Starting phenix.real_space_refine on Sun Sep 29 23:28:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5juy_8178/09_2024/5juy_8178.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5juy_8178/09_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_8178/09_2024/5juy_8178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5juy_8178/09_2024/5juy_8178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5juy_8178/09_2024/5juy_8178.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5juy_8178/09_2024/5juy_8178.cif" } 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. Time to flip 43 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 33.32, per 1000 atoms: 0.44 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.69 Conformation dependent library (CDL) restraints added in 7.5 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... Secondary structure from input PDB file: 291 helices and 119 sheets defined 33.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.36 Creating SS restraints... Processing helix chain 'A' and resid 107 through 114 Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.919A pdb=" N VAL A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.563A pdb=" N LEU A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.700A pdb=" N ASP A 207 " --> pdb=" O CYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 Processing helix chain 'A' and resid 247 through 254 removed outlier: 3.915A pdb=" N ALA A 253 " --> pdb=" O TRP A 249 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 300 Processing helix chain 'A' and resid 302 through 307 Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.966A pdb=" N SER A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 334 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 337 through 345 Processing helix chain 'A' and resid 363 through 374 removed outlier: 3.998A pdb=" N ALA A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) 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) removed outlier: 3.847A pdb=" N MET A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 385 removed outlier: 3.814A pdb=" N THR A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 407 through 421 removed outlier: 3.965A pdb=" N ILE A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 479 through 494 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 496 through 505 removed outlier: 3.631A pdb=" N LEU A 500 " --> pdb=" O MET A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 removed outlier: 3.708A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 530 removed outlier: 4.500A pdb=" N LEU A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 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) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.583A pdb=" N LEU A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 587 Processing helix chain 'A' and resid 598 through 602 removed outlier: 4.003A pdb=" N LYS A 601 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 915 removed outlier: 3.501A pdb=" N CYS A 915 " --> pdb=" O THR A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 915' Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 21 through 24 Processing helix chain 'B' and resid 25 through 32 Processing helix chain 'B' and resid 36 through 45 Processing helix chain 'B' and resid 48 through 61 Processing helix chain 'B' and resid 64 through 78 Processing helix chain 'B' and resid 80 through 89 removed outlier: 4.651A pdb=" N ASP B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 114 Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.919A pdb=" N VAL B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 166 Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.563A pdb=" N LEU B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 207 removed outlier: 3.700A pdb=" N ASP B 207 " --> pdb=" O CYS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 234 removed outlier: 3.500A pdb=" N ALA B 223 " --> pdb=" O ASN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 254 removed outlier: 3.915A pdb=" N ALA B 253 " --> pdb=" O TRP B 249 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE B 254 " --> pdb=" O VAL B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 300 Processing helix chain 'B' and resid 302 through 307 Proline residue: B 307 - end of helix Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.966A pdb=" N SER B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 315 " --> pdb=" O HIS B 311 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 334 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 337 through 345 Processing helix chain 'B' and resid 363 through 374 removed outlier: 3.998A pdb=" N ALA B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) 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) removed outlier: 3.847A pdb=" N MET B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 385 removed outlier: 3.813A pdb=" N THR B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 397 through 405 Processing helix chain 'B' and resid 407 through 421 removed outlier: 3.965A pdb=" N ILE B 414 " --> pdb=" O GLU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 479 through 494 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 496 through 505 removed outlier: 3.630A pdb=" N LEU B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 removed outlier: 3.708A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 530 removed outlier: 4.499A pdb=" N LEU B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 552 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) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.583A pdb=" N LEU B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 587 Processing helix chain 'B' and resid 598 through 602 removed outlier: 4.002A pdb=" N LYS B 601 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 915 removed outlier: 3.501A pdb=" N CYS B 915 " --> pdb=" O THR B 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 915' Processing helix chain 'C' and resid 107 through 114 Processing helix chain 'C' and resid 129 through 142 removed outlier: 3.918A pdb=" N VAL C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 135 " --> pdb=" O LYS C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 166 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.562A pdb=" N LEU C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 207 removed outlier: 3.700A pdb=" N ASP C 207 " --> pdb=" O CYS C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 234 Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.915A pdb=" N ALA C 253 " --> pdb=" O TRP C 249 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE C 254 " --> pdb=" O VAL C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 300 Processing helix chain 'C' and resid 302 through 307 Proline residue: C 307 - end of helix Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.966A pdb=" N SER C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 315 " --> pdb=" O HIS C 311 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 334 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 337 through 345 Processing helix chain 'C' and resid 363 through 374 removed outlier: 3.998A pdb=" N ALA C 367 " --> pdb=" O ALA C 363 " (cutoff:3.500A) 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) removed outlier: 3.847A pdb=" N MET C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 385 removed outlier: 3.813A pdb=" N THR C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 397 through 405 Processing helix chain 'C' and resid 407 through 421 removed outlier: 3.965A pdb=" N ILE C 414 " --> pdb=" O GLU C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 479 through 494 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 496 through 505 removed outlier: 3.632A pdb=" N LEU C 500 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 517 removed outlier: 3.707A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 530 removed outlier: 4.500A pdb=" N LEU C 522 " --> pdb=" O GLY C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 552 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) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.583A pdb=" N LEU C 566 " --> pdb=" O ASN C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 587 Processing helix chain 'C' and resid 598 through 602 removed outlier: 4.003A pdb=" N LYS C 601 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 915 removed outlier: 3.501A pdb=" N CYS C 915 " --> pdb=" O THR C 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 911 through 915' Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 12 through 20 Processing helix chain 'D' and resid 21 through 24 Processing helix chain 'D' and resid 25 through 32 Processing helix chain 'D' and resid 36 through 45 Processing helix chain 'D' and resid 48 through 61 Processing helix chain 'D' and resid 64 through 78 Processing helix chain 'D' and resid 80 through 89 removed outlier: 4.650A pdb=" N ASP D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 114 Processing helix chain 'D' and resid 129 through 142 removed outlier: 3.918A pdb=" N VAL D 133 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 166 Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.563A pdb=" N LEU D 174 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 207 removed outlier: 3.699A pdb=" N ASP D 207 " --> pdb=" O CYS D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 234 removed outlier: 3.500A pdb=" N ALA D 223 " --> pdb=" O ASN D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 254 removed outlier: 3.915A pdb=" N ALA D 253 " --> pdb=" O TRP D 249 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE D 254 " --> pdb=" O VAL D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 300 Processing helix chain 'D' and resid 302 through 307 Proline residue: D 307 - end of helix Processing helix chain 'D' and resid 308 through 318 removed outlier: 3.966A pdb=" N SER D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS D 315 " --> pdb=" O HIS D 311 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 334 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 337 through 345 Processing helix chain 'D' and resid 363 through 374 removed outlier: 3.998A pdb=" N ALA D 367 " --> pdb=" O ALA D 363 " (cutoff:3.500A) 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) removed outlier: 3.846A pdb=" N MET D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 385 removed outlier: 3.813A pdb=" N THR D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 389 Processing helix chain 'D' and resid 397 through 405 Processing helix chain 'D' and resid 407 through 421 removed outlier: 3.965A pdb=" N ILE D 414 " --> pdb=" O GLU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 449 Processing helix chain 'D' and resid 452 through 468 Processing helix chain 'D' and resid 479 through 494 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 496 through 505 