Starting phenix.real_space_refine on Fri Dec 8 20:39:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qb8_4489/12_2023/6qb8_4489_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qb8_4489/12_2023/6qb8_4489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qb8_4489/12_2023/6qb8_4489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qb8_4489/12_2023/6qb8_4489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qb8_4489/12_2023/6qb8_4489_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qb8_4489/12_2023/6qb8_4489_updated.pdb" } resolution = 3.97 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= 0.042 sd= 0.162 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 377 5.16 5 C 37640 2.51 5 N 10462 2.21 5 O 11552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a ASP 48": "OD1" <-> "OD2" Residue "a ARG 185": "NH1" <-> "NH2" Residue "a ARG 189": "NH1" <-> "NH2" Residue "a ARG 266": "NH1" <-> "NH2" Residue "a ASP 358": "OD1" <-> "OD2" Residue "a GLU 479": "OE1" <-> "OE2" Residue "a ARG 480": "NH1" <-> "NH2" Residue "b GLU 351": "OE1" <-> "OE2" Residue "b ASP 384": "OD1" <-> "OD2" Residue "b ARG 481": "NH1" <-> "NH2" Residue "d GLU 135": "OE1" <-> "OE2" Residue "d ASP 220": "OD1" <-> "OD2" Residue "d ARG 280": "NH1" <-> "NH2" Residue "d TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 306": "NH1" <-> "NH2" Residue "d ASP 307": "OD1" <-> "OD2" Residue "d GLU 331": "OE1" <-> "OE2" Residue "d GLU 360": "OE1" <-> "OE2" Residue "d ASP 407": "OD1" <-> "OD2" Residue "d GLU 479": "OE1" <-> "OE2" Residue "d ARG 539": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 126": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e ARG 142": "NH1" <-> "NH2" Residue "e GLU 163": "OE1" <-> "OE2" Residue "e ARG 183": "NH1" <-> "NH2" Residue "e ARG 201": "NH1" <-> "NH2" Residue "e ARG 202": "NH1" <-> "NH2" Residue "e GLU 212": "OE1" <-> "OE2" Residue "e ARG 218": "NH1" <-> "NH2" Residue "e TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 340": "NH1" <-> "NH2" Residue "e ARG 344": "NH1" <-> "NH2" Residue "e GLU 351": "OE1" <-> "OE2" Residue "e ASP 369": "OD1" <-> "OD2" Residue "e ARG 381": "NH1" <-> "NH2" Residue "e ARG 400": "NH1" <-> "NH2" Residue "e ARG 410": "NH1" <-> "NH2" Residue "e ARG 414": "NH1" <-> "NH2" Residue "e ARG 449": "NH1" <-> "NH2" Residue "e ARG 478": "NH1" <-> "NH2" Residue "e ARG 480": "NH1" <-> "NH2" Residue "e ARG 534": "NH1" <-> "NH2" Residue "e GLU 540": "OE1" <-> "OE2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g ASP 147": "OD1" <-> "OD2" Residue "g ASP 149": "OD1" <-> "OD2" Residue "g ARG 189": "NH1" <-> "NH2" Residue "g ARG 229": "NH1" <-> "NH2" Residue "g ARG 338": "NH1" <-> "NH2" Residue "g ASP 356": "OD1" <-> "OD2" Residue "g TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 93": "OE1" <-> "OE2" Residue "h ASP 192": "OD1" <-> "OD2" Residue "h ASP 272": "OD1" <-> "OD2" Residue "h GLU 283": "OE1" <-> "OE2" Residue "h ARG 310": "NH1" <-> "NH2" Residue "h PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 137": "NH1" <-> "NH2" Residue "q ARG 155": "NH1" <-> "NH2" Residue "q ASP 158": "OD1" <-> "OD2" Residue "q ARG 165": "NH1" <-> "NH2" Residue "q GLU 176": "OE1" <-> "OE2" Residue "q PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 285": "OD1" <-> "OD2" Residue "q TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 382": "OD1" <-> "OD2" Residue "q ASP 386": "OD1" <-> "OD2" Residue "q PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 491": "OD1" <-> "OD2" Residue "z ARG 28": "NH1" <-> "NH2" Residue "z ARG 35": "NH1" <-> "NH2" Residue "z GLU 112": "OE1" <-> "OE2" Residue "z ARG 117": "NH1" <-> "NH2" Residue "z GLU 128": "OE1" <-> "OE2" Residue "z ARG 141": "NH1" <-> "NH2" Residue "z ARG 145": "NH1" <-> "NH2" Residue "z ARG 153": "NH1" <-> "NH2" Residue "z ARG 157": "NH1" <-> "NH2" Residue "z GLU 163": "OE1" <-> "OE2" Residue "z GLU 184": "OE1" <-> "OE2" Residue "z ARG 208": "NH1" <-> "NH2" Residue "z ARG 217": "NH1" <-> "NH2" Residue "z ARG 224": "NH1" <-> "NH2" Residue "z PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 264": "NH1" <-> "NH2" Residue "z ARG 270": "NH1" <-> "NH2" Residue "z ARG 279": "NH1" <-> "NH2" Residue "z ASP 284": "OD1" <-> "OD2" Residue "z ARG 318": "NH1" <-> "NH2" Residue "z ARG 319": "NH1" <-> "NH2" Residue "z ASP 342": "OD1" <-> "OD2" Residue "z ARG 370": "NH1" <-> "NH2" Residue "z ARG 392": "NH1" <-> "NH2" Residue "z ARG 396": "NH1" <-> "NH2" Residue "z ARG 432": "NH1" <-> "NH2" Residue "z GLU 469": "OE1" <-> "OE2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 480": "NH1" <-> "NH2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B ARG 481": "NH1" <-> "NH2" Residue "D ASP 159": "OD1" <-> "OD2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D ARG 539": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "E ARG 142": "NH1" <-> "NH2" Residue "E ARG 183": "NH1" <-> "NH2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E ARG 218": "NH1" <-> "NH2" Residue "E TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 340": "NH1" <-> "NH2" Residue "E ARG 344": "NH1" <-> "NH2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E ARG 381": "NH1" <-> "NH2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E ARG 400": "NH1" <-> "NH2" Residue "E ARG 410": "NH1" <-> "NH2" Residue "E ARG 414": "NH1" <-> "NH2" Residue "E GLU 444": "OE1" <-> "OE2" Residue "E ARG 449": "NH1" <-> "NH2" Residue "E ARG 478": "NH1" <-> "NH2" Residue "E ARG 480": "NH1" <-> "NH2" Residue "E ARG 534": "NH1" <-> "NH2" Residue "E GLU 541": "OE1" <-> "OE2" Residue "G ASP 147": "OD1" <-> "OD2" Residue "G ARG 189": "NH1" <-> "NH2" Residue "G ARG 229": "NH1" <-> "NH2" Residue "G TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 338": "NH1" <-> "NH2" Residue "G ASP 356": "OD1" <-> "OD2" Residue "G GLU 510": "OE1" <-> "OE2" Residue "H ASP 70": "OD1" <-> "OD2" Residue "H TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 279": "OE1" <-> "OE2" Residue "H ARG 306": "NH1" <-> "NH2" Residue "Q TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 137": "NH1" <-> "NH2" Residue "Q ARG 155": "NH1" <-> "NH2" Residue "Q ASP 158": "OD1" <-> "OD2" Residue "Q ARG 165": "NH1" <-> "NH2" Residue "Q GLU 176": "OE1" <-> "OE2" Residue "Q PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 285": "OD1" <-> "OD2" Residue "Q TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 382": "OD1" <-> "OD2" Residue "Q ASP 386": "OD1" <-> "OD2" Residue "Q PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 491": "OD1" <-> "OD2" Residue "Z ARG 28": "NH1" <-> "NH2" Residue "Z ARG 35": "NH1" <-> "NH2" Residue "Z ARG 117": "NH1" <-> "NH2" Residue "Z ARG 141": "NH1" <-> "NH2" Residue "Z ARG 145": "NH1" <-> "NH2" Residue "Z ARG 153": "NH1" <-> "NH2" Residue "Z ARG 157": "NH1" <-> "NH2" Residue "Z ARG 208": "NH1" <-> "NH2" Residue "Z ARG 217": "NH1" <-> "NH2" Residue "Z ARG 224": "NH1" <-> "NH2" Residue "Z GLU 255": "OE1" <-> "OE2" Residue "Z ARG 264": "NH1" <-> "NH2" Residue "Z ARG 270": "NH1" <-> "NH2" Residue "Z ARG 279": "NH1" <-> "NH2" Residue "Z ASP 286": "OD1" <-> "OD2" Residue "Z ARG 318": "NH1" <-> "NH2" Residue "Z ARG 319": "NH1" <-> "NH2" Residue "Z ARG 370": "NH1" <-> "NH2" Residue "Z ARG 392": "NH1" <-> "NH2" Residue "Z ARG 396": "NH1" <-> "NH2" Residue "Z ARG 432": "NH1" <-> "NH2" Residue "Z PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 469": "OE1" <-> "OE2" Residue "Z ARG 523": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 60035 Number of models: 1 Model: "" Number of chains: 18 Chain: "a" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3709 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 11, 'TRANS': 478} Chain breaks: 2 Chain: "b" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3590 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 8, 'TRANS': 469} Chain breaks: 1 Chain: "d" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3673 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 475} Chain breaks: 1 Chain: "e" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3882 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 14, 'TRANS': 490} Chain breaks: 1 Chain: "g" Number of atoms: 3678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3678 