allowed : 1.09 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.07), residues: 9403 helix: -2.89 (0.07), residues: 2892 sheet: -0.74 (0.10), residues: 1792 loop : -2.11 (0.07), residues: 4719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 184 HIS 0.010 0.001 HIS E 614 PHE 0.021 0.002 PHE F1213 TYR 0.014 0.002 TYR G 382 ARG 0.010 0.001 ARG G 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 899 time to evaluate : 6.666 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8506 (tpt) cc_final: 0.8104 (ttp) REVERT: B 155 MET cc_start: 0.8708 (tpt) cc_final: 0.8368 (ttp) REVERT: B 250 VAL cc_start: 0.9234 (t) cc_final: 0.8809 (p) REVERT: B 522 LEU cc_start: 0.8846 (tp) cc_final: 0.8591 (tp) REVERT: C 522 LEU cc_start: 0.8967 (tp) cc_final: 0.8700 (tp) REVERT: D 443 ASP cc_start: 0.7537 (m-30) cc_final: 0.7312 (m-30) REVERT: D 522 LEU cc_start: 0.9054 (tp) cc_final: 0.8824 (tp) REVERT: E 155 MET cc_start: 0.8482 (tpt) cc_final: 0.8160 (ttp) REVERT: E 522 LEU cc_start: 0.8696 (tp) cc_final: 0.8326 (tp) REVERT: F 155 MET cc_start: 0.8547 (tpt) cc_final: 0.8222 (ttm) REVERT: G 155 MET cc_start: 0.8589 (tpt) cc_final: 0.8026 (ttm) REVERT: G 522 LEU cc_start: 0.8929 (tp) cc_final: 0.8582 (tp) REVERT: I 80 MET cc_start: 0.5622 (ttt) cc_final: 0.4624 (ttt) REVERT: K 80 MET cc_start: 0.5035 (ttt) cc_final: 0.4351 (ttt) REVERT: L 10 PHE cc_start: 0.3041 (t80) cc_final: 0.2579 (t80) REVERT: L 80 MET cc_start: 0.5025 (ttt) cc_final: 0.4540 (ttt) REVERT: O 93 ARG cc_start: 0.0785 (OUTLIER) cc_final: -0.0514 (tpt-90) REVERT: P 1 MET cc_start: 0.0326 (ttm) cc_final: -0.0204 (mtp) outliers start: 60 outliers final: 5 residues processed: 944 average time/residue: 0.7440 time to fit residues: 1172.7895 Evaluate side-chains 408 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 402 time to evaluate : 6.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 937 random chunks: chunk 791 optimal weight: 20.0000 chunk 710 optimal weight: 5.9990 chunk 394 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 479 optimal weight: 5.9990 chunk 379 optimal weight: 0.8980 chunk 734 optimal weight: 0.6980 chunk 284 optimal weight: 6.9990 chunk 446 optimal weight: 30.0000 chunk 546 optimal weight: 0.8980 chunk 850 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 235 HIS A 416 GLN A 562 ASN A 602 ASN A 620 HIS A 703 ASN A 712 HIS A 782 ASN A 819 ASN ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 HIS A1126 HIS B 11 GLN B 51 GLN B 201 ASN B 214 GLN B 416 GLN B 562 ASN B 602 ASN B 620 HIS B 703 ASN B 782 ASN B 819 ASN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 HIS C 201 ASN C 214 GLN C 235 HIS C 416 GLN C 429 ASN C 562 ASN C 602 ASN C 620 HIS C 703 ASN C 782 ASN C 819 ASN C 852 ASN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1126 HIS D 11 GLN D 51 GLN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN D 416 GLN D 562 ASN D 602 ASN D 620 HIS D 703 ASN D 712 HIS D 782 ASN D 819 ASN ** D 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1126 HIS E 11 GLN E 45 ASN E 51 GLN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN E 235 HIS E 416 GLN E 562 ASN E 602 ASN E 620 HIS E 703 ASN E 782 ASN E 819 ASN ** E 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1126 HIS ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 GLN F 235 HIS F 416 GLN ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN F 620 HIS F 703 ASN F 782 ASN F 819 ASN ** F 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1126 HIS G 11 GLN G 45 ASN G 51 GLN ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 GLN G 416 GLN ** G 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 ASN G 620 HIS G 703 ASN G 782 ASN G 819 ASN G1043 HIS G1126 HIS ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 ASN O 44 GLN P 44 GLN Q 44 GLN R 44 GLN Total number of N/Q/H flips: 88 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5599 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 77677 Z= 0.202 Angle : 0.608 11.454 105068 Z= 0.315 Chirality : 0.042 0.176 11597 Planarity : 0.003 0.057 13339 Dihedral : 8.123 132.977 10336 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.31 % Favored : 95.54 % Rotamer: Outliers : 0.02 % Allowed : 1.59 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -1.41 (0.08), residues: 9403 helix: -0.40 (0.09), residues: 2842 sheet: -0.40 (0.11), residues: 1959 loop : -1.49 (0.08), residues: 4602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 184 HIS 0.007 0.001 HIS E 235 PHE 0.016 0.001 PHE G 526 TYR 0.019 