removed outlier: 3.631A pdb=" N LEU D 500 " --> pdb=" O MET D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 517 removed outlier: 3.708A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 530 removed outlier: 4.499A pdb=" N LEU D 522 " --> pdb=" O GLY D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 552 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) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.584A pdb=" N LEU D 566 " --> pdb=" O ASN D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 587 Processing helix chain 'D' and resid 598 through 602 removed outlier: 4.002A pdb=" N LYS D 601 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 915 removed outlier: 3.501A pdb=" N CYS D 915 " --> pdb=" O THR D 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 911 through 915' Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 12 through 20 Processing helix chain 'E' and resid 21 through 24 Processing helix chain 'E' and resid 25 through 32 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 64 through 78 Processing helix chain 'E' and resid 80 through 89 removed outlier: 4.650A pdb=" N ASP E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 114 Processing helix chain 'E' and resid 129 through 142 removed outlier: 3.919A pdb=" N VAL E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 166 Processing helix chain 'E' and resid 170 through 178 removed outlier: 3.563A pdb=" N LEU E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 207 removed outlier: 3.699A pdb=" N ASP E 207 " --> pdb=" O CYS E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 234 removed outlier: 3.500A pdb=" N ALA E 223 " --> pdb=" O ASN E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 254 removed outlier: 3.915A pdb=" N ALA E 253 " --> pdb=" O TRP E 249 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE E 254 " --> pdb=" O VAL E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 302 through 307 Proline residue: E 307 - end of helix Processing helix chain 'E' and resid 308 through 318 removed outlier: 3.965A pdb=" N SER E 312 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS E 315 " --> pdb=" O HIS E 311 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 334 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 337 through 345 Processing helix chain 'E' and resid 363 through 374 removed outlier: 3.998A pdb=" N ALA E 367 " --> pdb=" O ALA E 363 " (cutoff:3.500A) 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) removed outlier: 3.847A pdb=" N MET E 374 " --> pdb=" O ILE E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 385 removed outlier: 3.814A pdb=" N THR E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 397 through 405 Processing helix chain 'E' and resid 407 through 421 removed outlier: 3.965A pdb=" N ILE E 414 " --> pdb=" O GLU E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 449 Processing helix chain 'E' and resid 452 through 468 Processing helix chain 'E' and resid 479 through 494 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 496 through 505 removed outlier: 3.631A pdb=" N LEU E 500 " --> pdb=" O MET E 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 517 removed outlier: 3.707A pdb=" N ILE E 510 " --> pdb=" O SER E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 530 removed outlier: 4.500A pdb=" N LEU E 522 " --> pdb=" O GLY E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 552 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) Processing helix chain 'E' and resid 562 through 568 removed outlier: 3.583A pdb=" N LEU E 566 " --> pdb=" O ASN E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 587 Processing helix chain 'E' and resid 598 through 602 removed outlier: 4.003A pdb=" N LYS E 601 " --> pdb=" O ILE E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 911 through 915 removed outlier: 3.501A pdb=" N CYS E 915 " --> pdb=" O THR E 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 911 through 915' Processing helix chain 'F' and resid 107 through 114 Processing helix chain 'F' and resid 129 through 142 removed outlier: 3.919A pdb=" N VAL F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 135 " --> pdb=" O LYS F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 166 Processing helix chain 'F' and resid 170 through 178 removed outlier: 3.563A pdb=" N LEU F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 207 removed outlier: 3.700A pdb=" N ASP F 207 " --> pdb=" O CYS F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 234 Processing helix chain 'F' and resid 247 through 255 removed outlier: 3.915A pdb=" N ALA F 253 " --> pdb=" O TRP F 249 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE F 254 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP F 255 " --> pdb=" O LEU F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 300 Processing helix chain 'F' and resid 302 through 307 Proline residue: F 307 - end of helix Processing helix chain 'F' and resid 308 through 318 removed outlier: 3.966A pdb=" N SER F 312 " --> pdb=" O GLU F 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 314 " --> pdb=" O ALA F 310 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS F 315 " --> pdb=" O HIS F 311 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU F 316 " --> pdb=" O SER F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 334 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 337 through 345 Processing helix chain 'F' and resid 363 through 374 removed outlier: 3.998A pdb=" N ALA F 367 " --> pdb=" O ALA F 363 " (cutoff:3.500A) 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) removed outlier: 3.846A pdb=" N MET F 374 " --> pdb=" O ILE F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 385 removed outlier: 3.814A pdb=" N THR F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 389 Processing helix chain 'F' and resid 397 through 405 Processing helix chain 'F' and resid 407 through 421 removed outlier: 3.965A pdb=" N ILE F 414 " --> pdb=" O GLU F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 449 Processing helix chain 'F' and resid 452 through 468 Processing helix chain 'F' and resid 479 through 494 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 496 through 505 removed outlier: 3.630A pdb=" N LEU F 500 " --> pdb=" O MET F 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 517 removed outlier: 3.707A pdb=" N ILE F 510 " --> pdb=" O SER F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 530 removed outlier: 4.499A pdb=" N LEU F 522 " --> pdb=" O GLY F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 552 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) Processing helix chain 'F' and resid 562 through 568 removed outlier: 3.583A pdb=" N LEU F 566 " --> pdb=" O ASN F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 587 Processing helix chain 'F' and resid 598 through 602 removed outlier: 4.003A pdb=" N LYS F 601 " --> pdb=" O ILE F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 911 through 915 removed outlier: 3.501A pdb=" N CYS F 915 " --> pdb=" O THR F 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 911 through 915' Processing helix chain 'G' and resid 2 through 12 Processing helix chain 'G' and resid 12 through 20 Processing helix chain 'G' and resid 21 through 24 Processing helix chain 'G' and resid 25 through 32 Processing helix chain 'G' and resid 36 through 45 Processing helix chain 'G' and resid 48 through 61 Processing helix chain 'G' and resid 64 through 78 Processing helix chain 'G' and resid 80 through 89 removed outlier: 4.652A pdb=" N ASP G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 114 Processing helix chain 'G' and resid 129 through 142 removed outlier: 3.918A pdb=" N VAL G 133 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 166 Processing helix chain 'G' and resid 170 through 178 removed outlier: 3.563A pdb=" N LEU G 174 " --> pdb=" O ASP G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 207 removed outlier: 3.699A pdb=" N ASP G 207 " --> pdb=" O CYS G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 234 Processing helix chain 'G' and resid 247 through 254 removed outlier: 3.914A pdb=" N ALA G 253 " --> pdb=" O TRP G 249 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE G 254 " --> pdb=" O VAL G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 300 Processing helix chain 'G' and resid 302 through 307 Proline residue: G 307 - end of helix Processing helix chain 'G' and resid 308 through 318 removed outlier: 3.965A pdb=" N SER G 312 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 314 " --> pdb=" O ALA G 310 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS G 315 " --> pdb=" O HIS G 311 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU G 316 " --> pdb=" O SER G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 334 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 337 through 345 Processing helix chain 'G' and resid 363 through 374 removed outlier: 3.999A pdb=" N ALA G 367 " --> pdb=" O ALA G 363 " (cutoff:3.500A) 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) removed outlier: 3.847A pdb=" N MET G 374 " --> pdb=" O ILE G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 385 removed outlier: 3.813A pdb=" N THR G 384 " --> pdb=" O LYS G 380 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP G 385 " --> pdb=" O ASP G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 389 Processing helix chain 'G' and resid 397 through 405 Processing helix chain 'G' and resid 407 through 421 removed outlier: 3.965A pdb=" N ILE G 414 " --> pdb=" O GLU G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 449 Processing helix chain 'G' and resid 452 through 468 Processing helix chain 'G' and resid 479 through 494 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 496 through 505 removed outlier: 3.632A pdb=" N LEU G 500 " --> pdb=" O MET G 496 " (cutoff:3.500A) Processing helix chain 'G' and resid 506 through 517 removed outlier: 3.707A pdb=" N ILE G 510 " --> pdb=" O SER G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 518 through 530 removed outlier: 4.500A pdb=" N LEU G 522 " --> pdb=" O GLY G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 534 through 552 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) Processing helix chain 'G' and resid 562 through 568 removed outlier: 3.583A pdb=" N LEU G 566 " --> pdb=" O ASN G 562 " (cutoff:3.500A) Processing helix chain 'G' and resid 574 through 587 Processing helix chain 'G' and resid 598 through 602 removed outlier: 4.003A pdb=" N LYS G 601 " --> pdb=" O ILE G 598 " (cutoff:3.500A) Processing helix chain 'G' and resid 911 through 915 removed outlier: 3.501A pdb=" N CYS G 915 " --> pdb=" O THR G 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 911 through 915' Processing helix chain 'H' and resid 2 through 14 Processing helix chain 'H' and resid 49 through 54 Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 70 through 75 