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 16, 'TRANS': 460} Chain breaks: 1 Chain: "h" Number of atoms: 3834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3834 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 14, 'TRANS': 485} Chain breaks: 1 Chain: "q" Number of atoms: 3692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3692 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 12, 'TRANS': 470} Chain breaks: 1 Chain: "z" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3894 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 13, 'TRANS': 494} Chain breaks: 1 Chain: "A" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3742 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 11, 'TRANS': 482} Chain breaks: 2 Chain: "B" Number of atoms: 3698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3698 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 8, 'TRANS': 483} Chain breaks: 1 Chain: "D" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3655 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 473} Chain breaks: 1 Chain: "E" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3863 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 14, 'TRANS': 488} Chain breaks: 1 Chain: "G" Number of atoms: 3741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3741 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 16, 'TRANS': 468} Chain breaks: 1 Chain: "H" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3825 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 14, 'TRANS': 484} Chain breaks: 1 Chain: "Q" Number of atoms: 3692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3692 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 12, 'TRANS': 470} Chain breaks: 1 Chain: "Z" Number of atoms: 3813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3813 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 13, 'TRANS': 483} Chain breaks: 1 Chain: "q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.01, per 1000 atoms: 0.38 Number of scatterers: 60035 At special positions: 0 Unit cell: (176.73, 191.8, 190.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 377 16.00 P 4 15.00 O 11552 8.00 N 10462 7.00 C 37640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS h 330 " - pdb=" SG CYS h 349 " distance=2.03 Simple disulfide: pdb=" SG CYS H 326 " - pdb=" SG CYS H 345 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.45 Conformation dependent library (CDL) restraints added in 8.0 seconds 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14660 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 295 helices and 72 sheets defined 47.5% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.89 Creating SS restraints... Processing helix chain 'a' and resid 17 through 31 removed outlier: 3.693A pdb=" N ILE a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA a 29 " --> pdb=" O ALA a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 72 through 83 removed outlier: 3.789A pdb=" N CYS a 76 " --> pdb=" O LYS a 73 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU a 77 " --> pdb=" O VAL a 74 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA a 79 " --> pdb=" O CYS a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 110 removed outlier: 3.663A pdb=" N ALA a 97 " --> pdb=" O VAL a 93 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 132 removed outlier: 3.691A pdb=" N LYS a 126 " --> pdb=" O ARG a 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 146 through 156 removed outlier: 3.703A pdb=" N SER a 155 " --> pdb=" O ALA a 151 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET a 156 " --> pdb=" O ALA a 152 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 178 removed outlier: 3.527A pdb=" N MET a 171 " --> pdb=" O PHE a 167 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA a 178 " --> pdb=" O ASP a 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 273 through 281 removed outlier: 4.303A pdb=" N THR a 281 " --> pdb=" O LYS a 277 " (cutoff:3.500A) Processing helix chain 'a' and resid 296 through 299 No H-bonds generated for 'chain 'a' and resid 296 through 299' Processing helix chain 'a' and resid 313 through 323 removed outlier: 3.927A pdb=" N ARG a 318 " --> pdb=" O ARG a 314 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA a 322 " --> pdb=" O ARG a 318 " (cutoff:3.500A) Processing helix chain 'a' and resid 386 through 403 removed outlier: 3.818A pdb=" N ALA a 395 " --> pdb=" O SER a 391 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU a 396 " --> pdb=" O LEU a 392 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS a 397 " --> pdb=" O HIS a 393 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG a 401 " --> pdb=" O CYS a 397 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL a 402 " --> pdb=" O VAL a 398 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU a 403 " --> pdb=" O VAL a 399 " (cutoff:3.500A) Processing helix chain 'a' and resid 414 through 429 removed outlier: 3.657A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN a 425 " --> pdb=" O ILE a 421 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 435 through 455 removed outlier: 3.938A pdb=" N ALA a 439 " --> pdb=" O GLN a 435 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU a 440 " --> pdb=" O LEU a 436 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix removed outlier: 3.565A pdb=" N VAL a 454 " --> pdb=" O ASN a 450 " (cutoff:3.500A) Processing helix chain 'a' and resid 460 through 472 removed outlier: 3.991A pdb=" N VAL a 464 " --> pdb=" O SER a 460 " (cutoff:3.500A) Processing helix chain 'a' and resid 507 through 526 removed outlier: 3.615A pdb=" N THR a 518 " --> pdb=" O LEU a 514 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR a 523 " --> pdb=" O GLU a 519 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE a 524 " --> pdb=" O ALA a 520 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 39 removed outlier: 3.581A pdb=" N VAL b 39 " --> pdb=" O ILE b 35 " (cutoff:3.500A) Processing helix chain 'b' and resid 68 through 72 removed outlier: 3.584A pdb=" N LYS b 72 " --> pdb=" O ALA b 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 68 through 72' Processing helix chain 'b' and resid 79 through 95 removed outlier: 3.539A pdb=" N VAL b 83 " --> pdb=" O PRO b 79 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU b 84 " --> pdb=" O ALA b 80 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU b 94 " --> pdb=" O VAL b 90 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL b 95 " --> pdb=" O GLN b 91 " (cutoff:3.500A) Processing helix chain 'b' and resid 99 through 118 removed outlier: 3.770A pdb=" N SER b 115 " --> pdb=" O ARG b 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 143 removed outlier: 3.623A pdb=" N ALA b 136 " --> pdb=" O GLU b 132 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU b 141 " --> pdb=" O ALA b 137 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU b 142 " --> pdb=" O ARG b 138 " (cutoff:3.500A) Processing helix chain 'b' and resid 157 through 165 removed outlier: 3.878A pdb=" N ILE b 162 " --> pdb=" O ASP b 158 " (cutoff:3.500A) Processing helix chain 'b' and resid 176 through 184 Processing helix chain 'b' and resid 209 through 211 No H-bonds generated for 'chain 'b' and resid 209 through 211' Processing helix chain 'b' and resid 264 through 283 removed outlier: 3.641A pdb=" N LEU b 283 " --> pdb=" O VAL b 279 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 307 removed outlier: 3.768A pdb=" N LEU b 303 " --> pdb=" O TYR b 299 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA b 307 " --> pdb=" O LEU b 303 " (cutoff:3.500A) Processing helix chain 'b' and resid 317 through 324 removed outlier: 3.662A pdb=" N ARG b 322 " --> pdb=" O ALA b 318 " (cutoff:3.500A) Processing helix chain 'b' and resid 381 through 402 removed outlier: 3.697A pdb=" N GLU b 387 " --> pdb=" O LEU b 383 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL b 396 " --> pdb=" O ASP b 392 " (cutoff:3.500A) Processing helix chain 'b' and resid 412 through 425 Processing helix chain 'b' and resid 431 through 452 removed outlier: 3.679A pdb=" N MET b 436 " --> pdb=" O ALA b 433 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER b 438 " --> pdb=" O