0.001 TYR E 594 ARG 0.012 0.000 ARG M 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 536 time to evaluate : 6.768 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8381 (tpt) cc_final: 0.7785 (ttp) REVERT: A 443 ASP cc_start: 0.7394 (m-30) cc_final: 0.7139 (m-30) REVERT: A 739 MET cc_start: 0.5000 (mpp) cc_final: 0.4696 (mmm) REVERT: A 814 MET cc_start: 0.2724 (mpp) cc_final: 0.1332 (mmm) REVERT: B 155 MET cc_start: 0.8514 (tpt) cc_final: 0.8246 (ttp) REVERT: B 231 MET cc_start: 0.8406 (mmm) cc_final: 0.8105 (mmm) REVERT: B 250 VAL cc_start: 0.9256 (t) cc_final: 0.8902 (p) REVERT: B 687 MET cc_start: 0.7892 (mmt) cc_final: 0.7523 (mmm) REVERT: B 688 THR cc_start: 0.6910 (m) cc_final: 0.6604 (m) REVERT: B 814 MET cc_start: 0.2503 (mpp) cc_final: 0.0996 (mmm) REVERT: C 406 MET cc_start: 0.8328 (ptp) cc_final: 0.7059 (ptp) REVERT: C 522 LEU cc_start: 0.8606 (tp) cc_final: 0.8316 (tp) REVERT: D 921 MET cc_start: 0.8385 (mpp) cc_final: 0.7962 (mpp) REVERT: D 1191 MET cc_start: 0.7388 (tmm) cc_final: 0.7148 (tmm) REVERT: E 155 MET cc_start: 0.8551 (tpt) cc_final: 0.8059 (ttp) REVERT: E 406 MET cc_start: 0.8324 (ptp) cc_final: 0.7599 (ptm) REVERT: E 814 MET cc_start: 0.2327 (mpp) cc_final: 0.0622 (mmm) REVERT: F 155 MET cc_start: 0.8597 (tpt) cc_final: 0.8113 (ttm) REVERT: F 232 LEU cc_start: 0.9242 (tp) cc_final: 0.9021 (tp) REVERT: F 688 THR cc_start: 0.6752 (m) cc_final: 0.5971 (m) REVERT: F 814 MET cc_start: 0.2512 (mpp) cc_final: 0.1075 (mmm) REVERT: G 155 MET cc_start: 0.8450 (tpt) cc_final: 0.7814 (ttm) REVERT: G 374 MET cc_start: 0.8263 (mmp) cc_final: 0.7888 (mmp) REVERT: G 406 MET cc_start: 0.8343 (ptm) cc_final: 0.7777 (ptm) REVERT: G 688 THR cc_start: 0.6061 (m) cc_final: 0.5375 (m) REVERT: G 739 MET cc_start: 0.5667 (mpp) cc_final: 0.5178 (mmm) REVERT: G 814 MET cc_start: 0.3104 (mpp) cc_final: 0.0863 (mmm) REVERT: I 80 MET cc_start: 0.5878 (ttt) cc_final: 0.5022 (ttt) REVERT: L 80 MET cc_start: 0.5271 (ttt) cc_final: 0.4752 (ttt) outliers start: 2 outliers final: 1 residues processed: 538 average time/residue: 0.6855 time to fit residues: 644.4383 Evaluate side-chains 367 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 366 time to evaluate : 6.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 937 random chunks: chunk 472 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 708 optimal weight: 20.0000 chunk 579 optimal weight: 0.5980 chunk 234 optimal weight: 5.9990 chunk 852 optimal weight: 20.0000 chunk 920 optimal weight: 10.0000 chunk 759 optimal weight: 1.9990 chunk 845 optimal weight: 30.0000 chunk 290 optimal weight: 9.9990 chunk 683 optimal weight: 30.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS A 614 HIS A 776 ASN A 881 HIS ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 ASN B 471 HIS B 614 HIS B 712 HIS B 776 ASN B 881 HIS ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN B1043 HIS C 471 HIS C 614 HIS C 712 HIS C 776 ASN C 881 HIS ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 931 GLN C1043 HIS D 88 HIS ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 HIS D 471 HIS D 614 HIS D 776 ASN D 881 HIS ** D 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 931 GLN D1043 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS E 88 HIS E 471 HIS E 614 HIS E 712 HIS E 776 ASN E 881 HIS ** E 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 931 GLN E1043 HIS E1176 HIS ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 471 HIS F 562 ASN F 614 HIS F 712 HIS F 776 ASN F 881 HIS ** F 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 931 GLN F1043 HIS ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 HIS ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 471 HIS G 543 ASN G 562 ASN G 614 HIS G 712 HIS G 776 ASN G 881 HIS G 931 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 ASN K 33 HIS K 70 ASN L 33 HIS ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 70 ASN N 33 HIS N 70 ASN O 24 GLN P 38 HIS R 92 ASN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 77677 Z= 0.413 Angle : 0.735 15.277 105068 Z= 0.371 Chirality : 0.045 0.244 11597 Planarity : 0.004 0.064 13339 Dihedral : 8.466 166.922 10336 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.73 % Favored : 94.12 % Rotamer: Outliers : 0.15 % Allowed : 2.26 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -1.28 (0.08), residues: 9403 helix: -0.22 (0.09), residues: 2856 sheet: -0.46 (0.11), residues: 1979 loop : -1.39 (0.09), residues: 4568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 