removed outlier: 3.682A pdb=" N ILE H 75 " --> pdb=" O PRO H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 102 removed outlier: 3.673A pdb=" N ARG H 91 " --> pdb=" O LYS H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 14 Processing helix chain 'I' and resid 49 through 54 Processing helix chain 'I' and resid 62 through 68 Processing helix chain 'I' and resid 70 through 75 removed outlier: 3.682A pdb=" N ILE I 75 " --> pdb=" O PRO I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 102 removed outlier: 3.673A pdb=" N ARG I 91 " --> pdb=" O LYS I 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 14 Processing helix chain 'J' and resid 49 through 54 Processing helix chain 'J' and resid 62 through 68 Processing helix chain 'J' and resid 70 through 75 removed outlier: 3.682A pdb=" N ILE J 75 " --> pdb=" O PRO J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 102 removed outlier: 3.673A pdb=" N ARG J 91 " --> pdb=" O LYS J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 14 Processing helix chain 'K' and resid 49 through 54 Processing helix chain 'K' and resid 62 through 68 Processing helix chain 'K' and resid 70 through 75 removed outlier: 3.682A pdb=" N ILE K 75 " --> pdb=" O PRO K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 102 removed outlier: 3.673A pdb=" N ARG K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 14 Processing helix chain 'L' and resid 49 through 54 Processing helix chain 'L' and resid 62 through 68 Processing helix chain 'L' and resid 70 through 75 removed outlier: 3.682A pdb=" N ILE L 75 " --> pdb=" O PRO L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 102 removed outlier: 3.673A pdb=" N ARG L 91 " --> pdb=" O LYS L 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 14 Processing helix chain 'M' and resid 49 through 54 Processing helix chain 'M' and resid 62 through 68 Processing helix chain 'M' and resid 70 through 75 removed outlier: 3.683A pdb=" N ILE M 75 " --> pdb=" O PRO M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 102 removed outlier: 3.673A pdb=" N ARG M 91 " --> pdb=" O LYS M 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 14 Processing helix chain 'N' and resid 49 through 54 Processing helix chain 'N' and resid 62 through 68 Processing helix chain 'N' and resid 70 through 75 removed outlier: 3.682A pdb=" N ILE N 75 " --> pdb=" O PRO N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 102 removed outlier: 3.674A pdb=" N ARG N 91 " --> pdb=" O LYS N 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 12 Processing helix chain 'O' and resid 12 through 20 Processing helix chain 'O' and resid 25 through 32 Processing helix chain 'O' and resid 36 through 45 Processing helix chain 'O' and resid 50 through 63 removed outlier: 3.720A pdb=" N GLU O 63 " --> pdb=" O ILE O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 80 Processing helix chain 'O' and resid 82 through 94 removed outlier: 3.757A pdb=" N ASN O 92 " --> pdb=" O PHE O 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 12 Processing helix chain 'P' and resid 12 through 20 Processing helix chain 'P' and resid 25 through 32 Processing helix chain 'P' and resid 36 through 45 Processing helix chain 'P' and resid 50 through 63 removed outlier: 3.721A pdb=" N GLU P 63 " --> pdb=" O ILE P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 80 Processing helix chain 'P' and resid 82 through 94 removed outlier: 3.753A pdb=" N ASN P 92 " --> pdb=" O PHE P 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 12 Processing helix chain 'Q' and resid 12 through 20 Processing helix chain 'Q' and resid 25 through 32 Processing helix chain 'Q' and resid 36 through 45 Processing helix chain 'Q' and resid 50 through 63 removed outlier: 3.722A pdb=" N GLU Q 63 " --> pdb=" O ILE Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 80 Processing helix chain 'Q' and resid 82 through 94 removed outlier: 3.753A pdb=" N ASN Q 92 " --> pdb=" O PHE Q 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 12 Processing helix chain 'R' and resid 12 through 20 Processing helix chain 'R' and resid 25 through 32 Processing helix chain 'R' and resid 36 through 45 Processing helix chain 'R' and resid 50 through 63 removed outlier: 3.719A pdb=" N GLU R 63 " --> pdb=" O ILE R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 80 Processing helix chain 'R' and resid 82 through 94 removed outlier: 3.757A pdb=" N ASN R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 153 removed outlier: 6.547A pdb=" N GLY A 148 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU A 262 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 150 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR A 264 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 152 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 261 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 263 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 425 through 428 Processing sheet with id=AA3, first strand: chain 'A' and resid 609 through 611 Processing sheet with id=AA4, first strand: chain 'A' and resid 618 through 620 removed outlier: 4.844A pdb=" N GLY A 634 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) 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=AA5, first strand: chain 'A' and resid 660 through 663 removed outlier: 7.316A pdb=" N CYS A 675 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N CYS A 663 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ALA A 673 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS A 693 " --> pdb=" O ILE A 683 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN A 685 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU A 691 " --> pdb=" O ASN A 685 " (cutoff:3.500A) Processing sheet with id=AA6, 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=AA7, 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=AA8, first strand: chain 'A' and resid 801 through 806 removed outlier: 4.872A pdb=" N CYS A 803 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA A 816 " --> pdb=" O CYS A 803 " (cutoff:3.500A) Processing sheet with id=AA9, 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=AB1, first strand: chain 'A' and resid 922 through 931 removed outlier: 6.565A pdb=" N GLU A 925 " --> pdb=" O VAL A 940 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 940 " --> pdb=" O GLU A 925 " (cutoff:3.500A) Processing sheet with id=AB2, 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=AB3, first strand: chain 'A' and resid 1006 through 1010 removed outlier: 4.319A pdb=" N HIS A1008 " --> pdb=" O SER A1021 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER A1022 " --> pdb=" O GLU A1026 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU A1026 " --> pdb=" O SER A1022 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1049 through 1052 Processing sheet with id=AB5, first strand: chain 'A' and resid 1089 through 1093 removed outlier: 5.304A pdb=" N SER A1090 " --> pdb=" O SER A1104 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER A1104 " --> pdb=" O SER A1090 " (cutoff:3.500A) 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=AB6, first strand: chain 'A' and resid 1132 through 1135 Processing sheet with id=AB7, first strand: chain 'A' and resid 1184 through 1185 Processing sheet with id=AB8, first strand: chain 'A' and resid 1224 through 1225 removed outlier: 3.720A pdb=" N HIS A1224 " --> pdb=" O VAL A1233 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A1233 " --> pdb=" O HIS A1224 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 148 through 153 removed outlier: 6.547A pdb=" N GLY B 148 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU B 262 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B 150 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR B 264 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE B 152 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 261 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B 263 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 425 through 428 Processing sheet with id=AC2, first strand: chain 'B' and resid 609 through 611 Processing sheet with id=AC3, first strand: chain 'B' and resid 618 through 620 removed outlier: 4.844A pdb=" N GLY B 634 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR B 638 " --> pdb=" O GLY B 634 " (cutoff:3.500A) 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=AC4, first strand: chain 'B' and resid 660 through 663 removed outlier: 7.316A pdb=" N CYS B 675 " --> pdb=" O LEU B 661 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N CYS B 663 " --> pdb=" O ALA B 673 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ALA B 673 " --> pdb=" O CYS B 663 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N HIS B 693 " --> pdb=" O ILE B 683 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN B 685 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU B 691 " --> pdb=" O ASN B 685 " (cutoff:3.500A) Processing sheet with id=AC5, 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=AC6, 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=AC7, first strand: chain 'B' and resid 801 through 806 removed outlier: 4.872A pdb=" N CYS B 803 " --> pdb=" O ALA B 816 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA B 816 " --> pdb=" O CYS B 803 " (cutoff:3.500A) Processing sheet with id=AC8, 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=AC9, first strand: chain 'B' and resid 922 through 931 removed outlier: 6.566A pdb=" N GLU B 925 " --> pdb=" O VAL B 940 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL B 940 " --> pdb=" O GLU B 925 " (cutoff:3.500A) Processing sheet with id=AD1, 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=AD2, first strand: chain 'B' and resid 1006 through 1010 removed outlier: 4.319A pdb=" N HIS B1008 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER B1022 " --> pdb=" O GLU B1026 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU B1026 " --> pdb=" O SER B1022 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1049 through 1052 Processing sheet with id=AD4, first strand: chain 'B' and resid 1089 through 1093 removed outlier: 5.304A pdb=" N SER B1090 " --> pdb=" O SER B1104 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER B1104 " --> pdb=" O SER B1090 " (cutoff:3.500A) 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=AD5, first strand: chain 'B' and resid 1132 through 1135 Processing sheet with id=AD6, first strand: chain 'B' and resid 1184 through 1185 Processing sheet with id=AD7, first strand: chain 'B' and resid 1224 through 1225 removed outlier: 3.720A pdb=" N HIS B1224 " --> pdb=" O VAL B1233 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B1233 " --> pdb=" O HIS B1224 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 148 through 153 removed outlier: 6.547A pdb=" N GLY C 148 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU C 262 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 