ALA b 435 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA b 442 " --> pdb=" O TYR b 439 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU b 446 " --> pdb=" O LEU b 443 " (cutoff:3.500A) Proline residue: b 447 - end of helix removed outlier: 3.905A pdb=" N ILE b 450 " --> pdb=" O PRO b 447 " (cutoff:3.500A) Processing helix chain 'b' and resid 461 through 470 removed outlier: 3.765A pdb=" N SER b 470 " --> pdb=" O ARG b 466 " (cutoff:3.500A) Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 516 removed outlier: 4.407A pdb=" N GLN b 502 " --> pdb=" O GLN b 498 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA b 508 " --> pdb=" O LEU b 504 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 46 removed outlier: 3.633A pdb=" N SER d 36 " --> pdb=" O GLN d 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 51 No H-bonds generated for 'chain 'd' and resid 49 through 51' Processing helix chain 'd' and resid 74 through 80 Processing helix chain 'd' and resid 86 through 101 removed outlier: 3.551A pdb=" N LEU d 91 " --> pdb=" O ALA d 87 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER d 95 " --> pdb=" O LEU d 91 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS d 96 " --> pdb=" O VAL d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 126 removed outlier: 3.601A pdb=" N ALA d 113 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU d 123 " --> pdb=" O SER d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 150 removed outlier: 3.790A pdb=" N ASP d 150 " --> pdb=" O GLU d 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 161 through 170 Processing helix chain 'd' and resid 180 through 193 Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 218 through 220 No H-bonds generated for 'chain 'd' and resid 218 through 220' Processing helix chain 'd' and resid 279 through 293 Processing helix chain 'd' and resid 311 through 318 removed outlier: 3.644A pdb=" N PHE d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) Processing helix chain 'd' and resid 330 through 340 removed outlier: 4.181A pdb=" N GLU d 334 " --> pdb=" O ARG d 330 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE d 335 " --> pdb=" O GLU d 331 " (cutoff:3.500A) Processing helix chain 'd' and resid 353 through 355 No H-bonds generated for 'chain 'd' and resid 353 through 355' Processing helix chain 'd' and resid 367 through 369 No H-bonds generated for 'chain 'd' and resid 367 through 369' Processing helix chain 'd' and resid 396 through 412 removed outlier: 4.031A pdb=" N ALA d 401 " --> pdb=" O VAL d 397 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU d 402 " --> pdb=" O ILE d 398 " (cutoff:3.500A) Processing helix chain 'd' and resid 414 through 417 No H-bonds generated for 'chain 'd' and resid 414 through 417' Processing helix chain 'd' and resid 427 through 442 Processing helix chain 'd' and resid 446 through 468 removed outlier: 3.737A pdb=" N TYR d 449 " --> pdb=" O MET d 446 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL d 451 " --> pdb=" O SER d 448 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP d 456 " --> pdb=" O ALA d 453 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA d 457 " --> pdb=" O PHE d 454 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL d 460 " --> pdb=" O ALA d 457 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE d 461 " --> pdb=" O MET d 458 " (cutoff:3.500A) Proline residue: d 462 - end of helix removed outlier: 4.088A pdb=" N ASN d 468 " --> pdb=" O LEU d 465 " (cutoff:3.500A) Processing helix chain 'd' and resid 473 through 486 Processing helix chain 'd' and resid 503 through 506 No H-bonds generated for 'chain 'd' and resid 503 through 506' Processing helix chain 'd' and resid 512 through 531 Processing helix chain 'e' and resid 30 through 44 removed outlier: 3.560A pdb=" N VAL e 44 " --> pdb=" O ALA e 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 51 Processing helix chain 'e' and resid 74 through 80 removed outlier: 3.684A pdb=" N SER e 79 " --> pdb=" O ALA e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 101 removed outlier: 3.631A pdb=" N SER e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP e 100 " --> pdb=" O LYS e 96 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 126 removed outlier: 3.890A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU e 123 " --> pdb=" O GLU e 119 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 150 removed outlier: 4.328A pdb=" N GLU e 146 " --> pdb=" O ARG e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 164 through 168 Processing helix chain 'e' and resid 177 through 180 removed outlier: 3.944A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 177 through 180' Processing helix chain 'e' and resid 182 through 195 removed outlier: 3.535A pdb=" N ALA e 189 " --> pdb=" O MET e 185 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU e 194 " --> pdb=" O VAL e 190 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR e 195 " --> pdb=" O ASN e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 272 through 286 Processing helix chain 'e' and resid 309 through 317 Processing helix chain 'e' and resid 330 through 333 No H-bonds generated for 'chain 'e' and resid 330 through 333' Processing helix chain 'e' and resid 350 through 352 No H-bonds generated for 'chain 'e' and resid 350 through 352' Processing helix chain 'e' and resid 392 through 408 removed outlier: 3.690A pdb=" N LEU e 402 " --> pdb=" O ALA e 398 " (cutoff:3.500A) Processing helix chain 'e' and resid 410 through 412 No H-bonds generated for 'chain 'e' and resid 410 through 412' Processing helix chain 'e' and resid 424 through 436 Processing helix chain 'e' and resid 442 through 466 removed outlier: 4.190A pdb=" N ASP e 453 " --> pdb=" O ARG e 449 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE e 458 " --> pdb=" O ALA e 454 " (cutoff:3.500A) Proline residue: e 459 - end of helix removed outlier: 3.676A pdb=" N LEU e 462 " --> pdb=" O ILE e 458 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER e 466 " --> pdb=" O LEU e 462 " (cutoff:3.500A) Processing helix chain 'e' and resid 472 through 483 Processing helix chain 'e' and resid 501 through 504 No H-bonds generated for 'chain 'e' and resid 501 through 504' Processing helix chain 'e' and resid 510 through 529 removed outlier: 4.119A pdb=" N GLN e 516 " --> pdb=" O GLY e 512 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET e 523 " --> pdb=" O LEU e 519 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET e 526 " --> pdb=" O GLN e 522 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 35 removed outlier: 3.906A pdb=" N ILE g 32 " --> pdb=" O ALA g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 68 removed outlier: 3.903A pdb=" N GLU g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 87 removed outlier: 3.655A pdb=" N SER g 83 " --> pdb=" O MET g 79 " (cutoff:3.500A) Processing helix chain 'g' and resid 94 through 112 removed outlier: 3.706A pdb=" N ILE g 98 " --> pdb=" O THR g 94 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY g 102 " --> pdb=" O ILE g 98 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET g 104 " --> pdb=" O LEU g 100 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU g 109 " --> pdb=" O LEU g 105 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS g 110 " --> pdb=" O SER g 106 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE g 111 " --> pdb=" O VAL g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 138 removed outlier: 3.503A pdb=" N ASP g 131 " --> pdb=" O LYS g 127 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER g 134 " --> pdb=" O ASP g 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU g 136 " --> pdb=" O MET g 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS g 137 " --> pdb=" O ILE g 133 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 158 Processing helix chain 'g' and resid 168 through 181 removed outlier: 4.555A pdb=" N ASN g 173 " --> pdb=" O SER g 169 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU g 176 " --> pdb=" O CYS g 172 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS g 180 " --> pdb=" O LEU g 176 " (cutoff:3.500A) Processing helix chain 'g' and resid 208 through 210 