404 HIS 0.011 0.002 HIS B 183 PHE 0.034 0.002 PHE G 786 TYR 0.019 0.002 TYR D 24 ARG 0.009 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 450 time to evaluate : 7.799 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 687 MET cc_start: 0.7673 (mmt) cc_final: 0.7406 (mmt) REVERT: A 739 MET cc_start: 0.4670 (mpp) cc_final: 0.4458 (mmm) REVERT: A 814 MET cc_start: 0.2184 (mpp) cc_final: 0.1380 (mmm) REVERT: B 29 MET cc_start: 0.3124 (mpp) cc_final: 0.2386 (mpp) REVERT: B 687 MET cc_start: 0.8121 (mmt) cc_final: 0.7888 (mmt) REVERT: C 155 MET cc_start: 0.8651 (tpt) cc_final: 0.8066 (ttm) REVERT: C 814 MET cc_start: 0.3329 (mpp) cc_final: 0.1474 (mmm) REVERT: C 1191 MET cc_start: 0.7241 (tmm) cc_final: 0.6613 (tmm) REVERT: D 921 MET cc_start: 0.8553 (mpp) cc_final: 0.8103 (mpp) REVERT: E 26 MET cc_start: 0.0684 (ptt) cc_final: 0.0360 (mtp) REVERT: E 406 MET cc_start: 0.8241 (ptp) cc_final: 0.7925 (ptm) REVERT: E 522 LEU cc_start: 0.8683 (tp) cc_final: 0.8388 (tp) REVERT: E 814 MET cc_start: 0.1695 (mpp) cc_final: 0.0537 (mmm) REVERT: F 814 MET cc_start: 0.2449 (mpp) cc_final: 0.1202 (mmm) REVERT: G 368 MET cc_start: 0.9312 (mmt) cc_final: 0.9074 (mpp) REVERT: G 739 MET cc_start: 0.5289 (mpp) cc_final: 0.4951 (mmt) REVERT: H 80 MET cc_start: 0.5898 (ttt) cc_final: 0.4794 (ttt) REVERT: I 80 MET cc_start: 0.6213 (ttt) cc_final: 0.5800 (ttt) REVERT: J 80 MET cc_start: 0.5604 (ttt) cc_final: 0.5295 (ttt) REVERT: K 80 MET cc_start: 0.6075 (ttt) cc_final: 0.5759 (ttt) REVERT: L 80 MET cc_start: 0.5779 (ttt) cc_final: 0.5180 (ttt) REVERT: N 80 MET cc_start: 0.5724 (ttt) cc_final: 0.4819 (ttt) outliers start: 13 outliers final: 7 residues processed: 463 average time/residue: 0.6691 time to fit residues: 545.4729 Evaluate side-chains 326 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 319 time to evaluate : 6.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 937 random chunks: chunk 842 optimal weight: 6.9990 chunk 640 optimal weight: 0.1980 chunk 442 optimal weight: 30.0000 chunk 94 optimal weight: 9.9990 chunk 406 optimal weight: 3.9990 chunk 572 optimal weight: 40.0000 chunk 855 optimal weight: 5.9990 chunk 905 optimal weight: 5.9990 chunk 446 optimal weight: 40.0000 chunk 810 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 543 ASN A 562 ASN ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN B 49 GLN B 235 HIS B 543 ASN ** B 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 562 ASN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 562 ASN ** D 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 543 ASN F 171 HIS ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 HIS G 171 HIS ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 235 HIS H 70 ASN ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 77677 Z= 0.355 Angle : 0.665 13.617 105068 Z= 0.338 Chirality : 0.043 0.190 11597 Planarity : 0.003 0.061 13339 Dihedral : 8.247 160.621 10336 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.74 % Favored : 94.11 % Rotamer: Outliers : 0.05 % Allowed : 2.12 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -1.13 (0.08), residues: 9403 helix: -0.05 (0.09), residues: 2802 sheet: -0.43 (0.11), residues: 1949 loop : -1.29 (0.09), residues: 4652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 184 HIS 0.008 0.001 HIS B 183 PHE 0.026 0.002 PHE A 822 TYR 0.020 0.002 TYR I 97 ARG 0.014 0.001 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 400 time to evaluate : 6.727 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 687 MET cc_start: 0.7904 (mmt) cc_final: 0.7684 (mmt) REVERT: A 739 MET cc_start: 0.4656 (mpp) cc_final: 0.4447 (mmm) REVERT: A 797 MET cc_start: -0.0721 (tmm) cc_final: -0.1179 (ttt) REVERT: A 814 MET cc_start: 0.2394 (mpp) cc_final: 0.1496 (mmm) REVERT: B 29 MET cc_start: 0.3336 (mpp) cc_final: 0.1226 (mpp) REVERT: B 32 ASP cc_start: 0.5434 (m-30) cc_final: 0.4903 (t0) REVERT: B 231 MET cc_start: 0.8189 (mmm) cc_final: 0.7617 (mmm) REVERT: B 687 MET cc_start: 0.8045 (mmt) cc_final: 0.7811 (mmt) REVERT: B 814 MET cc_start: 0.3581 (mpp) cc_final: 0.1717 (mmm) REVERT: B 1191 MET cc_start: 0.7131 (tmm) cc_final: 0.6863 (tmm) REVERT: C 797 MET cc_start: -0.0610 (tmm) cc_final: -0.1310 (ttt) REVERT: D 431 LYS cc_start: 0.6432 (tptt) cc_final: 0.5831 (tppt) REVERT: D 814 MET cc_start: 0.3969 (mpp) cc_final: 0.2056 (mmm) REVERT: D 921 MET cc_start: 0.8674 (mpp) cc_final: 0.8274 (mpp) REVERT: E 814 MET cc_start: 0.3001 (mpp) cc_final: 0.1512 (mmm) REVERT: F 814 MET cc_start: 0.3407 (mpp) cc_final: 0.2004 (mmm) REVERT: G 59 MET cc_start: 0.3997 (mtp) cc_final: 0.3778 (mtp) REVERT: G 739 MET cc_start: 0.5673 (mpp) cc_final: 0.5247 (mmm) REVERT: G 814 MET cc_start: 0.3733 (mpp) cc_final: 0.2050 (mmm) REVERT: H 80 MET cc_start: 0.6598 (ttt) cc_final: 0.5306 (ttt) REVERT: I 80 MET cc_start: 0.6509 (ttt) cc_final: 0.5697 (ttt) REVERT: J 80 MET cc_start: 0.6009 (ttt) cc_final: 0.5433 (ttt) outliers start: 4 outliers final: 2 residues processed: 404 average time/residue: 0.6643 time to fit residues: 477.2983 Evaluate side-chains 325 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 323 time to evaluate : 6.