150 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR C 264 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE C 152 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 261 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR C 263 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 425 through 428 Processing sheet with id=AE1, first strand: chain 'C' and resid 609 through 611 Processing sheet with id=AE2, first strand: chain 'C' and resid 618 through 620 removed outlier: 4.844A pdb=" N GLY C 634 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR C 638 " --> pdb=" O GLY C 634 " (cutoff:3.500A) 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=AE3, first strand: chain 'C' and resid 660 through 663 removed outlier: 7.316A pdb=" N CYS C 675 " --> pdb=" O LEU C 661 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N CYS C 663 " --> pdb=" O ALA C 673 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ALA C 673 " --> pdb=" O CYS C 663 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS C 693 " --> pdb=" O ILE C 683 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN C 685 " --> pdb=" O LEU C 691 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU C 691 " --> pdb=" O ASN C 685 " (cutoff:3.500A) Processing sheet with id=AE4, 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=AE5, 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=AE6, first strand: chain 'C' and resid 801 through 806 removed outlier: 4.872A pdb=" N CYS C 803 " --> pdb=" O ALA C 816 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA C 816 " --> pdb=" O CYS C 803 " (cutoff:3.500A) Processing sheet with id=AE7, 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=AE8, first strand: chain 'C' and resid 922 through 931 removed outlier: 6.566A pdb=" N GLU C 925 " --> pdb=" O VAL C 940 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL C 940 " --> pdb=" O GLU C 925 " (cutoff:3.500A) Processing sheet with id=AE9, 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=AF1, first strand: chain 'C' and resid 1006 through 1010 removed outlier: 4.318A pdb=" N HIS C1008 " --> pdb=" O SER C1021 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER C1022 " --> pdb=" O GLU C1026 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU C1026 " --> pdb=" O SER C1022 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1049 through 1052 Processing sheet with id=AF3, first strand: chain 'C' and resid 1089 through 1093 removed outlier: 5.304A pdb=" N SER C1090 " --> pdb=" O SER C1104 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER C1104 " --> pdb=" O SER C1090 " (cutoff:3.500A) 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=AF4, first strand: chain 'C' and resid 1132 through 1135 Processing sheet with id=AF5, first strand: chain 'C' and resid 1184 through 1185 Processing sheet with id=AF6, first strand: chain 'C' and resid 1224 through 1225 removed outlier: 3.720A pdb=" N HIS C1224 " --> pdb=" O VAL C1233 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C1233 " --> pdb=" O HIS C1224 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 148 through 153 removed outlier: 6.547A pdb=" N GLY D 148 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU D 262 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL D 150 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR D 264 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 152 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 261 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 263 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 425 through 428 Processing sheet with id=AF9, first strand: chain 'D' and resid 609 through 611 Processing sheet with id=AG1, first strand: chain 'D' and resid 618 through 620 removed outlier: 4.844A pdb=" N GLY D 634 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR D 638 " --> pdb=" O GLY D 634 " (cutoff:3.500A) 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=AG2, first strand: chain 'D' and resid 660 through 663 removed outlier: 7.316A pdb=" N CYS D 675 " --> pdb=" O LEU D 661 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N CYS D 663 " --> pdb=" O ALA D 673 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ALA D 673 " --> pdb=" O CYS D 663 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS D 693 " --> pdb=" O ILE D 683 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN D 685 " --> pdb=" O LEU D 691 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU D 691 " --> pdb=" O ASN D 685 " (cutoff:3.500A) Processing sheet with id=AG3, 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=AG4, 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=AG5, first strand: chain 'D' and resid 801 through 806 removed outlier: 4.873A pdb=" N CYS D 803 " --> pdb=" O ALA D 816 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA D 816 " --> pdb=" O CYS D 803 " (cutoff:3.500A) Processing sheet with id=AG6, 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=AG7, first strand: chain 'D' and resid 922 through 931 removed outlier: 6.566A pdb=" N GLU D 925 " --> pdb=" O VAL D 940 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL D 940 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing sheet with id=AG8, 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=AG9, first strand: chain 'D' and resid 1006 through 1010 removed outlier: 4.319A pdb=" N HIS D1008 " --> pdb=" O SER D1021 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER D1022 " --> pdb=" O GLU D1026 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU D1026 " --> pdb=" O SER D1022 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 1049 through 1052 Processing sheet with id=AH2, first strand: chain 'D' and resid 1089 through 1093 removed outlier: 5.304A pdb=" N SER D1090 " --> pdb=" O SER D1104 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER D1104 " --> pdb=" O SER D1090 " (cutoff:3.500A) 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=AH3, first strand: chain 'D' and resid 1132 through 1135 Processing sheet with id=AH4, first strand: chain 'D' and resid 1184 through 1185 Processing sheet with id=AH5, first strand: chain 'D' and resid 1224 through 1225 removed outlier: 3.720A pdb=" N HIS D1224 " --> pdb=" O VAL D1233 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D1233 " --> pdb=" O HIS D1224 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 148 through 153 removed outlier: 6.547A pdb=" N GLY E 148 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU E 262 " --> pdb=" O GLY E 148 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL E 150 " --> pdb=" O LEU E 262 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR E 264 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE E 152 " --> pdb=" O THR E 264 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 261 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR E 263 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 425 through 428 Processing sheet with id=AH8, first strand: chain 'E' and resid 609 through 611 Processing sheet with id=AH9, first strand: chain 'E' and resid 618 through 620 removed outlier: 4.844A pdb=" N GLY E 634 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR E 638 " --> pdb=" O GLY E 634 " (cutoff:3.500A) 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=AI1, first strand: chain 'E' and resid 660 through 663 removed outlier: 7.315A pdb=" N CYS E 675 " --> pdb=" O LEU E 661 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N CYS E 663 " --> pdb=" O ALA E 673 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ALA E 673 " --> pdb=" O CYS E 663 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N HIS E 693 " --> pdb=" O ILE E 683 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN E 685 " --> pdb=" O LEU E 691 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU E 691 " --> pdb=" O ASN E 685 " (cutoff:3.500A) Processing sheet with id=AI2, 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=AI3, 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=AI4, first strand: chain 'E' and resid 801 through 806 removed outlier: 4.873A pdb=" N CYS E 803 " --> pdb=" O ALA E 816 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA E 816 " --> pdb=" O CYS E 803 " (cutoff:3.500A) Processing sheet with id=AI5, 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=AI6, first strand: chain 'E' and resid 922 through 931 removed outlier: 6.565A pdb=" N GLU E 925 " --> pdb=" O VAL E 940 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL E 940 " --> pdb=" O GLU E 925 " (cutoff:3.500A) Processing sheet with id=AI7, 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=AI8, first strand: chain 'E' and resid 1006 through 1010 removed outlier: 4.319A pdb=" N HIS E1008 " --> pdb=" O SER E1021 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER E1022 " --> pdb=" O GLU E1026 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU E1026 " --> pdb=" O SER E1022 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 1049 through 1052 Processing sheet with id=AJ1, first strand: chain 'E' and resid 1089 through 1093 removed outlier: 5.304A pdb=" N SER E1090 " --> pdb=" O SER E1104 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER E1104 " --> pdb=" O SER E1090 " (cutoff:3.500A) 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=AJ2, first strand: chain 'E' and resid 1132 through 1135 Processing sheet with id=AJ3, first strand: chain 'E' and resid 1184 through 1185 Processing sheet with id=AJ4, first strand: chain 'E' and resid 1224 through 1225 removed outlier: 3.719A pdb=" N HIS E1224 " --> pdb=" O VAL E1233 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E1233 " --> pdb=" O HIS E1224 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'F' and resid 148 through 153 removed outlier: 6.546A pdb=" N GLY F 148 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU F 262 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL F 150 " --> pdb=" O LEU F 262 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR F 264 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE F 152 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 261 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR F 263 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 425 through 428 Processing sheet with id=AJ7, first strand: chain 'F' and resid 609 through 611 Processing sheet with id=AJ8, first strand: chain 'F' and resid 618 through 620 removed outlier: 4.845A pdb=" N GLY F 634 " --> pdb=" O THR F 638 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR F 638 " --> pdb=" O GLY F 634 " (cutoff:3.500A) 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=AJ9, first strand: chain 'F' and resid 660 through 663 removed outlier: 7.316A pdb=" N CYS F 675 " --> pdb=" O LEU F 661 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N CYS F 663 " --> pdb=" O ALA F 673 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ALA F 673 " --> pdb=" O CYS F 663 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS F 693 " --> pdb=" O ILE F 683 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN F 685 " --> pdb=" O LEU F 691 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU F 691 " --> pdb=" O ASN F 685 " (cutoff:3.500A) Processing sheet with id=AK1, 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=AK2, 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=AK3, first strand: chain 'F' and resid 801 through 806 removed outlier: 4.873A pdb=" N CYS F 803 " --> pdb=" O ALA F 816 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA F 816 " --> pdb=" O CYS F 803 " (cutoff:3.500A) Processing sheet with id=AK4, 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=AK5, first strand: chain 'F' and resid 922 through 931 removed outlier: 6.566A pdb=" N GLU F 925 " --> pdb=" O VAL F 940 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL F 940 " --> pdb=" O GLU F 925 " (cutoff:3.500A) Processing sheet with id=AK6, 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=AK7, first strand: chain 'F' and resid 1006 through 1010 removed outlier: 4.318A pdb=" N HIS F1008 " --> pdb=" O SER F1021 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER F1022 " --> pdb=" O GLU F1026 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU F1026 " --> pdb=" O SER F1022 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'F' and resid 1049 through 1052 Processing sheet with id=AK9, first strand: chain 'F' and resid 1089 through 1093 removed outlier: 5.305A pdb=" N SER F1090 " --> pdb=" O SER F1104 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER F1104 " --> pdb=" O SER F1090 " (cutoff:3.500A) 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=AL1, first strand: chain 'F' and resid 1132 through 1135 Processing sheet with id=AL2, first strand: chain 'F' and resid 1184 through 1185 Processing sheet with id=AL3, first strand: chain 'F' and resid 1224 through 1225 removed outlier: 3.720A pdb=" N HIS F1224 " --> pdb=" O VAL F1233 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F1233 " --> pdb=" O HIS F1224 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'G' and resid 148 through 153 removed outlier: 6.548A pdb=" N GLY G 148 " --> pdb=" O ILE G 260 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU G 262 " --> pdb=" O GLY G 148 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL G 150 " --> pdb=" O LEU G 262 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR G 264 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE G 152 " --> pdb=" O THR G 264 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 261 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR G 263 " --> pdb=" O LEU G 242 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'G' and resid 425 through 428 Processing sheet with id=AL6, first strand: chain 'G' and resid 609 through 611 Processing sheet with id=AL7, first strand: chain 'G' and resid 618 through 620 removed outlier: 4.844A pdb=" N GLY G 634 " --> pdb=" O THR G 638 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR G 638 " --> pdb=" O GLY G 634 " (cutoff:3.500A) 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=AL8, first strand: chain 'G' and resid 660 through 663 removed outlier: 7.316A pdb=" N CYS G 675 " --> pdb=" O LEU G 661 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N CYS G 663 " --> pdb=" O ALA G 673 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ALA G 673 " --> pdb=" O CYS G 663 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS G 693 " --> pdb=" O ILE G 683 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN G 685 " --> pdb=" O LEU G 691 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU G 691 " --> pdb=" O ASN G 685 " (cutoff:3.500A) Processing sheet with id=AL9, 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=AM1, 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=AM2, first strand: chain 'G' and resid 801 through 806 removed outlier: 4.872A pdb=" N CYS G 803 " --> pdb=" O ALA G 816 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA G 816 " --> pdb=" O CYS G 803 " (cutoff:3.500A) Processing sheet with id=AM3, 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=AM4, first strand: chain 'G' and resid 922 through 931 removed outlier: 6.566A pdb=" N GLU G 925 " --> pdb=" O VAL G 940 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL G 940 " --> pdb=" O GLU G 925 " (cutoff:3.500A) Processing sheet with id=AM5, 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=AM6, first strand: chain 'G' and resid 1006 through 1010 removed outlier: 4.318A pdb=" N HIS G1008 " --> pdb=" O SER G1021 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER G1022 " --> pdb=" O GLU G1026 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU G1026 " --> pdb=" O SER G1022 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'G' and resid 1049 through 1052 Processing sheet with id=AM8, first strand: chain 'G' and resid 1089 through 1093 removed outlier: 5.303A pdb=" N SER G1090 " --> pdb=" O SER G1104 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER G1104 " --> pdb=" O SER G1090 " (cutoff:3.500A) 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=AM9, first strand: chain 'G' and resid 1132 through 1135 Processing sheet with id=AN1, first strand: chain 'G' and resid 1184 through 1185 Processing sheet with id=AN2, first strand: chain 'G' and resid 1224 through 1225 removed outlier: 3.720A pdb=" N HIS G1224 " --> pdb=" O VAL G1233 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL G1233 " --> pdb=" O HIS G1224 " (cutoff:3.500A) 2856 hydrogen bonds defined for protein. 7968 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: 42.69 Time building geometry restraints manager: 16.61 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: 0.00 - 4.56: 104230 4.56 - 9.13: 740 9.13 - 13.69: 70 13.69 - 18.25: 14 18.25 - 22.82: 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: 22391 2.83 - 3.52: 102920 3.52 - 4.21: 170497 4.21 - 4.90: 291756 Nonbonded interactions: 587598 Sorted by model distance: nonbonded pdb=" OE2 GLU D 316 " pdb=" NE2 GLN D 346 " model vdw 1.447 3.120 nonbonded pdb=" OE2 GLU B 316 " pdb=" NE2 GLN B 346 " model vdw 1.447 3.120 nonbonded pdb=" OE2 GLU F 316 " pdb=" NE2 GLN F 346 " model vdw 1.447 3.120 nonbonded pdb=" OE2 GLU G 316 " pdb=" NE2 GLN G 346 " model vdw 1.447 3.120 nonbonded pdb=" OE2 GLU A 316 " pdb=" NE2 GLN A 346 " model vdw 1.447 3.120 ... (remaining 587593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 2.210 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: 0.050 Extract box with map and model: 2.270 Check model and map are aligned: 0.430 Set scattering table: 0.540 Process input model: 146.350 Find NCS groups from input model: 4.000 Set up NCS constraints: 0.440 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:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.620 ------------------------------------------------------------------------------- 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= 0.590 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 : 6.629 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: 0.7517 time to fit residues: 1196.7155 Evaluate side-chains 408 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 402 time to evaluate : 6.595 ------------------------------------------------------------------------------- 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: 7.9990 chunk 394 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 479 optimal weight: 5.9990 chunk 379 optimal weight: 0.9990 chunk 734 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 446 optimal weight: 30.0000 chunk 546 optimal weight: 9.9990 chunk 850 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 416 GLN A 471 HIS ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN A 602 ASN A 614 HIS A 620 HIS A 703 ASN A 712 HIS A 782 ASN A 819 ASN A 881 HIS ** A1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 HIS A1126 HIS B 11 GLN B 12 HIS B 51 GLN B 214 GLN B 416 GLN B 471 HIS ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN B 602 ASN B 620 HIS B 703 ASN B 712 HIS B 782 ASN B 819 ASN B 881 HIS ** B1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 HIS C 201 ASN C 214 GLN C 235 HIS C 416 GLN C 471 HIS ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C 620 HIS C 703 ASN C 712 HIS C 782 ASN C 819 ASN C 852 ASN C 881 HIS ** C1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1043 HIS C1126 HIS D 11 GLN D 51 GLN D 214 GLN D 416 GLN D 471 HIS ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 ASN D 602 ASN D 620 HIS D 703 ASN D 712 HIS D 782 ASN D 819 ASN D 881 HIS D1126 HIS E 11 GLN E 12 HIS E 45 ASN E 51 GLN E 214 GLN E 235 HIS E 416 GLN E 471 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN E 602 ASN E 620 HIS E 703 ASN E 712 HIS E 782 ASN E 819 ASN E 881 HIS E1126 HIS F 214 GLN F 416 GLN F 471 HIS ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN F 620 HIS F 703 ASN F 712 HIS F 782 ASN F 819 ASN F 881 HIS ** F 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1126 HIS G 11 GLN G 12 HIS G 45 ASN G 51 GLN G 77 HIS G 214 GLN G 416 GLN G 471 HIS ** G 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 ASN G 620 HIS G 703 ASN G 712 HIS G 782 ASN G 819 ASN G 881 HIS ** G1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1043 HIS G1126 HIS ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 44 GLN P 38 HIS P 44 GLN Q 44 GLN ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN R 92 ASN Total number of N/Q/H flips: 110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5667 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 77677 Z= 0.297 Angle : 0.678 9.843 105068 Z= 0.354 Chirality : 0.044 0.200 11597 Planarity : 0.004 0.050 13339 Dihedral : 8.101 124.025 10336 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.67 % Favored : 95.18 % Rotamer: Outliers : 0.04 % Allowed : 1.64 % Favored : 98.32 % 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: -1.48 (0.08), residues: 9403 helix: -0.49 (0.09), residues: 2874 sheet: -0.51 (0.11), residues: 1988 loop : -1.47 (0.08), residues: 4541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 184 HIS 0.009 0.001 HIS F 235 PHE 0.015 0.002 PHE F 526 TYR 0.017 0.002 TYR E 594 ARG 0.011 0.001 ARG N 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 541 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 538 time to evaluate : 6.752 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: 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: 0.8424 (tpt) cc_final: 0.7743 (ttp) REVERT: A 687 MET cc_start: 0.7450 (mmt) cc_final: 0.7146 (mmt) REVERT: A 739 MET cc_start: 0.5025 (mpp) cc_final: 0.4718 (mmt) REVERT: A 814 MET cc_start: 0.2230 (mpp) cc_final: 0.1295 (mmm) REVERT: B 155 MET cc_start: 0.8712 (tpt) cc_final: 0.8395 (ttp) REVERT: B 231 MET cc_start: 0.8305 (mmm) cc_final: 0.8087 (mmm) REVERT: B 687 MET cc_start: 0.7901 (mmt) cc_final: 0.7554 (mmm) REVERT: C 374 MET cc_start: 0.8273 (mmp) cc_final: 0.7989 (mmt) REVERT: C 522 LEU cc_start: 0.8526 (tp) cc_final: 0.8315 (tp) REVERT: D 29 MET cc_start: 0.1215 (mtp) cc_final: 0.0960 (mtt) REVERT: D 921 MET cc_start: 0.8391 (mpp) cc_final: 0.8053 (mpp) REVERT: E 155 MET cc_start: 0.8596 (tpt) cc_final: 0.8204 (ttp) REVERT: E 406 MET cc_start: 0.8266 (ptp) cc_final: 0.7592 (ptm) REVERT: E 814 MET cc_start: 0.2081 (mpp) cc_final: 0.0717 (mmm) REVERT: F 155 MET cc_start: 0.8632 (tpt) cc_final: 0.8172 (ttm) REVERT: F 374 MET cc_start: 0.8370 (mmp) cc_final: 0.8061 (mmt) REVERT: F 688 THR cc_start: 0.6819 (m) cc_final: 0.6172 (m) REVERT: F 814 MET cc_start: 0.2355 (mpp) cc_final: 0.1138 (mmm) REVERT: G 55 MET cc_start: 0.3275 (ttt) cc_final: 0.3053 (ttt) REVERT: G 155 MET cc_start: 0.8460 (tpt) cc_final: 0.7825 (ttm) REVERT: G 739 MET cc_start: 0.5593 (mpp) cc_final: 0.5151 (mmt) REVERT: G 814 MET cc_start: 0.3242 (mpp) cc_final: 0.1426 (mmm) REVERT: I 80 MET cc_start: 0.6140 (ttt) cc_final: 0.5681 (ttt) REVERT: L 80 MET cc_start: 0.5258 (ttt) cc_final: 0.4807 (ttt) outliers start: 3 outliers final: 1 residues processed: 541 average time/residue: 0.7170 time to fit residues: 679.9652 Evaluate side-chains 353 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 352 time to evaluate : 6.624 ------------------------------------------------------------------------------- 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: 2.9990 chunk 264 optimal weight: 3.9990 chunk 708 optimal weight: 10.0000 chunk 579 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 chunk 852 optimal weight: 10.0000 chunk 920 optimal weight: 8.9990 chunk 759 optimal weight: 0.9980 chunk 845 optimal weight: 20.0000 chunk 290 optimal weight: 9.9990 chunk 683 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN ** A1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 HIS ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN ** B1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1043 HIS ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 HIS C 620 HIS ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 931 GLN ** C1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS D 171 HIS D 614 HIS ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 931 GLN D1043 HIS E 77 HIS E 88 HIS E 614 HIS E 881 HIS E 931 GLN E1043 HIS E1176 HIS F 171 HIS F 235 HIS F 562 ASN F 614 HIS F 881 HIS F 931 GLN F1043 HIS G 88 HIS G 235 HIS ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 562 ASN G 614 HIS G 844 GLN G 931 GLN ** G1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1224 HIS H 33 HIS ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 ASN J 33 HIS J 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 ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 77677 Z= 0.433 Angle : 0.759 12.717 105068 Z= 0.389 Chirality : 0.046 0.230 11597 Planarity : 0.004 0.073 13339 Dihedral : 8.466 165.785 10336 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.26 % Favored : 94.59 % Rotamer: Outliers : 0.08 % Allowed : 2.71 % Favored : 97.21 % 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: -1.29 (0.08), residues: 9403 helix: -0.15 (0.09), residues: 2919 sheet: -0.57 (0.11), residues: 1902 loop : -1.41 (0.09), residues: 4582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 184 HIS 0.011 0.002 HIS B 183 PHE 0.032 0.002 PHE A 334 TYR 0.028 0.002 TYR F 109 ARG 0.007 0.001 ARG O 11 *********************** 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 447 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 440 time to evaluate : 6.657 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 687 MET cc_start: 0.7594 (mmt) cc_final: 0.7326 (mmt) REVERT: A 739 MET cc_start: 0.4667 (mpp) cc_final: 0.4401 (mmm) REVERT: A 814 MET cc_start: 0.1865 (mpp) cc_final: 0.1123 (mmm) REVERT: B 687 MET cc_start: 0.8072 (mmt) cc_final: 0.7864 (mmt) REVERT: B 814 MET cc_start: 0.3485 (mpp) cc_final: 0.1813 (mmm) REVERT: C 797 MET cc_start: -0.0511 (tmm) cc_final: -0.0755 (ttp) REVERT: C 1191 MET cc_start: 0.7129 (tmm) cc_final: 0.6457 (tmm) REVERT: D 274 MET cc_start: 0.8173 (pmm) cc_final: 0.7924 (pmm) REVERT: D 921 MET cc_start: 0.8515 (mpp) cc_final: 0.8184 (mpp) REVERT: D 1191 MET cc_start: 0.7135 (tmm) cc_final: 0.6757 (tmm) REVERT: E 59 MET cc_start: 0.1694 (ttp) cc_final: 0.1185 (tpp) REVERT: E 406 MET cc_start: 0.8322 (ptp) cc_final: 0.7979 (ptm) REVERT: E 522 LEU cc_start: 0.8634 (tp) cc_final: 0.8431 (tp) REVERT: E 814 MET cc_start: 0.1578 (mpp) cc_final: 0.0512 (mmm) REVERT: F 406 MET cc_start: 0.7946 (ptp) cc_final: 0.7725 (ptp) REVERT: F 814 MET cc_start: 0.2395 (mpp) cc_final: 0.1247 (mmm) REVERT: G 243 ASP cc_start: 0.8727 (t0) cc_final: 0.8164 (t0) REVERT: G 374 MET cc_start: 0.8374 (mmp) cc_final: 0.8106 (mmt) REVERT: G 739 MET cc_start: 0.5314 (mpp) cc_final: 0.4947 (mmt) REVERT: G 797 MET cc_start: 0.0768 (tmm) cc_final: 0.0216 (ttp) REVERT: I 80 MET cc_start: 0.6633 (ttt) cc_final: 0.6109 (ttt) REVERT: L 80 MET cc_start: 0.5939 (ttt) cc_final: 0.5267 (ttt) REVERT: M 80 MET cc_start: 0.6449 (ttt) cc_final: 0.5632 (ttt) REVERT: P 39 MET cc_start: 0.4074 (mtt) cc_final: 0.3847 (mtt) outliers start: 7 outliers final: 6 residues processed: 447 average time/residue: 0.7152 time to fit residues: 564.5706 Evaluate side-chains 329 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 323 time to evaluate : 6.647 ------------------------------------------------------------------------------- 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: 20.0000 chunk 640 optimal weight: 0.7980 chunk 442 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 406 optimal weight: 4.9990 chunk 572 optimal weight: 40.0000 chunk 855 optimal weight: 20.0000 chunk 905 optimal weight: 8.9990 chunk 446 optimal weight: 0.0970 chunk 810 optimal weight: 20.0000 chunk 244 optimal weight: 0.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 171 HIS A 620 HIS A 881 HIS ** A1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 HIS B 201 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 HIS B 881 HIS ** B1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 HIS D 562 ASN D 620 HIS D 881 HIS ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 620 HIS F 620 HIS ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 844 GLN ** G1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN O 92 ASN P 92 ASN Q 38 HIS ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5800 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 77677 Z= 0.262 Angle : 0.609 10.132 105068 Z= 0.315 Chirality : 0.042 0.184 11597 Planarity : 0.003 0.059 13339 Dihedral : 8.112 145.308 10336 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 0.01 % Allowed : 1.77 % Favored : 98.22 % 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: -0.93 (0.08), residues: 9403 helix: 0.28 (0.09), residues: 2932 sheet: -0.47 (0.11), residues: 1929 loop : -1.24 (0.09), residues: 4542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 184 HIS 0.006 0.001 HIS A 171 PHE 0.032 0.002 PHE G 822 TYR 0.013 0.002 TYR F 109 ARG 0.005 0.000 ARG A 337 *********************** 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 438 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 437 time to evaluate : 6.895 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: A 687 MET cc_start: 0.7717 (mmt) cc_final: 0.7486 (mmt) REVERT: A 739 MET cc_start: 0.4687 (mpp) cc_final: 0.4463 (mmm) REVERT: A 814 MET cc_start: 0.2339 (mpp) cc_final: 0.1314 (mmm) REVERT: B 197 MET cc_start: 0.7575 (mtm) cc_final: 0.7367 (mtp) REVERT: B 231 MET cc_start: 0.8060 (mmm) cc_final: 0.7787 (mmm) REVERT: B 374 MET cc_start: 0.8363 (mmp) cc_final: 0.8085 (mmt) REVERT: B 814 MET cc_start: 0.3477 (mpp) cc_final: 0.1587 (mmm) REVERT: C 374 MET cc_start: 0.8316 (mmp) cc_final: 0.7989 (mmt) REVERT: C 797 MET cc_start: -0.0225 (tmm) cc_final: -0.0994 (ttp) REVERT: C 814 MET cc_start: 0.3768 (mpp) cc_final: 0.2080 (mmm) REVERT: D 797 MET cc_start: -0.0144 (tmm) cc_final: -0.1135 (ttp) REVERT: D 814 MET cc_start: 0.3943 (mpp) cc_final: 0.2080 (mmm) REVERT: D 921 MET cc_start: 0.8457 (mpp) cc_final: 0.8177 (mpp) REVERT: E 59 MET cc_start: 0.1978 (ttp) cc_final: 0.1340 (tpp) REVERT: E 166 GLU cc_start: 0.8311 (tp30) cc_final: 0.8035 (tp30) REVERT: E 374 MET cc_start: 0.8460 (mmp) cc_final: 0.8246 (mmt) REVERT: E 406 MET cc_start: 0.8180 (ptp) cc_final: 0.7853 (ptm) REVERT: E 814 MET cc_start: 0.2993 (mpp) cc_final: 0.1620 (mmm) REVERT: F 374 MET cc_start: 0.8412 (mmp) cc_final: 0.8152 (mmt) REVERT: F 814 MET cc_start: 0.3301 (mpp) cc_final: 0.1944 (mmm) REVERT: G 155 MET cc_start: 0.8091 (ttp) cc_final: 0.7864 (ttp) REVERT: G 243 ASP cc_start: 0.8635 (t0) cc_final: 0.8028 (t0) REVERT: G 739 MET cc_start: 0.5638 (mpp) cc_final: 0.5198 (mmm) REVERT: G 797 MET cc_start: 0.0350 (tmm) cc_final: -0.0517 (ttp) REVERT: G 814 MET cc_start: 0.3755 (mpp) cc_final: 0.2100 (mmm) REVERT: L 80 MET cc_start: 0.6004 (ttt) cc_final: 0.5365 (ttt) REVERT: N 80 MET cc_start: 0.5470 (ttt) cc_final: 0.4673 (ttt) outliers start: 1 outliers final: 0 residues processed: 438 average time/residue: 0.6971 time to fit residues: 546.1484 Evaluate side-chains 339 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 6.641 ------------------------------------------------------------------------------- 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: 2.9990 chunk 13 optimal weight: 2.9990 chunk 674 optimal weight: 9.9990 chunk 373 optimal weight: 1.9990 chunk 772 optimal weight: 20.0000 chunk 626 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 462 optimal weight: 30.0000 chunk 812 optimal weight: 10.0000 chunk 228 optimal weight: 0.0070 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 562 ASN ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 924 GLN F 171 HIS ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 ASN ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5776 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 77677 Z= 0.206 Angle : 0.568 9.630 105068 Z= 0.295 Chirality : 0.041 0.180 11597 Planarity : 0.003 0.074 13339 Dihedral : 7.866 139.557 10336 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.08 % Favored : 94.77 % Rotamer: Outliers : 0.02 % Allowed : 1.38 % Favored : 98.60 % 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: -0.71 (0.08), residues: 9403 helix: 0.54 (0.09), residues: 2947 sheet: -0.36 (0.11), residues: 1979 loop : -1.17 (0.09), residues: 4477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 404 HIS 0.006 0.001 HIS E 620 PHE 0.022 0.001 PHE A 822 TYR 0.014 0.001 TYR F 845 ARG 0.004 0.000 ARG O 56 *********************** 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 436 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 434 time to evaluate : 6.688 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 739 MET cc_start: 0.4634 (mpp) cc_final: 0.4422 (mmm) REVERT: A 814 MET cc_start: 0.2363 (mpp) cc_final: 0.1603 (mmm) REVERT: B 197 MET cc_start: 0.7609 (mtm) cc_final: 0.7407 (mtp) REVERT: C 374 MET cc_start: 0.8347 (mmp) cc_final: 0.8013 (mmt) REVERT: D 29 MET cc_start: 0.1743 (mtp) cc_final: 0.1020 (mmm) REVERT: D 155 MET cc_start: 0.8210 (ttp) cc_final: 0.8009 (ttp) REVERT: D 374 MET cc_start: 0.8424 (mmp) cc_final: 0.8093 (mmt) REVERT: D 797 MET cc_start: 0.0366 (tmm) cc_final: -0.0597 (ttp) REVERT: D 814 MET cc_start: 0.3988 (mpp) cc_final: 0.2154 (mmm) REVERT: D 921 MET cc_start: 0.8439 (mpp) cc_final: 0.8174 (mpp) REVERT: E 59 MET cc_start: 0.1584 (ttp) cc_final: 0.1087 (tpp) REVERT: E 166 GLU cc_start: 0.8359 (tp30) cc_final: 0.7949 (tp30) REVERT: E 406 MET cc_start: 0.8199 (ptp) cc_final: 0.7885 (ptm) REVERT: E 522 LEU cc_start: 0.8414 (tp) cc_final: 0.8206 (tp) REVERT: E 797 MET cc_start: -0.0066 (tmm) cc_final: -0.0484 (ttp) REVERT: E 814 MET cc_start: 0.3263 (mpp) cc_final: 0.1872 (mmm) REVERT: F 374 MET cc_start: 0.8340 (mmp) cc_final: 0.8099 (mmt) REVERT: F 814 MET cc_start: 0.3201 (mpp) cc_final: 0.1783 (mmm) REVERT: G 155 MET cc_start: 0.8143 (ttp) cc_final: 0.7878 (ttp) REVERT: G 243 ASP cc_start: 0.8634 (t0) cc_final: 0.8058 (t0) REVERT: G 406 MET cc_start: 0.8004 (ptt) cc_final: 0.7520 (ptm) REVERT: G 739 MET cc_start: 0.5681 (mpp) cc_final: 0.5208 (mmm) REVERT: G 797 MET cc_start: 0.0216 (tmm) cc_final: -0.0718 (ttt) REVERT: G 814 MET cc_start: 0.3678 (mpp) cc_final: 0.2097 (mmm) REVERT: H 80 MET cc_start: 0.6161 (ttt) cc_final: 0.5250 (ttt) REVERT: I 80 MET cc_start: 0.6068 (ttt) cc_final: 0.5562 (ttp) REVERT: L 80 MET cc_start: 0.6039 (ttt) cc_final: 0.5428 (ttt) REVERT: N 80 MET cc_start: 0.5417 (ttt) cc_final: 0.4664 (ttt) outliers start: 2 outliers final: 0 residues processed: 436 average time/residue: 0.6703 time to fit residues: 526.1356 Evaluate side-chains 338 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 6.698 ------------------------------------------------------------------------------- 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: 7.9990 chunk 815 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 531 optimal weight: 7.9990 chunk 223 optimal weight: 20.0000 chunk 906 optimal weight: 8.9990 chunk 752 optimal weight: 6.9990 chunk 419 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 299 optimal weight: 30.0000 chunk 475 optimal weight: 0.7980 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN A 454 GLN A 469 GLN A 562 ASN A 599 ASN ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 ASN B 171 HIS B 620 HIS B 693 HIS B 844 GLN ** B1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1224 HIS C 121 GLN C 153 HIS C 171 HIS ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN C 599 ASN ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 HIS ** C1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1176 HIS ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN ** D 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 GLN E 543 ASN E 599 ASN E 693 HIS ** E1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 HIS ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN F 469 GLN F 543 ASN F 599 ASN ** F 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 GLN G 599 ASN G 620 HIS G 628 GLN G 827 HIS G 844 GLN ** G1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1176 HIS G1211 GLN L 52 ASN L 70 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.5569 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= 0.499 Angle : 0.793 14.007 105068 Z= 0.407 Chirality : 0.047 0.211 11597 Planarity : 0.004 0.050 13339 Dihedral : 8.606 146.792 10336 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.59 % Favored : 93.26 % Rotamer: Outliers : 0.01 % Allowed : 2.01 % Favored : 97.98 % 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: -1.24 (0.08), residues: 9403 helix: -0.05 (0.09), residues: 2927 sheet: -0.78 (0.11), residues: 1918 loop : -1.31 (0.09), residues: 4558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP C 404 HIS 0.012 0.002 HIS F 183 PHE 0.029 0.003 PHE D 822 TYR 0.029 0.003 TYR A 109 ARG 0.008 0.001 ARG O 10 *********************** 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 365 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 364 time to evaluate : 6.710 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 814 MET cc_start: 0.2206 (mpp) cc_final: 0.1704 (mmm) REVERT: A 889 MET cc_start: 0.5806 (tmm) cc_final: 0.5450 (tmm) REVERT: A 921 MET cc_start: 0.8624 (mpp) cc_final: 0.8393 (mpp) REVERT: B 32 ASP cc_start: 0.4890 (m-30) cc_final: 0.4441 (t0) REVERT: B 231 MET cc_start: 0.8152 (mmm) cc_final: 0.7628 (mmm) REVERT: B 687 MET cc_start: 0.7701 (mmm) cc_final: 0.7412 (mmm) REVERT: B 814 MET cc_start: 0.3951 (mpp) cc_final: 0.2099 (mmm) REVERT: C 243 ASP cc_start: 0.9039 (t0) cc_final: 0.8818 (t0) REVERT: C 797 MET cc_start: 0.0773 (tmm) cc_final: 0.0389 (ttp) REVERT: C 1191 MET cc_start: 0.7115 (tmm) cc_final: 0.5798 (tmm) REVERT: D 687 MET cc_start: 0.8009 (mmm) cc_final: 0.7791 (mmm) REVERT: D 797 MET cc_start: 0.0686 (tmm) cc_final: -0.0077 (ttp) REVERT: D 921 MET cc_start: 0.8558 (mpp) cc_final: 0.8161 (mpp) REVERT: E 1 MET cc_start: 0.5918 (tmm) cc_final: 0.3030 (pmm) REVERT: E 59 MET cc_start: 0.2176 (ttp) cc_final: 0.1621 (tpp) REVERT: E 406 MET cc_start: 0.8180 (ptp) cc_final: 0.7875 (ptm) REVERT: E 814 MET cc_start: 0.2625 (mpp) cc_final: 0.1519 (mmm) REVERT: F 814 MET cc_start: 0.3181 (mpp) cc_final: 0.1963 (mmm) REVERT: G 739 MET cc_start: 0.5527 (mpp) cc_final: 0.5100 (mmt) REVERT: G 814 MET cc_start: 0.3852 (mpp) cc_final: 0.2302 (mmm) REVERT: I 80 MET cc_start: 0.6626 (ttt) cc_final: 0.6181 (ttp) REVERT: K 80 MET cc_start: 0.6658 (ttt) cc_final: 0.6231 (ttt) REVERT: L 80 MET cc_start: 0.6620 (ttt) cc_final: 0.5861 (ttt) REVERT: M 80 MET cc_start: 0.6756 (ttt) cc_final: 0.5967 (ttt) REVERT: N 80 MET cc_start: 0.6304 (ttt) cc_final: 0.5460 (ttt) outliers start: 1 outliers final: 0 residues processed: 365 average time/residue: 0.6789 time to fit residues: 446.1255 Evaluate side-chains 295 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 6.701 ------------------------------------------------------------------------------- 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: 4.9990 chunk 102 optimal weight: 10.0000 chunk 516 optimal weight: 4.9990 chunk 662 optimal weight: 30.0000 chunk 512 optimal weight: 0.7980 chunk 763 optimal weight: 7.9990 chunk 506 optimal weight: 0.7980 chunk 903 optimal weight: 9.9990 chunk 565 optimal weight: 30.0000 chunk 550 optimal weight: 0.2980 chunk 416 optimal weight: 9.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN B 454 GLN B 844 GLN B1002 HIS ** C 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN D1002 HIS ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1084 HIS ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN G 844 GLN L 52 ASN M 54 ASN ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 77677 Z= 0.236 Angle : 0.590 9.957 105068 Z= 0.308 Chirality : 0.042 0.176 11597 Planarity : 0.003 0.047 13339 Dihedral : 8.112 136.669 10336 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.18 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: 0.35 (0.09), residues: 2957 sheet: -0.69 (0.12), residues: 1890 loop : -1.19 (0.09), residues: 4556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 404 HIS 0.006 0.001 HIS D 620 PHE 0.019 0.001 PHE F 418 TYR 0.017 0.001 TYR K 97 ARG 0.008 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 395 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 6.639 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 814 MET cc_start: 0.2310 (mpp) cc_final: 0.1724 (mmm) REVERT: A 921 MET cc_start: 0.8609 (mpp) cc_final: 0.8177 (mpp) REVERT: A 1191 MET cc_start: 0.7061 (tmm) cc_final: 0.6793 (tmm) REVERT: B 814 MET cc_start: 0.3863 (mpp) cc_final: 0.2019 (mmm) REVERT: C 374 MET cc_start: 0.8347 (mmp) cc_final: 0.7970 (mmt) REVERT: C 797 MET cc_start: 0.1018 (tmm) cc_final: 0.0701 (ttp) REVERT: D 155 MET cc_start: 0.8304 (ttp) cc_final: 0.8030 (ttp) REVERT: D 687 MET cc_start: 0.8066 (mmm) cc_final: 0.7658 (mpp) REVERT: D 797 MET cc_start: 0.0521 (tmm) cc_final: -0.0075 (ttp) REVERT: D 921 MET cc_start: 0.8578 (mpp) cc_final: 0.8187 (mpp) REVERT: E 1 MET cc_start: 0.5086 (tmm) cc_final: 0.2358 (pmm) REVERT: E 59 MET cc_start: 0.1915 (ttp) cc_final: 0.1572 (tpp) REVERT: E 406 MET cc_start: 0.8106 (ptp) cc_final: 0.7882 (ptm) REVERT: E 814 MET cc_start: 0.2656 (mpp) cc_final: 0.1516 (mmm) REVERT: F 374 MET cc_start: 0.8403 (mmp) cc_final: 0.8174 (mmt) REVERT: F 814 MET cc_start: 0.3462 (mpp) cc_final: 0.2085 (mmm) REVERT: G 243 ASP cc_start: 0.8702 (t0) cc_final: 0.8384 (t0) REVERT: G 739 MET cc_start: 0.5507 (mpp) cc_final: 0.5210 (mmt) REVERT: G 797 MET cc_start: -0.0694 (tmm) cc_final: -0.0914 (ttt) REVERT: G 814 MET cc_start: 0.3781 (mpp) cc_final: 0.2203 (mmm) REVERT: H 80 MET cc_start: 0.6491 (ttt) cc_final: 0.5535 (ttt) REVERT: I 80 MET cc_start: 0.6679 (ttt) cc_final: 0.6405 (ttp) REVERT: N 80 MET cc_start: 0.5971 (ttt) cc_final: 0.5120 (ttt) REVERT: P 40 ILE cc_start: 0.4826 (mt) cc_final: 0.4596 (mt) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.6616 time to fit residues: 471.1323 Evaluate side-chains 316 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 6.568 ------------------------------------------------------------------------------- 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: 8.9990 chunk 360 optimal weight: 0.5980 chunk 539 optimal weight: 9.9990 chunk 272 optimal weight: 0.6980 chunk 177 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 574 optimal weight: 20.0000 chunk 615 optimal weight: 0.0070 chunk 446 optimal weight: 9.9990 chunk 84 optimal weight: 0.0770 chunk 709 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN C 599 ASN C 881 HIS C1084 HIS ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 HIS ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 599 ASN F 599 ASN F1084 HIS ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 599 ASN ** G1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 ASN M 70 ASN Q 92 ASN ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5761 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 77677 Z= 0.138 Angle : 0.541 10.356 105068 Z= 0.283 Chirality : 0.041 0.193 11597 Planarity : 0.003 0.038 13339 Dihedral : 7.491 121.188 10336 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -0.57 (0.08), residues: 9403 helix: 0.73 (0.09), residues: 2979 sheet: -0.37 (0.12), residues: 1872 loop : -1.10 (0.09), residues: 4552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 404 HIS 0.007 0.001 HIS E1084 PHE 0.022 0.001 PHE D 822 TYR 0.013 0.001 TYR K 97 ARG 0.007 0.000 ARG G 6 *********************** 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 431 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 6.687 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 814 MET cc_start: 0.2077 (mpp) cc_final: 0.1394 (mmm) REVERT: A 921 MET cc_start: 0.8589 (mpp) cc_final: 0.8151 (mpp) REVERT: B 503 LEU cc_start: 0.9108 (tp) cc_final: 0.8779 (tt) REVERT: B 814 MET cc_start: 0.3844 (mpp) cc_final: 0.2094 (mmm) REVERT: C 374 MET cc_start: 0.8307 (mmp) cc_final: 0.7964 (mmt) REVERT: D 1 MET cc_start: -0.0830 (tmm) cc_final: -0.1055 (tmm) REVERT: D 29 MET cc_start: 0.1742 (mtp) cc_final: 0.1156 (mmm) REVERT: D 687 MET cc_start: 0.8008 (mmm) cc_final: 0.7579 (mpp) REVERT: D 814 MET cc_start: 0.3654 (mpp) cc_final: 0.1786 (mmm) REVERT: D 921 MET cc_start: 0.8549 (mpp) cc_final: 0.8134 (mpp) REVERT: E 1 MET cc_start: 0.4949 (tmm) cc_final: 0.2212 (pmm) REVERT: E 59 MET cc_start: 0.1960 (ttp) cc_final: 0.1649 (tpp) REVERT: E 166 GLU cc_start: 0.8310 (tp30) cc_final: 0.8068 (tp30) REVERT: E 406 MET cc_start: 0.8014 (ptp) cc_final: 0.7777 (ptp) REVERT: E 411 VAL cc_start: 0.9317 (t) cc_final: 0.9068 (p) REVERT: E 814 MET cc_start: 0.2943 (mpp) cc_final: 0.1513 (mmm) REVERT: F 374 MET cc_start: 0.8350 (mmp) cc_final: 0.7976 (mmt) REVERT: F 814 MET cc_start: 0.3420 (mpp) cc_final: 0.2017 (mmm) REVERT: G 155 MET cc_start: 0.8088 (ttp) cc_final: 0.7721 (ttp) REVERT: G 202 LEU cc_start: 0.9399 (tp) cc_final: 0.8903 (tp) REVERT: G 243 ASP cc_start: 0.8563 (t0) cc_final: 0.8186 (t0) REVERT: G 797 MET cc_start: -0.0562 (tmm) cc_final: -0.0883 (ttt) REVERT: G 814 MET cc_start: 0.3731 (mpp) cc_final: 0.2122 (mmm) REVERT: H 80 MET cc_start: 0.6379 (ttt) cc_final: 0.5472 (ttt) REVERT: I 80 MET cc_start: 0.6360 (ttt) cc_final: 0.5974 (ttp) REVERT: Q 44 GLN cc_start: 0.3498 (mt0) cc_final: 0.2993 (tm-30) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.6973 time to fit residues: 542.5161 Evaluate side-chains 342 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 6.708 ------------------------------------------------------------------------------- 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: 20.0000 chunk 865 optimal weight: 0.9980 chunk 789 optimal weight: 9.9990 chunk 841 optimal weight: 20.0000 chunk 864 optimal weight: 0.0470 chunk 506 optimal weight: 0.5980 chunk 366 optimal weight: 1.9990 chunk 660 optimal weight: 20.0000 chunk 258 optimal weight: 0.9980 chunk 760 optimal weight: 10.0000 chunk 795 optimal weight: 9.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 HIS B 7 ASN C1084 HIS ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 HIS ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN F 543 ASN F1084 HIS F1224 HIS ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 ASN N 70 ASN ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5763 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 77677 Z= 0.149 Angle : 0.542 11.555 105068 Z= 0.281 Chirality : 0.041 0.175 11597 Planarity : 0.003 0.038 13339 Dihedral : 7.209 114.252 10336 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.98 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -0.43 (0.09), residues: 9403 helix: 0.88 (0.09), residues: 2976 sheet: -0.23 (0.12), residues: 1865 loop : -1.07 (0.09), residues: 4562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.001 TRP C 597 HIS 0.005 0.001 HIS E 620 PHE 0.028 0.001 PHE C 623 TYR 0.018 0.001 TYR A 845 ARG 0.006 0.000 ARG O 10 *********************** 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 412 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 6.735 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: A 374 MET cc_start: 0.8366 (mmp) cc_final: 0.8026 (mmt) REVERT: A 814 MET cc_start: 0.2114 (mpp) cc_final: 0.1424 (mmm) REVERT: A 921 MET cc_start: 0.8607 (mpp) cc_final: 0.8139 (mpp) REVERT: B 197 MET cc_start: 0.7629 (mtm) cc_final: 0.7418 (mtp) REVERT: B 374 MET cc_start: 0.8291 (mmp) cc_final: 0.7929 (mmt) REVERT: B 431 LYS cc_start: 0.6123 (tppt) cc_final: 0.5863 (tppt) REVERT: B 814 MET cc_start: 0.3863 (mpp) cc_final: 0.2076 (mmm) REVERT: C 374 MET cc_start: 0.8240 (mmp) cc_final: 0.7935 (mmt) REVERT: D 374 MET cc_start: 0.8266 (mmp) cc_final: 0.7857 (mmt) REVERT: D 687 MET cc_start: 0.7941 (mmm) cc_final: 0.7514 (mpp) REVERT: D 797 MET cc_start: 0.0348 (tmm) cc_final: -0.0410 (ttp) REVERT: D 814 MET cc_start: 0.3666 (mpp) cc_final: 0.1827 (mmm) REVERT: D 921 MET cc_start: 0.8565 (mpp) cc_final: 0.8136 (mpp) REVERT: E 1 MET cc_start: 0.5163 (tmm) cc_final: 0.2624 (pmm) REVERT: E 59 MET cc_start: 0.2146 (ttp) cc_final: 0.1639 (tpp) REVERT: E 166 GLU cc_start: 0.8332 (tp30) cc_final: 0.8068 (tp30) REVERT: E 406 MET cc_start: 0.8103 (ptp) cc_final: 0.7810 (ptp) REVERT: E 411 VAL cc_start: 0.9373 (t) cc_final: 0.9095 (p) REVERT: E 814 MET cc_start: 0.2838 (mpp) cc_final: 0.1523 (mmm) REVERT: F 202 LEU cc_start: 0.9221 (tt) cc_final: 0.8910 (tt) REVERT: F 374 MET cc_start: 0.8272 (mmp) cc_final: 0.7978 (mmt) REVERT: F 797 MET cc_start: -0.1183 (ttt) cc_final: -0.1447 (ttt) REVERT: F 814 MET cc_start: 0.3423 (mpp) cc_final: 0.2002 (mmm) REVERT: G 55 MET cc_start: 0.4505 (ttm) cc_final: 0.3532 (ptm) REVERT: G 155 MET cc_start: 0.8123 (ttp) cc_final: 0.7793 (ttp) REVERT: G 202 LEU cc_start: 0.9408 (tp) cc_final: 0.8912 (tp) REVERT: G 374 MET cc_start: 0.8312 (mmp) cc_final: 0.8103 (tpp) REVERT: G 797 MET cc_start: -0.0332 (tmm) cc_final: -0.0990 (ttt) REVERT: G 814 MET cc_start: 0.3756 (mpp) cc_final: 0.2187 (mmm) REVERT: I 80 MET cc_start: 0.6593 (ttt) cc_final: 0.6219 (ttp) REVERT: L 80 MET cc_start: 0.5755 (ttp) cc_final: 0.5312 (mtp) REVERT: M 80 MET cc_start: 0.6719 (ttt) cc_final: 0.5982 (ttt) REVERT: Q 44 GLN cc_start: 0.3478 (mt0) cc_final: 0.2968 (tm-30) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.6714 time to fit residues: 502.8887 Evaluate side-chains 340 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 6.630 ------------------------------------------------------------------------------- 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: 7.9990 chunk 552 optimal weight: 4.9990 chunk 889 optimal weight: 10.0000 chunk 543 optimal weight: 20.0000 chunk 422 optimal weight: 30.0000 chunk 618 optimal weight: 0.9990 chunk 933 optimal weight: 0.8980 chunk 859 optimal weight: 6.9990 chunk 743 optimal weight: 0.8980 chunk 77 optimal weight: 30.0000 chunk 574 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 HIS B 171 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN F 201 ASN ** F1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5865 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 77677 Z= 0.278 Angle : 0.606 11.956 105068 Z= 0.314 Chirality : 0.042 0.210 11597 Planarity : 0.003 0.038 13339 Dihedral : 7.562 125.577 10336 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -0.57 (0.09), residues: 9403 helix: 0.76 (0.09), residues: 2962 sheet: -0.33 (0.12), residues: 1830 loop : -1.13 (0.09), residues: 4611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP E 404 HIS 0.006 0.001 HIS E 620 PHE 0.024 0.002 PHE G 526 TYR 0.017 0.001 TYR J 97 ARG 0.005 0.000 ARG O 10 ********************** 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 380 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 6.577 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 374 MET cc_start: 0.8387 (mmp) cc_final: 0.8143 (mmt) REVERT: A 814 MET cc_start: 0.2179 (mpp) cc_final: 0.1424 (mmm) REVERT: A 921 MET cc_start: 0.8669 (mpp) cc_final: 0.8145 (mpp) REVERT: B 431 LYS cc_start: 0.6155 (tppt) cc_final: 0.5945 (tppt) REVERT: B 814 MET cc_start: 0.3925 (mpp) cc_final: 0.2105 (mmm) REVERT: C 374 MET cc_start: 0.8383 (mmp) cc_final: 0.8113 (mmt) REVERT: C 814 MET cc_start: 0.3901 (mpp) cc_final: 0.1688 (ptt) REVERT: D 155 MET cc_start: 0.8421 (ttp) cc_final: 0.8180 (ttp) REVERT: D 687 MET cc_start: 0.8063 (mmm) cc_final: 0.7595 (mpp) REVERT: D 797 MET cc_start: 0.0373 (tmm) cc_final: -0.0358 (ttp) REVERT: D 814 MET cc_start: 0.3750 (mpp) cc_final: 0.1911 (mmm) REVERT: D 921 MET cc_start: 0.8589 (mpp) cc_final: 0.8150 (mpp) REVERT: E 1 MET cc_start: 0.5161 (tmm) cc_final: 0.3166 (pmm) REVERT: E 59 MET cc_start: 0.2010 (ttp) cc_final: 0.1588 (tpp) REVERT: E 166 GLU cc_start: 0.8382 (tp30) cc_final: 0.8158 (tp30) REVERT: E 374 MET cc_start: 0.8487 (mmp) cc_final: 0.8249 (mmt) REVERT: E 814 MET cc_start: 0.2795 (mpp) cc_final: 0.1560 (mmm) REVERT: F 797 MET cc_start: -0.0727 (ttt) cc_final: -0.1030 (ttt) REVERT: F 814 MET cc_start: 0.3131 (mpp) cc_final: 0.1950 (mmm) REVERT: G 55 MET cc_start: 0.4396 (ttm) cc_final: 0.3989 (ttp) REVERT: G 155 MET cc_start: 0.8279 (ttp) cc_final: 0.8013 (ttp) REVERT: G 243 ASP cc_start: 0.8675 (t0) cc_final: 0.8474 (t0) REVERT: G 797 MET cc_start: -0.0329 (tmm) cc_final: -0.0770 (ttt) REVERT: G 814 MET cc_start: 0.3854 (mpp) cc_final: 0.2282 (mmm) REVERT: H 80 MET cc_start: 0.5953 (ttp) cc_final: 0.5183 (mtp) REVERT: I 80 MET cc_start: 0.6726 (ttt) cc_final: 0.6337 (ttp) REVERT: L 80 MET cc_start: 0.5672 (ttp) cc_final: 0.5277 (mtp) REVERT: M 80 MET cc_start: 0.6775 (ttt) cc_final: 0.6068 (ttt) REVERT: Q 44 GLN cc_start: 0.3904 (mt0) cc_final: 0.3024 (tm-30) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.6673 time to fit residues: 461.4400 Evaluate side-chains 326 residues out of total 8414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 6.384 ------------------------------------------------------------------------------- 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: 9.9990 chunk 590 optimal weight: 40.0000 chunk 791 optimal weight: 3.9990 chunk 227 optimal weight: 0.0980 chunk 685 optimal weight: 8.9990 chunk 109 optimal weight: 0.3980 chunk 206 optimal weight: 30.0000 chunk 744 optimal weight: 5.9990 chunk 311 optimal weight: 20.0000 chunk 764 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS A1084 HIS C 171 HIS ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1126 HIS ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 886 HIS ** F1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 599 ASN G 886 HIS H 52 ASN L 52 ASN O 38 HIS ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.110973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.093807 restraints weight = 344938.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.093679 restraints weight = 659342.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.092657 restraints weight = 334459.339| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.6334 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= 0.347 Angle : 0.667 14.472 105068 Z= 0.345 Chirality : 0.044 0.307 11597 Planarity : 0.003 0.040 13339 Dihedral : 7.972 137.485 10336 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.50 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -0.89 (0.08), residues: 9403 helix: 0.44 (0.09), residues: 2961 sheet: -0.63 (0.12), residues: 1812 loop : -1.23 (0.09), residues: 4630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP E 404 HIS 0.009 0.001 HIS B 183 PHE 0.028 0.002 PHE A 126 TYR 0.017 0.002 TYR J 97 ARG 0.009 0.001 ARG L 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11966.99 seconds wall clock time: 213 minutes 10.24 seconds (12790.24 seconds total)