No H-bonds generated for 'chain 'g' and resid 208 through 210' Processing helix chain 'g' and resid 275 through 283 removed outlier: 4.484A pdb=" N ILE g 282 " --> pdb=" O CYS g 278 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLN g 283 " --> pdb=" O GLU g 279 " (cutoff:3.500A) Processing helix chain 'g' and resid 297 through 306 removed outlier: 3.504A pdb=" N ALA g 306 " --> pdb=" O TYR g 302 " (cutoff:3.500A) Processing helix chain 'g' and resid 316 through 326 removed outlier: 3.610A pdb=" N ARG g 321 " --> pdb=" O THR g 317 " (cutoff:3.500A) Processing helix chain 'g' and resid 339 through 341 No H-bonds generated for 'chain 'g' and resid 339 through 341' Processing helix chain 'g' and resid 383 through 402 Processing helix chain 'g' and resid 412 through 425 removed outlier: 3.597A pdb=" N LYS g 424 " --> pdb=" O ALA g 420 " (cutoff:3.500A) Processing helix chain 'g' and resid 432 through 454 removed outlier: 3.594A pdb=" N ALA g 440 " --> pdb=" O TYR g 436 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU g 443 " --> pdb=" O VAL g 439 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLU g 444 " --> pdb=" O ALA g 440 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N VAL g 445 " --> pdb=" O GLN g 441 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE g 446 " --> pdb=" O ALA g 442 " (cutoff:3.500A) Proline residue: g 447 - end of helix removed outlier: 3.709A pdb=" N LEU g 450 " --> pdb=" O ILE g 446 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS g 454 " --> pdb=" O LEU g 450 " (cutoff:3.500A) Processing helix chain 'g' and resid 459 through 467 Processing helix chain 'g' and resid 489 through 492 No H-bonds generated for 'chain 'g' and resid 489 through 492' Processing helix chain 'g' and resid 498 through 517 Processing helix chain 'h' and resid 18 through 34 removed outlier: 3.571A pdb=" N LEU h 22 " --> pdb=" O ILE h 19 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL h 23 " --> pdb=" O PRO h 20 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER h 24 " --> pdb=" O GLN h 21 " (cutoff:3.500A) Processing helix chain 'h' and resid 37 through 39 No H-bonds generated for 'chain 'h' and resid 37 through 39' Processing helix chain 'h' and resid 62 through 67 Processing helix chain 'h' and resid 78 through 93 removed outlier: 3.567A pdb=" N THR h 82 " --> pdb=" O PRO h 78 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU h 83 " --> pdb=" O ALA h 79 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL h 84 " --> pdb=" O ALA h 80 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE h 86 " --> pdb=" O THR h 82 " (cutoff:3.500A) Processing helix chain 'h' and resid 100 through 116 removed outlier: 3.941A pdb=" N ALA h 105 " --> pdb=" O VAL h 101 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL h 112 " --> pdb=" O PHE h 108 " (cutoff:3.500A) Proline residue: h 114 - end of helix Processing helix chain 'h' and resid 122 through 142 removed outlier: 4.500A pdb=" N LYS h 141 " --> pdb=" O VAL h 137 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU h 142 " --> pdb=" O ASN h 138 " (cutoff:3.500A) Processing helix chain 'h' and resid 157 through 166 removed outlier: 3.850A pdb=" N THR h 165 " --> pdb=" O LYS h 161 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA h 166 " --> pdb=" O CYS h 162 " (cutoff:3.500A) Processing helix chain 'h' and resid 176 through 188 removed outlier: 3.768A pdb=" N MET h 182 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP h 185 " --> pdb=" O LYS h 181 " (cutoff:3.500A) Processing helix chain 'h' and resid 267 through 284 removed outlier: 4.012A pdb=" N VAL h 271 " --> pdb=" O TYR h 267 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU h 282 " --> pdb=" O LEU h 278 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU h 283 " --> pdb=" O TYR h 279 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS h 284 " --> pdb=" O ASP h 280 " (cutoff:3.500A) Processing helix chain 'h' and resid 304 through 307 No H-bonds generated for 'chain 'h' and resid 304 through 307' Processing helix chain 'h' and resid 320 through 329 removed outlier: 3.801A pdb=" N THR h 326 " --> pdb=" O ASP h 322 " (cutoff:3.500A) Processing helix chain 'h' and resid 383 through 391 removed outlier: 4.129A pdb=" N GLU h 387 " --> pdb=" O GLN h 384 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR h 389 " --> pdb=" O MET h 386 " (cutoff:3.500A) Processing helix chain 'h' and resid 393 through 405 removed outlier: 3.871A pdb=" N MET h 398 " --> pdb=" O HIS h 394 " (cutoff:3.500A) Processing helix chain 'h' and resid 416 through 430 removed outlier: 3.587A pdb=" N ARG h 429 " --> pdb=" O ARG h 425 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR h 430 " --> pdb=" O ASP h 426 " (cutoff:3.500A) Processing helix chain 'h' and resid 434 through 446 removed outlier: 3.741A pdb=" N LEU h 437 " --> pdb=" O LYS h 434 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE h 439 " --> pdb=" O GLN h 436 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS h 444 " --> pdb=" O ALA h 441 " (cutoff:3.500A) Processing helix chain 'h' and resid 448 through 457 Processing helix chain 'h' and resid 463 through 474 removed outlier: 3.780A pdb=" N LYS h 467 " --> pdb=" O ASN h 463 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU h 468 " --> pdb=" O ILE h 464 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG h 471 " --> pdb=" O LYS h 467 " (cutoff:3.500A) Processing helix chain 'h' and resid 500 through 519 removed outlier: 3.514A pdb=" N ILE h 517 " --> pdb=" O ALA h 513 " (cutoff:3.500A) Processing helix chain 'q' and resid 30 through 44 removed outlier: 3.879A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 73 Processing helix chain 'q' and resid 81 through 94 removed outlier: 3.863A pdb=" N MET q 85 " --> pdb=" O PRO q 81 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE q 86 " --> pdb=" O ALA q 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 121 removed outlier: 3.655A pdb=" N GLU q 117 " --> pdb=" O GLU q 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 125 through 145 removed outlier: 4.039A pdb=" N ILE q 129 " --> pdb=" O VAL q 125 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU q 130 " --> pdb=" O SER q 126 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU q 141 " --> pdb=" O ARG q 137 " (cutoff:3.500A) Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 157 through 163 removed outlier: 3.813A pdb=" N SER q 162 " --> pdb=" O ASP q 158 " (cutoff:3.500A) Processing helix chain 'q' and resid 165 through 171 Processing helix chain 'q' and resid 174 through 186 removed outlier: 4.400A pdb=" N PHE q 178 " --> pdb=" O ASN q 175 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU q 179 " --> pdb=" O GLU q 176 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS q 181 " --> pdb=" O PHE q 178 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA q 184 " --> pdb=" O LYS q 181 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA q 186 " --> pdb=" O ILE q 183 " (cutoff:3.500A) Processing helix chain 'q' and resid 188 through 190 No H-bonds generated for 'chain 'q' and resid 188 through 190' Processing helix chain 'q' and resid 212 through 214 No H-bonds generated for 'chain 'q' and resid 212 through 214' Processing helix chain 'q' and resid 263 through 284 Processing helix chain 'q' and resid 299 through 307 Processing helix chain 'q' and resid 320 through 328 removed outlier: 4.279A pdb=" N CYS q 325 " --> pdb=" O LEU q 321 " (cutoff:3.500A) Processing helix chain 'q' and resid 355 through 357 No H-bonds generated for 'chain 'q' and resid 355 through 357' Processing helix chain 'q' and resid 385 through 404 removed outlier: 3.742A pdb=" N ASP q 394 " --> pdb=" O ARG q 390 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR q 398 " --> pdb=" O ASP q 394 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG q 404 " --> pdb=" O LYS q 400 " (cutoff:3.500A) Processing helix chain 'q' and resid 414 through 427 removed outlier: 3.679A pdb=" N THR q 424 " --> pdb=" O ALA q 420 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 456 removed outlier: 4.409A pdb=" N ILE q 438 " --> pdb=" O GLN q 435 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA q 442 " --> pdb=" O LYS q 439 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU q 443 " --> pdb=" O LYS q 440 " (cutoff:3.500A) Proline residue: q 449 - end of helix removed outlier: 4.145A pdb=" N GLU q 454 " --> pdb=" O ALA q 451 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN q 455 " --> pdb=" O LEU q 452 " (cutoff:3.500A) Processing helix chain 'q' and resid 460 through 473 removed outlier: 3.702A pdb=" N GLN q 472 " --> pdb=" O TYR q 468 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU q 473 " --> pdb=" O ALA q 469 " (cutoff:3.500A) Processing helix chain 'q' and resid 492 through 495 No H-bonds generated for 'chain 'q' and resid 492 through 495' Processing helix chain 'q' and resid 501 through 519 removed outlier: 3.561A pdb=" N LYS q 509 " --> pdb=" O TYR q 505 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR q 512 " --> pdb=" O ILE q 508 " (cutoff:3.500A) Processing helix chain 'z' and resid 14 through 37 removed outlier: 4.114A pdb=" N VAL z 33 " --> pdb=" O GLY z 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 66 removed outlier: 3.507A pdb=" N HIS z 65 " --> pdb=" O ASN z 61 " (cutoff:3.500A) Processing helix chain 'z' and resid 72 through 88 removed outlier: 3.665A pdb=" N LEU z 76 " --> pdb=" O PRO z 72 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE z 87 " --> pdb=" O ALA z 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 92 through 110 removed outlier: 3.846A pdb=" N LYS z 104 " --> pdb=" O GLY z 100 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 116 through 137 removed outlier: 3.660A pdb=" N GLU z 128 " --> pdb=" O GLU z 124 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE z 133 " --> pdb=" O LYS z 129 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU z 136 " --> pdb=" O GLN z 132 " (cutoff:3.500A) Processing helix chain 'z' and resid 145 through 157 removed outlier: 4.232A pdb=" N VAL z 151 " --> pdb=" O THR z 147 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 4.795A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA z 171 " --> pdb=" O VAL z 167 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL z 173 " --> pdb=" O THR z 169 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER z 175 " --> pdb=" O ALA z 171 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE z 179 " --> pdb=" O SER z 175 " (cutoff:3.500A) Processing helix chain 'z' and resid 254 through 257 No H-bonds generated for 'chain 'z' and resid 254 through 257' Processing helix chain 'z' and resid 259 through 279 removed outlier: 3.664A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 306 removed outlier: 4.065A pdb=" N ASP z 303 " --> pdb=" O PRO z 299 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 326 Processing helix chain 'z' and resid 336 through 338 No H-bonds generated for 'chain 'z' and resid 336 through 338' Processing helix chain 'z' and resid 341 through 343 No H-bonds generated for 'chain 'z' and resid 341 through 343' Processing helix chain 'z' and resid 381 through 403 Processing helix chain 'z' and resid 413 through 422 Processing helix chain 'z' and resid 434 through 444 removed outlier: 3.656A pdb=" N ASP z 442 " --> pdb=" O GLN z 438 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA z 443 " --> pdb=" O ALA z 439 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU z 444 " --> pdb=" O PHE z 440 " (cutoff:3.500A) Processing helix chain 'z' and resid 446 through 453 removed outlier: 3.507A pdb=" N ALA z 452 " --> pdb=" O PRO z 448 " (cutoff:3.500A) Processing helix chain 'z' and resid 461 through 466 Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 498 through 517 removed outlier: 4.389A pdb=" N LEU z 517 " --> pdb=" O THR z 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 31 removed outlier: 4.012A pdb=" N ILE A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 70 through 86 removed outlier: 4.319A pdb=" N GLU A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.873A pdb=" N ALA A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 133 removed outlier: 3.763A pdb=" N ARG A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.779A pdb=" N MET A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 178 removed outlier: 3.554A pdb=" N VAL A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 175 " --> pdb=" O MET A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 273 through 280 Processing helix chain 'A' and resid 296 through 302 removed outlier: 5.058A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'A' and resid 386 through 403 removed outlier: 3.693A pdb=" N VAL A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 401 " --> pdb=" O CYS A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.744A pdb=" N ASN A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 443 removed outlier: 4.316A pdb=" N LEU A 436 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 438 " --> pdb=" O GLN A 435 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG A 443 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.931A pdb=" N VAL A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 21 through 38 removed outlier: 4.129A pdb=" N ARG B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 118 removed outlier: 3.544A pdb=" N SER B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 144 removed outlier: 3.781A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 165 Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 264 through 282 Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 381 through 402 removed outlier: 4.927A pdb=" N ALA B 386 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 388 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 389 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 393 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 394 " --> pdb=" O HIS B 391 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 397 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 431 through 452 removed outlier: 3.974A pdb=" N MET B 436 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER B 438 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 445 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.700A pdb=" N ILE B 450 " --> pdb=" O PRO B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 471 removed outlier: 3.995A pdb=" N GLU B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 515 removed outlier: 3.803A pdb=" N GLN B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.594A pdb=" N SER D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 removed outlier: 3.739A pdb=" N LEU D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 126 removed outlier: 3.839A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 113 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 180 through 193 Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 285 through 293 Processing helix chain 'D' and resid 311 through 316 Processing helix chain 'D' and resid 330 through 340 removed outlier: 4.034A pdb=" N GLU D 334 " --> pdb=" O ARG D 330 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 369 No H-bonds generated for 'chain 'D' and resid 367 through 369' Processing helix chain 'D' and resid 396 through 412 removed outlier: 4.113A pdb=" N ALA D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 417 No H-bonds generated for 'chain 'D' and resid 414 through 417' Processing helix chain 'D' and resid 427 through 442 removed outlier: 3.683A pdb=" N THR D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 468 removed outlier: 3.871A pdb=" N TYR D 449 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL D 451 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP D 456 " --> pdb=" O ALA D 453 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA D 457 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL D 460 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE D 461 " --> pdb=" O MET D 458 " (cutoff:3.500A) Proline residue: D 462 - end of helix removed outlier: 4.263A pdb=" N ASN D 468 " --> pdb=" O LEU D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 486 removed outlier: 3.720A pdb=" N GLN D 486 " --> pdb=" O ASN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 506 No H-bonds generated for 'chain 'D' and resid 503 through 506' Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 30 through 48 removed outlier: 3.541A pdb=" N LYS E 35 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS E 37 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE E 38 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET E 39 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS E 42 " --> pdb=" O MET E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 80 Processing helix chain 'E' and resid 86 through 96 Processing helix chain 'E' and resid 106 through 125 removed outlier: 3.691A pdb=" N VAL E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 150 removed outlier: 4.198A pdb=" N GLU E 146 " --> pdb=" O ARG E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 173 removed outlier: 3.797A pdb=" N THR E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR E 172 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 173 " --> pdb=" O ALA E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 195 removed outlier: 4.997A pdb=" N ARG E 183 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET E 185 " --> pdb=" O HIS E 182 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ALA E 186 " --> pdb=" O ARG E 183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL E 193 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 295 removed outlier: 4.383A pdb=" N GLN E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 330 through 336 removed outlier: 4.248A pdb=" N ALA E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 408 removed outlier: 4.154A pdb=" N LEU E 402 " --> pdb=" O ALA E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 412 No H-bonds generated for 'chain 'E' and resid 410 through 412' Processing helix chain 'E' and resid 424 through 436 removed outlier: 3.598A pdb=" N ALA E 432 " --> pdb=" O SER E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 465 removed outlier: 4.025A pdb=" N ARG E 449 " --> pdb=" O TYR E 446 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA E 452 " --> pdb=" O ARG E 449 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP E 453 " --> pdb=" O ALA E 450 " (cutoff:3.500A) Proline residue: E 459 - end of helix removed outlier: 3.625A pdb=" N LEU E 462 " --> pdb=" O PRO E 459 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU E 464 " --> pdb=" O ALA E 461 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN E 465 " --> pdb=" O LEU E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 483 removed outlier: 3.893A pdb=" N MET E 474 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'E' and resid 510 through 528 removed outlier: 3.539A pdb=" N GLN E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET E 523 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET E 526 " --> pdb=" O GLN E 522 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 33 Processing helix chain 'G' and resid 62 through 68 removed outlier: 3.846A pdb=" N GLU G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 88 removed outlier: 3.544A pdb=" N SER G 83 " --> pdb=" O MET G 79 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU G 88 " --> pdb=" O ARG G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 112 removed outlier: 3.748A pdb=" N ILE G 98 " --> pdb=" O THR G 94 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU G 103 " --> pdb=" O ILE G 99 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET G 104 " --> pdb=" O LEU G 100 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS G 110 " --> pdb=" O SER G 106 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE G 111 " --> pdb=" O VAL G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 138 removed outlier: 3.732A pdb=" N SER G 134 " --> pdb=" O ASP G 130 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 158 Processing helix chain 'G' and resid 168 through 179 removed outlier: 4.722A pdb=" N ASN G 173 " --> pdb=" O SER G 169 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU G 176 " --> pdb=" O CYS G 172 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA G 178 " --> pdb=" O ILE G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 210 No H-bonds generated for 'chain 'G' and resid 208 through 210' Processing helix chain 'G' and resid 276 through 283 removed outlier: 3.825A pdb=" N ILE G 282 " --> pdb=" O CYS G 278 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLN G 283 " --> pdb=" O GLU G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 306 removed outlier: 3.688A pdb=" N ALA G 306 " --> pdb=" O TYR G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 326 removed outlier: 3.920A pdb=" N ARG G 321 " --> pdb=" O THR G 317 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS G 326 " --> pdb=" O ILE G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 341 No H-bonds generated for 'chain 'G' and resid 339 through 341' Processing helix chain 'G' and resid 383 through 403 Processing helix chain 'G' and resid 412 through 424 removed outlier: 3.558A pdb=" N LYS G 424 " --> pdb=" O ALA G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 442 removed outlier: 4.131A pdb=" N TRP G 434 " --> pdb=" O VAL G 431 " (cutoff:3.500A) Proline residue: G 435 - end of helix removed outlier: 3.999A pdb=" N VAL G 439 " --> pdb=" O TYR G 436 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA G 442 " --> pdb=" O VAL G 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 454 removed outlier: 3.717A pdb=" N LEU G 450 " --> pdb=" O ILE G 446 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS G 454 " --> pdb=" O LEU G 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 467 Processing helix chain 'G' and resid 489 through 492 No H-bonds generated for 'chain 'G' and resid 489 through 492' Processing helix chain 'G' and resid 498 through 517 removed outlier: 3.536A pdb=" N LEU G 514 " --> pdb=" O GLU G 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 36 removed outlier: 3.556A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 68 removed outlier: 3.770A pdb=" N LEU H 68 " --> pdb=" O THR H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 87 removed outlier: 5.048A pdb=" N ILE H 82 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP H 87 " --> pdb=" O ALA H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 Proline residue: H 110 - end of helix removed outlier: 3.948A pdb=" N GLU H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 138 removed outlier: 3.895A pdb=" N LYS H 137 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU H 138 " --> pdb=" O ASN H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 162 removed outlier: 3.831A pdb=" N CYS H 158 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA H 162 " --> pdb=" O ALA H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 186 removed outlier: 4.072A pdb=" N PHE H 174 " --> pdb=" O GLN H 170 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU H 186 " --> pdb=" O ALA H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 267 through 284 removed outlier: 4.086A pdb=" N ILE H 281 " --> pdb=" O LYS H 277 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS H 282 " --> pdb=" O LEU H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 304 Processing helix chain 'H' and resid 316 through 321 Processing helix chain 'H' and resid 353 through 355 No H-bonds generated for 'chain 'H' and resid 353 through 355' Processing helix chain 'H' and resid 381 through 388 Processing helix chain 'H' and resid 392 through 401 Processing helix chain 'H' and resid 411 through 425 removed outlier: 3.666A pdb=" N ARG H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 3.596A pdb=" N LEU H 433 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE H 435 " --> pdb=" O GLN H 432 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY H 436 " --> pdb=" O LEU H 433 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS H 440 " --> pdb=" O ALA H 437 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA H 441 " --> pdb=" O TYR H 438 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE H 444 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix removed outlier: 3.918A pdb=" N CYS H 450 " --> pdb=" O ARG H 447 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP H 451 " --> pdb=" O GLN H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 