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 937 random chunks: chunk 754 optimal weight: 6.9990 chunk 514 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 674 optimal weight: 6.9990 chunk 373 optimal weight: 0.6980 chunk 772 optimal weight: 30.0000 chunk 626 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 462 optimal weight: 10.0000 chunk 812 optimal weight: 10.0000 chunk 228 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 ASN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 924 GLN ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5795 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 77677 Z= 0.185 Angle : 0.550 11.914 105068 Z= 0.282 Chirality : 0.041 0.164 11597 Planarity : 0.003 0.039 13339 Dihedral : 7.843 161.266 10336 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.10 % Favored : 94.75 % Rotamer: Outliers : 0.01 % Allowed : 1.46 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.77 (0.08), residues: 9403 helix: 0.42 (0.10), residues: 2801 sheet: -0.29 (0.12), residues: 1954 loop : -1.16 (0.09), residues: 4648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 404 HIS 0.004 0.001 HIS J 33 PHE 0.017 0.001 PHE A 334 TYR 0.016 0.001 TYR J 97 ARG 0.006 0.000 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 425 time to evaluate : 6.848 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 687 MET cc_start: 0.8197 (mmm) cc_final: 0.7660 (mmt) REVERT: A 797 MET cc_start: -0.0534 (tmm) cc_final: -0.0980 (ttt) REVERT: A 814 MET cc_start: 0.2548 (mpp) cc_final: 0.1842 (mmm) REVERT: B 29 MET cc_start: 0.1822 (mpp) cc_final: 0.1249 (mpp) REVERT: B 32 ASP cc_start: 0.4912 (m-30) cc_final: 0.4528 (t0) REVERT: B 231 MET cc_start: 0.8139 (mmm) cc_final: 0.7918 (mmm) REVERT: B 385 ASP cc_start: 0.7973 (m-30) cc_final: 0.7642 (m-30) REVERT: B 687 MET cc_start: 0.8157 (mmt) cc_final: 0.7855 (mmt) REVERT: B 814 MET cc_start: 0.3506 (mpp) cc_final: 0.1639 (mmm) REVERT: C 814 MET cc_start: 0.4093 (mpp) cc_final: 0.2299 (mmm) REVERT: D 155 MET cc_start: 0.8338 (ttp) cc_final: 0.8023 (ttp) REVERT: D 431 LYS cc_start: 0.6056 (tptt) cc_final: 0.5499 (tppt) REVERT: D 814 MET cc_start: 0.3889 (mpp) cc_final: 0.2098 (mmm) REVERT: D 921 MET cc_start: 0.8674 (mpp) cc_final: 0.8307 (mpp) REVERT: E 166 GLU cc_start: 0.8173 (tp30) cc_final: 0.7934 (tp30) REVERT: E 797 MET cc_start: -0.2133 (tmm) cc_final: -0.2385 (ttp) REVERT: E 814 MET cc_start: 0.3235 (mpp) cc_final: 0.1801 (mmm) REVERT: F 155 MET cc_start: 0.8467 (ttp) cc_final: 0.8145 (ttp) REVERT: F 814 MET cc_start: 0.3268 (mpp) cc_final: 0.1688 (mmm) REVERT: G 155 MET cc_start: 0.8287 (ttp) cc_final: 0.7928 (ttp) REVERT: G 739 MET cc_start: 0.5629 (mpp) cc_final: 0.5240 (mmm) REVERT: G 797 MET cc_start: -0.0626 (tmm) cc_final: -0.0945 (ttt) REVERT: G 814 MET cc_start: 0.3592 (mpp) cc_final: 0.2006 (mmm) REVERT: I 80 MET cc_start: 0.6467 (ttt) cc_final: 0.6061 (ttt) REVERT: J 80 MET cc_start: 0.5980 (ttt) cc_final: 0.5520 (ttt) REVERT: K 80 MET cc_start: 0.6226 (ttt) cc_final: 0.5886 (ttt) REVERT: L 80 MET cc_start: 0.6117 (ttt) cc_final: 0.5470 (ttt) REVERT: M 80 MET cc_start: 0.6154 (ttt) cc_final: 0.5658 (ttt) outliers start: 1 outliers final: 0 residues processed: 426 average time/residue: 0.6579 time to fit residues: 508.4981 Evaluate side-chains 348 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 6.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 937 random chunks: chunk 304 optimal weight: 20.0000 chunk 815 optimal weight: 5.9990 chunk 179 optimal weight: 0.4980 chunk 531 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 chunk 906 optimal weight: 10.0000 chunk 752 optimal weight: 4.9990 chunk 419 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 299 optimal weight: 6.9990 chunk 475 optimal weight: 9.