470 removed outlier: 3.812A pdb=" N LEU H 464 " --> pdb=" O ILE H 460 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG H 467 " --> pdb=" O LYS H 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 515 removed outlier: 3.580A pdb=" N ILE H 513 " --> pdb=" O ALA H 509 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 44 removed outlier: 3.881A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 73 Processing helix chain 'Q' and resid 81 through 94 removed outlier: 3.863A pdb=" N MET Q 85 " --> pdb=" O PRO Q 81 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 121 removed outlier: 3.655A pdb=" N GLU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 145 removed outlier: 4.039A pdb=" N ILE Q 129 " --> pdb=" O VAL Q 125 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU Q 130 " --> pdb=" O SER Q 126 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU Q 141 " --> pdb=" O ARG Q 137 " (cutoff:3.500A) Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 157 through 163 removed outlier: 3.814A pdb=" N SER Q 162 " --> pdb=" O ASP Q 158 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 171 Processing helix chain 'Q' and resid 174 through 186 removed outlier: 4.400A pdb=" N PHE Q 178 " --> pdb=" O ASN Q 175 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU Q 179 " --> pdb=" O GLU Q 176 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS Q 181 " --> pdb=" O PHE Q 178 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA Q 184 " --> pdb=" O LYS Q 181 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA Q 186 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) Processing helix chain 'Q' and resid 188 through 190 No H-bonds generated for 'chain 'Q' and resid 188 through 190' Processing helix chain 'Q' and resid 212 through 214 No H-bonds generated for 'chain 'Q' and resid 212 through 214' Processing helix chain 'Q' and resid 263 through 284 Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'Q' and resid 320 through 328 removed outlier: 4.280A pdb=" N CYS Q 325 " --> pdb=" O LEU Q 321 " (cutoff:3.500A) Processing helix chain 'Q' and resid 355 through 357 No H-bonds generated for 'chain 'Q' and resid 355 through 357' Processing helix chain 'Q' and resid 385 through 404 removed outlier: 3.742A pdb=" N ASP Q 394 " --> pdb=" O ARG Q 390 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR Q 398 " --> pdb=" O ASP Q 394 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG Q 404 " --> pdb=" O LYS Q 400 " (cutoff:3.500A) Processing helix chain 'Q' and resid 414 through 427 removed outlier: 3.679A pdb=" N THR Q 424 " --> pdb=" O ALA Q 420 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 456 removed outlier: 4.409A pdb=" N ILE Q 438 " --> pdb=" O GLN Q 435 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA Q 442 " --> pdb=" O LYS Q 439 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU Q 443 " --> pdb=" O LYS Q 440 " (cutoff:3.500A) Proline residue: Q 449 - end of helix removed outlier: 4.145A pdb=" N GLU Q 454 " --> pdb=" O ALA Q 451 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN Q 455 " --> pdb=" O LEU Q 452 " (cutoff:3.500A) Processing helix chain 'Q' and resid 460 through 473 removed outlier: 3.702A pdb=" N GLN Q 472 " --> pdb=" O TYR Q 468 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU Q 473 " --> pdb=" O ALA Q 469 " (cutoff:3.500A) Processing helix chain 'Q' and resid 492 through 495 No H-bonds generated for 'chain 'Q' and resid 492 through 495' Processing helix chain 'Q' and resid 501 through 519 removed outlier: 3.560A pdb=" N LYS Q 509 " --> pdb=" O TYR Q 505 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR Q 512 " --> pdb=" O ILE Q 508 " (cutoff:3.500A) Processing helix chain 'Z' and resid 14 through 33 removed outlier: 3.930A pdb=" N ALA Z 26 " --> pdb=" O VAL Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 66 removed outlier: 3.757A pdb=" N HIS Z 65 " --> pdb=" O ASN Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 88 removed outlier: 4.186A pdb=" N LEU Z 76 " --> pdb=" O PRO Z 72 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE Z 77 " --> pdb=" O THR Z 73 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA Z 81 " --> pdb=" O ILE Z 77 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA Z 83 " --> pdb=" O LYS Z 79 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE Z 87 " --> pdb=" O ALA Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 110 removed outlier: 3.522A pdb=" N LYS Z 104 " --> pdb=" O GLY Z 100 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 137 removed outlier: 3.528A pdb=" N GLU Z 124 " --> pdb=" O THR Z 120 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS Z 129 " --> pdb=" O ALA Z 125 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU Z 136 " --> pdb=" O GLN Z 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 145 through 157 Processing helix chain 'Z' and resid 162 through 171 removed outlier: 4.701A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 173 through 178 Processing helix chain 'Z' and resid 259 through 278 Processing helix chain 'Z' and resid 299 through 306 Processing helix chain 'Z' and resid 319 through 326 removed outlier: 3.835A pdb=" N ARG Z 323 " --> pdb=" O ARG Z 319 " (cutoff:3.500A) Processing helix chain 'Z' and resid 382 through 403 Processing helix chain 'Z' and resid 413 through 424 removed outlier: 3.649A pdb=" N LYS Z 424 " --> pdb=" O GLU Z 420 " (cutoff:3.500A) Processing helix chain 'Z' and resid 434 through 443 Processing helix chain 'Z' and resid 446 through 454 Processing helix chain 'Z' and resid 461 through 466 Processing helix chain 'Z' and resid 498 through 516 removed outlier: 4.425A pdb=" N GLN Z 503 " --> pdb=" O CYS Z 499 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR Z 509 " --> pdb=" O LEU Z 505 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL Z 510 " --> pdb=" O HIS Z 506 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'a' and resid 195 through 200 removed outlier: 7.158A pdb=" N ALA a 373 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU a 198 " --> pdb=" O ALA a 373 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE a 375 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA a 200 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU a 377 " --> pdb=" O ALA a 200 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET a 209 " --> pdb=" O ILE a 376 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= C, first strand: chain 'a' and resid 234 through 237 removed outlier: 6.764A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= E, first strand: chain 'a' and resid 486 through 488 Processing sheet with id= F, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.324A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'b' and resid 290 through 292 Processing sheet with id= H, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= I, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= J, first strand: chain 'd' and resid 212 through 214 removed outlier: 5.924A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.650A pdb=" N LEU d 361 " --> pdb=" O THR d 377 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= M, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= N, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= O, first strand: chain 'e' and resid 248 through 250 removed outlier: 6.049A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= Q, first strand: chain 'g' and resid 47 through 50 Processing sheet with id= R, first strand: chain 'g' and resid 199 through 202 Processing sheet with id= S, first strand: chain 'g' and resid 216 through 219 Processing sheet with id= T, first strand: chain 'g' and resid 237 through 239 removed outlier: 7.132A pdb=" N VAL g 288 " --> pdb=" O VAL g 238 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'g' and resid 406 through 408 Processing sheet with id= V, first strand: chain 'g' and resid 477 through 479 Processing sheet with id= W, first strand: chain 'h' and resid 47 through 50 removed outlier: 3.560A pdb=" N ILE h 49 " --> pdb=" O THR h 57 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'h' and resid 202 through 205 removed outlier: 3.820A pdb=" N GLY h 380 " --> pdb=" O VAL h 204 