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1176 HIS ** B1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 HIS ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 77677 Z= 0.352 Angle : 0.653 13.867 105068 Z= 0.332 Chirality : 0.043 0.164 11597 Planarity : 0.003 0.068 13339 Dihedral : 8.057 165.688 10336 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.41 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.94 (0.08), residues: 9403 helix: 0.17 (0.10), residues: 2814 sheet: -0.39 (0.12), residues: 1888 loop : -1.18 (0.09), residues: 4701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 404 HIS 0.009 0.001 HIS B 183 PHE 0.028 0.002 PHE A 418 TYR 0.022 0.002 TYR D 467 ARG 0.006 0.001 ARG B 670 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 6.730 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 687 MET cc_start: 0.8120 (mmm) cc_final: 0.7776 (mmt) REVERT: A 797 MET cc_start: -0.0326 (tmm) cc_final: -0.0773 (ttt) REVERT: A 814 MET cc_start: 0.2117 (mpp) cc_final: 0.1515 (mmm) REVERT: A 889 MET cc_start: 0.5046 (tmm) cc_final: 0.4401 (tmm) REVERT: B 29 MET cc_start: 0.2752 (mpp) cc_final: 0.1854 (mpp) REVERT: B 32 ASP cc_start: 0.5505 (m-30) cc_final: 0.4856 (t0) REVERT: B 687 MET cc_start: 0.8208 (mmt) cc_final: 0.7861 (mmt) REVERT: B 814 MET cc_start: 0.4139 (mpp) cc_final: 0.2314 (mmm) REVERT: C 797 MET cc_start: 0.0585 (tmm) cc_final: 0.0099 (ttt) REVERT: C 814 MET cc_start: 0.4198 (mpp) cc_final: 0.2454 (mmm) REVERT: D 431 LYS cc_start: 0.6150 (tptt) cc_final: 0.5619 (tppt) REVERT: D 797 MET cc_start: -0.0221 (ttp) cc_final: -0.0740 (ttt) REVERT: D 814 MET cc_start: 0.3943 (mpp) cc_final: 0.2137 (mmm) REVERT: D 921 MET cc_start: 0.8797 (mpp) cc_final: 0.8359 (mpp) REVERT: E 166 GLU cc_start: 0.8436 (tp30) cc_final: 0.8081 (tp30) REVERT: E 814 MET cc_start: 0.3073 (mpp) cc_final: 0.1521 (mmm) REVERT: F 155 MET cc_start: 0.8617 (ttp) cc_final: 0.8301 (ttp) REVERT: F 814 MET cc_start: 0.3287 (mpp) cc_final: 0.1895 (mmm) REVERT: G 155 MET cc_start: 0.8413 (ttp) cc_final: 0.8105 (ttp) REVERT: G 739 MET cc_start: 0.5603 (mpp) cc_final: 0.5231 (mmm) REVERT: G 797 MET cc_start: -0.0811 (tmm) cc_final: -0.1057 (ttt) REVERT: G 814 MET cc_start: 0.3729 (mpp) cc_final: 0.2169 (mmm) REVERT: H 80 MET cc_start: 0.7018 (ttt) cc_final: 0.5648 (ttt) REVERT: I 80 MET cc_start: 0.6751 (ttt) cc_final: 0.5927 (ttt) REVERT: J 80 MET cc_start: 0.6235 (ttt) cc_final: 0.5677 (ttt) REVERT: K 80 MET cc_start: 0.6492 (ttt) cc_final: 0.6102 (ttt) REVERT: O 39 MET cc_start: 0.4498 (ttp) cc_final: 0.4229 (ttp) REVERT: P 1 MET cc_start: 0.3288 (mpp) cc_final: 0.2945 (mpp) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.6633 time to fit residues: 458.0646 Evaluate side-chains 322 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 6.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 937 random chunks: chunk 874 optimal weight: 0.7980 chunk 102 optimal weight: 20.0000 chunk 516 optimal weight: 2.9990 chunk 662 optimal weight: 10.0000 chunk 512 optimal weight: 2.9990 chunk 763 optimal weight: 5.9990 chunk 506 optimal weight: 0.8980 chunk 903 optimal weight: 5.9990 chunk 565 optimal weight: 4.9990 chunk 550 optimal weight: 5.9990 chunk 416 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN A1076 ASN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 HIS C1076 ASN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN ** F1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 620 HIS ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 77677 Z= 0.240 Angle : 0.571 12.120 105068 Z= 0.292 Chirality : 0.041 0.208 11597 Planarity : 0.003 0.039 13339 Dihedral : 7.724 167.461 10336 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.63 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.79 (0.08), residues: 9403 helix: 0.36 (0.10), residues: 2812 sheet: -0.31 (0.12), residues: 1896 loop : -1.13 (0.09), residues: 4695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 404 HIS 0.004 0.001 HIS F 620 PHE 0.026 0.001 PHE F 822 TYR 0.014 0.001 TYR I 97 ARG 0.007 0.000 ARG O 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 6.767 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 687 MET cc_start: 0.8033 (mmm) cc_final: 0.7673 (mmt) REVERT: A 797 MET cc_start: -0.0187 (tmm) cc_final: -0.0557 (ttt) REVERT: A 814 MET cc_start: 0.2111 (mpp) cc_final: 0.1485 (mmm) REVERT: A 889 MET cc_start: 0.5323 (tmm) cc_final: 0.4882 (tmm) REVERT: B 29 MET cc_start: 0.2144 (mpp) cc_final: 0.1304 (mpp) REVERT: B 32 ASP cc_start: 0.5082 (m-30) cc_final: 0.4734 (t0) REVERT: B 385 ASP cc_start: 0.7800 (m-30) cc_final: 0.7437 (m-30) REVERT: B 814 MET cc_start: 0.4303 (mpp) cc_final: 0.2174 (mmm) REVERT: B 889 MET cc_start: 0.5575 (tmm) cc_final: 0.5219 (tmm) REVERT: C 385 ASP cc_start: 0.7939 (m-30) cc_final: 0.7418 (m-30) REVERT: C 797 MET cc_start: 0.0513 (tmm) cc_final: -0.0098 (ttt) REVERT: C 814 MET cc_start: 0.4171 (mpp) cc_final: 0.2422 (mmm) REVERT: D 431 LYS cc_start: 0.6188 (tptt) cc_final: 0.5681 (tppt) REVERT: D 814 MET cc_start: 0.4328 (mpp) cc_final: 0.2498 (mmm) REVERT: D 921 MET cc_start: 0.8822 (mpp) cc_final: 0.8346 (mpp) REVERT: E 166 GLU cc_start: 0.8430 (tp30) cc_final: 0.7982 (tp30) REVERT: E 814 MET cc_start: 0.3062 (mpp) cc_final: 0.1495 (mmm) REVERT: F 155 MET cc_start: 0.8566 (ttp) cc_final: 0.8282 (ttp) REVERT: F 814 MET cc_start: 0.3480 (mpp) cc_final: 0.1930 (mmm) REVERT: G 55 MET cc_start: 0.4628 (ttm) cc_final: 0.3720 (ptm) REVERT: G 155 MET cc_start: 0.8318 (ttp) cc_final: 0.8041 (ttp) REVERT: G 814 MET cc_start: 0.3680 (mpp) cc_final: 0.2145 (mmm) REVERT: H 80 MET cc_start: 0.6551 (ttt) cc_final: 0.4958 (ttt) REVERT: I 80 MET cc_start: 0.6468 (ttt) cc_final: 0.5484 (ttt) REVERT: M 80 MET cc_start: 0.6117 (ttt) cc_final: 0.5505 (ttt) REVERT: P 40 ILE cc_start: 0.4908 (mt) cc_final: 0.4671 (mt) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.6537 time to fit residues: 474.6088 Evaluate side-chains 339 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 6.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 937 random chunks: chunk 558 optimal weight: 10.0000 chunk 360 optimal weight: 0.0060 chunk 539 optimal weight: 10.0000 chunk 272 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 574 optimal weight: 40.0000 chunk 615 optimal weight: 5.9990 chunk 446 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 709 optimal weight: 8.9990 overall best weight: 6.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 599 ASN A 620 HIS A1121 HIS ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 ASN B 620 HIS ** B 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1044 GLN ** B1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 599 ASN C 620 HIS C 713 HIS C 827 HIS C1176 HIS D 45 ASN D 171 HIS ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN D 620 HIS ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1044 GLN D1176 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 599 ASN E 620 HIS F 171 HIS F 599 ASN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 HIS ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 599 ASN G 827 HIS G1176 HIS ** G1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN L 70 ASN ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6032 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.153 77677 Z= 0.527 Angle : 0.814 15.962 105068 Z= 0.412 Chirality : 0.047 0.254 11597 Planarity : 0.004 0.059 13339 Dihedral : 8.552 163.078 10336 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.90 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -1.33 (0.08), residues: 9403 helix: -0.22 (0.09), residues: 2836 sheet: -0.79 (0.12), residues: 1872 loop : -1.28 (0.09), residues: 4695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 404 HIS 0.013 0.002 HIS A 183 PHE 0.043 0.003 PHE A 126 TYR 0.028 0.003 TYR F 109 ARG 0.007 0.001 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 6.820 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 797 MET cc_start: -0.0476 (tmm) cc_final: -0.0930 (ttt) REVERT: A 814 MET cc_start: 0.2469 (mpp) cc_final: 0.1615 (mmm) REVERT: B 29 MET cc_start: 0.2649 (mpp) cc_final: 0.1435 (mpp) REVERT: B 32 ASP cc_start: 0.6093 (m-30) cc_final: 0.5037 (t0) REVERT: B 814 MET cc_start: 0.4323 (mpp) cc_final: 0.2247 (mmm) REVERT: C 797 MET cc_start: 0.0851 (tmm) cc_final: 0.0160 (ttt) REVERT: C 814 MET cc_start: 0.3638 (mpp) cc_final: 0.2055 (mmm) REVERT: D 431 LYS cc_start: 0.6508 (tptt) cc_final: 0.5981 (tppt) REVERT: D 797 MET cc_start: 0.0663 (tmm) cc_final: 0.0255 (ttp) REVERT: D 814 MET cc_start: 0.4035 (mpp) cc_final: 0.2590 (mmm) REVERT: D 921 MET cc_start: 0.8880 (mpp) cc_final: 0.8319 (mpp) REVERT: E 797 MET cc_start: -0.0549 (ttt) cc_final: -0.0887 (ttt) REVERT: E 814 MET cc_start: 0.2759 (mpp) cc_final: 0.1463 (mmm) REVERT: F 155 MET cc_start: 0.8600 (ttp) cc_final: 0.8391 (ttp) REVERT: F 814 MET cc_start: 0.3279 (mpp) cc_final: 0.1937 (mmm) REVERT: F 889 MET cc_start: 0.6085 (tmm) cc_final: 0.5837 (tmm) REVERT: G 155 MET cc_start: 0.8462 (ttp) cc_final: 0.8204 (ttp) REVERT: G 814 MET cc_start: 0.3808 (mpp) cc_final: 0.2279 (mmm) REVERT: J 80 MET cc_start: 0.6614 (ttt) cc_final: 0.5893 (ttt) REVERT: K 80 MET cc_start: 0.5923 (ttp) cc_final: 0.5531 (mtp) REVERT: M 80 MET cc_start: 0.6489 (ttt) cc_final: 0.5968 (ttt) REVERT: P 1 MET cc_start: 0.2758 (mpp) cc_final: 0.2352 (mpp) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.6830 time to fit residues: 444.7559 Evaluate side-chains 292 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 6.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 937 random chunks: chunk 821 optimal weight: 30.0000 chunk 865 optimal weight: 8.9990 chunk 789 optimal weight: 4.9990 chunk 841 optimal weight: 20.0000 chunk 864 optimal weight: 10.0000 chunk 506 optimal weight: 0.9980 chunk 366 optimal weight: 0.9980 chunk 660 optimal weight: 1.9990 chunk 258 optimal weight: 0.8980 chunk 760 optimal weight: 0.9980 chunk 795 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 ASN ** B 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1044 GLN ** B1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1044 GLN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 732 GLN F 713 HIS G 12 HIS ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 ASN G 732 GLN ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN Q 38 HIS R 38 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 77677 Z= 0.162 Angle : 0.557 11.105 105068 Z= 0.288 Chirality : 0.041 0.200 11597 Planarity : 0.003 0.050 13339 Dihedral : 7.803 156.188 10336 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.39 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.88 (0.08), residues: 9403 helix: 0.31 (0.10), residues: 2814 sheet: -0.54 (0.12), residues: 1939 loop : -1.12 (0.09), residues: 4650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 404 HIS 0.005 0.001 HIS D 620 PHE 0.018 0.001 PHE F 822 TYR 0.016 0.001 TYR J 97 ARG 0.005 0.000 ARG C 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 6.821 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 687 MET cc_start: 0.7957 (mmm) cc_final: 0.7673 (mmt) REVERT: A 797 MET cc_start: 0.0028 (tmm) cc_final: -0.0430 (ttt) REVERT: A 814 MET cc_start: 0.2576 (mpp) cc_final: 0.1488 (mmm) REVERT: A 889 MET cc_start: 0.5430 (tmm) cc_final: 0.3837 (tmm) REVERT: B 29 MET cc_start: 0.1881 (mpp) cc_final: 0.1592 (mpp) REVERT: B 59 MET cc_start: 0.3071 (mmp) cc_final: 0.2702 (ptp) REVERT: B 385 ASP cc_start: 0.7979 (m-30) cc_final: 0.7574 (m-30) REVERT: B 503 LEU cc_start: 0.9102 (tp) cc_final: 0.8797 (tt) REVERT: B 687 MET cc_start: 0.7548 (mmp) cc_final: 0.6896 (mpp) REVERT: B 814 MET cc_start: 0.4191 (mpp) cc_final: 0.1956 (mmm) REVERT: C 385 ASP cc_start: 0.8054 (m-30) cc_final: 0.7415 (m-30) REVERT: C 797 MET cc_start: 0.0560 (tmm) cc_final: 0.0326 (ttp) REVERT: C 814 MET cc_start: 0.3500 (mpp) cc_final: 0.1962 (mmm) REVERT: C 1191 MET cc_start: 0.6947 (tmm) cc_final: 0.6590 (tmm) REVERT: D 814 MET cc_start: 0.4326 (mpp) cc_final: 0.2868 (mmm) REVERT: D 921 MET cc_start: 0.8866 (mpp) cc_final: 0.8324 (mpp) REVERT: E 166 GLU cc_start: 0.8299 (tp30) cc_final: 0.8056 (tp30) REVERT: E 797 MET cc_start: -0.0447 (ttt) cc_final: -0.0775 (ttp) REVERT: E 814 MET cc_start: 0.2899 (mpp) cc_final: 0.1645 (mmm) REVERT: F 155 MET cc_start: 0.8484 (ttp) cc_final: 0.8219 (ttp) REVERT: F 814 MET cc_start: 0.3490 (mpp) cc_final: 0.1973 (mmm) REVERT: G 155 MET cc_start: 0.8203 (ttp) cc_final: 0.7875 (ttp) REVERT: G 814 MET cc_start: 0.3902 (mpp) cc_final: 0.2254 (mmm) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.7064 time to fit residues: 531.5920 Evaluate side-chains 330 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 6.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 937 random chunks: chunk 838 optimal weight: 8.9990 chunk 552 optimal weight: 30.0000 chunk 889 optimal weight: 9.9990 chunk 543 optimal weight: 20.0000 chunk 422 optimal weight: 30.0000 chunk 618 optimal weight: 0.0970 chunk 933 optimal weight: 20.0000 chunk 859 optimal weight: 9.9990 chunk 743 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 574 optimal weight: 40.0000 overall best weight: 6.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 ASN A1076 ASN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 ASN ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 GLN ** B1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 429 ASN ** C1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1044 GLN ** D1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 GLN F 469 GLN ** F 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 827 HIS F1044 GLN ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN N 52 ASN O 38 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.158 77677 Z= 0.547 Angle : 0.810 16.294 105068 Z= 0.413 Chirality : 0.048 0.264 11597 Planarity : 0.004 0.068 13339 Dihedral : 8.502 154.276 10336 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.37 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -1.38 (0.08), residues: 9403 helix: -0.21 (0.09), residues: 2854 sheet: -0.96 (0.12), residues: 1872 loop : -1.29 (0.09), residues: 4677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 404 HIS 0.011 0.002 HIS G 77 PHE 0.046 0.003 PHE E 526 TYR 0.030 0.003 TYR G 109 ARG 0.010 0.001 ARG B 670 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18806 Ramachandran restraints generated. 9403 Oldfield, 0 Emsley, 9403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 6.683 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 797 MET cc_start: 0.0353 (tmm) cc_final: -0.0027 (ttt) REVERT: A 814 MET cc_start: 0.2838 (mpp) cc_final: 0.1663 (mmm) REVERT: A 889 MET cc_start: 0.5876 (tmm) cc_final: 0.5307 (tmm) REVERT: B 243 ASP cc_start: 0.8949 (t0) cc_final: 0.8658 (t0) REVERT: B 687 MET cc_start: 0.7802 (mmp) cc_final: 0.7241 (mpp) REVERT: C 814 MET cc_start: 0.3406 (mpp) cc_final: 0.1879 (mmm) REVERT: D 814 MET cc_start: 0.4564 (mpp) cc_final: 0.3068 (mmm) REVERT: D 921 MET cc_start: 0.8917 (mpp) cc_final: 0.8255 (mpp) REVERT: E 406 MET cc_start: 0.8365 (ptp) cc_final: 0.8126 (ptm) REVERT: E 814 MET cc_start: 0.2766 (mpp) cc_final: 0.1473 (mmm) REVERT: F 155 MET cc_start: 0.8599 (ttp) cc_final: 0.8379 (ttp) REVERT: G 55 MET cc_start: 0.4216 (ptm) cc_final: 0.3874 (ptm) REVERT: G 155 MET cc_start: 0.8482 (ttp) cc_final: 0.8192 (ttp) REVERT: G 687 MET cc_start: 0.7561 (mmp) cc_final: 0.7037 (mpp) REVERT: G 814 MET cc_start: 0.4045 (mpp) cc_final: 0.2424 (mmm) REVERT: G 889 MET cc_start: 0.6211 (tmm) cc_final: 0.5725 (tmm) REVERT: H 80 MET cc_start: 0.6841 (ttt) cc_final: 0.6066 (ttt) REVERT: L 80 MET cc_start: 0.6233 (ttp) cc_final: 0.5402 (mtp) REVERT: M 80 MET cc_start: 0.6394 (ttp) cc_final: 0.5731 (mtp) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.6685 time to fit residues: 414.2060 Evaluate side-chains 289 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 6.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 937 random chunks: chunk 455 optimal weight: 8.9990 chunk 590 optimal weight: 4.9990 chunk 791 optimal weight: 8.9990 chunk 227 optimal weight: 0.7980 chunk 685 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 206 optimal weight: 9.9990 chunk 744 optimal weight: 2.9990 chunk 311 optimal weight: 30.0000 chunk 764 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 701 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 GLN ** B 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 GLN ** B1224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 732 GLN ** C1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 HIS D 171 HIS ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN D 701 GLN ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1044 GLN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 ASN E 416 GLN F 121 GLN F 171 HIS F 701 GLN ** F1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1044 GLN G 121 GLN G 171 HIS ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.111113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.092700 restraints weight = 349036.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.090385 restraints weight = 510802.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.088947 restraints weight = 367974.645| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.6483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 77677 Z= 0.261 Angle : 0.604 10.224 105068 Z= 0.315 Chirality : 0.042 0.212 11597 Planarity : 0.003 0.052 13339 Dihedral : 8.099 142.496 10336 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.42 % Favored : 93.43 % Rotamer: Outliers : 0.05 % Allowed : 0.25 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -1.16 (0.08), residues: 9403 helix: 0.10 (0.10), residues: 2855 sheet: -0.90 (0.12), residues: 1910 loop : -1.21 (0.09), residues: 4638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP O 26 HIS 0.006 0.001 HIS B 183 PHE 0.035 0.002 PHE E 526 TYR 0.016 0.001 TYR J 97 ARG 0.009 0.001 ARG G 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11496.98 seconds wall clock time: 208 minutes 35.74 seconds (12515.74 seconds total)