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'h' and resid 241 through 243 removed outlier: 7.043A pdb=" N VAL h 292 " --> pdb=" O ALA h 242 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE h 313 " --> pdb=" O VAL h 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'h' and resid 353 through 357 Processing sheet with id= AA, first strand: chain 'h' and resid 409 through 411 Processing sheet with id= AB, first strand: chain 'h' and resid 479 through 481 Processing sheet with id= AC, first strand: chain 'q' and resid 54 through 56 Processing sheet with id= AD, first strand: chain 'q' and resid 204 through 208 removed outlier: 6.545A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'q' and resid 408 through 410 Processing sheet with id= AF, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= AG, first strand: chain 'z' and resid 45 through 47 removed outlier: 3.504A pdb=" N LYS z 55 " --> pdb=" O LEU z 47 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.662A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'z' and resid 209 through 211 Processing sheet with id= AJ, first strand: chain 'z' and resid 227 through 233 removed outlier: 3.711A pdb=" N TYR z 229 " --> pdb=" O GLY z 288 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'z' and resid 407 through 409 Processing sheet with id= AL, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= AM, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= AN, first strand: chain 'A' and resid 213 through 216 removed outlier: 3.703A pdb=" N LEU A 216 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE A 362 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU A 354 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= AP, first strand: chain 'B' and resid 50 through 52 removed outlier: 3.548A pdb=" N THR B 64 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N MET B 62 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'B' and resid 201 through 205 removed outlier: 5.687A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= AS, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= AT, first strand: chain 'D' and resid 212 through 214 removed outlier: 5.773A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'D' and resid 297 through 299 removed outlier: 5.287A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'D' and resid 362 through 367 removed outlier: 3.865A pdb=" N GLU D 363 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS D 375 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= AX, first strand: chain 'D' and resid 491 through 494 Processing sheet with id= AY, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= AZ, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= BA, first strand: chain 'G' and resid 47 through 49 Processing sheet with id= BB, first strand: chain 'G' and resid 199 through 202 Processing sheet with id= BC, first strand: chain 'G' and resid 216 through 219 Processing sheet with id= BD, first strand: chain 'G' and resid 237 through 239 removed outlier: 7.206A pdb=" N VAL G 288 " --> pdb=" O VAL G 238 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'G' and resid 406 through 408 Processing sheet with id= BF, first strand: chain 'G' and resid 477 through 479 Processing sheet with id= BG, first strand: chain 'H' and resid 47 through 49 Processing sheet with id= BH, first strand: chain 'H' and resid 197 through 200 removed outlier: 6.430A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'H' and resid 237 through 239 removed outlier: 6.485A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'H' and resid 349 through 353 removed outlier: 3.884A pdb=" N THR H 351 " --> pdb=" O TYR H 358 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU H 356 " --> pdb=" O ILE H 353 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= BL, first strand: chain 'H' and resid 475 through 477 Processing sheet with id= BM, first strand: chain 'Q' and resid 54 through 56 Processing sheet with id= BN, first strand: chain 'Q' and resid 204 through 208 removed outlier: 6.546A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE Q 207 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU Q 377 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain 'Q' and resid 408 through 410 Processing sheet with id= BP, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= BQ, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= BR, first strand: chain 'Z' and resid 191 through 197 removed outlier: 6.974A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'Z' and resid 209 through 211 removed outlier: 3.553A pdb=" N GLU Z 358 " --> pdb=" O LEU Z 355 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'Z' and resid 477 through 479 2379 hydrogen bonds defined for protein. 6480 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: 18.42 Time building geometry restraints manager: 19.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 19155 1.34 - 1.46: 11976 1.46 - 1.59: 28941 1.59 - 1.71: 6 1.71 - 1.84: 618 Bond restraints: 60696 Sorted by residual: bond pdb=" N ARG z 28 " pdb=" CA ARG z 28 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.23e-02 6.61e+03 7.51e+00 bond pdb=" N GLY e 30 " pdb=" CA GLY e 30 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.64e-02 3.72e+03 7.21e+00 bond pdb=" N SER E 539 " pdb=" CA SER E 539 " ideal model delta sigma weight residual 1.461 1.496 -0.034 1.30e-02 5.92e+03 7.04e+00 bond pdb=" N SER e 539 " pdb=" CA SER e 539 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.00e-02 1.00e+04 6.49e+00 bond pdb=" N ARG Z 28 " pdb=" CA ARG Z 28 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.22e+00 ... (remaining 60691 not shown) Histogram of bond angle deviations from ideal: 97.59 - 105.38: 933 105.38 - 113.18: 34619 113.18 - 120.97: 29167 120.97 - 128.76: 16904 128.76 - 136.55: 269 Bond angle restraints: 81892 Sorted by residual: angle pdb=" N VAL E 177 " pdb=" CA VAL E 177 " pdb=" C VAL E 177 " ideal model delta sigma weight residual 112.29 105.89 6.40 9.40e-01 1.13e+00 4.64e+01 angle pdb=" N ASN B 473 " pdb=" CA ASN B 473 " pdb=" C ASN B 473 " ideal model delta sigma weight residual 110.33 117.35 -7.02 1.29e+00 6.01e-01 2.96e+01 angle pdb=" CA LEU z 34 " pdb=" CB LEU z 34 " pdb=" CG LEU z 34 " ideal model delta sigma weight residual 116.30 97.59 18.71 3.50e+00 8.16e-02 2.86e+01 angle pdb=" N GLY a 162 " pdb=" CA GLY a 162 " pdb=" C GLY a 162 " ideal model delta sigma weight residual 113.27 120.07 -6.80 1.33e+00 5.65e-01 2.62e+01 angle pdb=" C LEU E 443 " pdb=" N GLU E 444 " pdb=" CA GLU E 444 " ideal model delta sigma weight residual 120.38 127.55 -7.17 1.46e+00 4.69e-01 2.41e+01 ... (remaining 81887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.97: 35601 26.97 - 53.93: 1827 53.93 - 80.90: 182 80.90 - 107.86: 10 107.86 - 134.83: 2 Dihedral angle restraints: 37622 sinusoidal: 15005 harmonic: 22617 Sorted by residual: dihedral pdb=" CA SER B 54 " pdb=" C SER B 54 " pdb=" N SER B 55 " pdb=" CA SER B 55 " ideal model delta harmonic sigma weight residual -180.00 -130.16 -49.84 0 5.00e+00 4.00e-02 9.94e+01 dihedral pdb=" CB CYS H 326 " pdb=" SG CYS H 326 " pdb=" SG CYS H 345 " pdb=" CB CYS H 345 " ideal model delta sinusoidal sigma weight residual 93.00 160.24 -67.24 1 1.00e+01 1.00e-02 5.89e+01 dihedral pdb=" CA ALA b 59 " pdb=" C ALA b 59 " pdb=" N SER b 60 " pdb=" CA SER b 60 " ideal model delta harmonic sigma weight residual -180.00 -142.64 -37.36 0 5.00e+00 4.00e-02 5.58e+01 ... (remaining 37619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 9141 0.103 - 0.207: 664 0.207 - 0.310: 38 0.310 - 0.414: 4 0.414 - 0.517: 1 Chirality restraints: 9848 Sorted by residual: chirality pdb=" CB ILE h 19 " pdb=" CA ILE h 19 " pdb=" CG1 ILE h 19 " pdb=" CG2 ILE h 19 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CB ILE a 376 " pdb=" CA ILE a 376 " pdb=" CG1 ILE a 376 " pdb=" CG2 ILE a 376 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CB ILE D 238 " pdb=" CA ILE D 238 " pdb=" CG1 ILE D 238 " pdb=" CG2 ILE D 238 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 9845 not shown) Planarity restraints: 10492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU e 538 " -0.033 2.00e-02 2.50e+03 6.61e-02 4.37e+01 pdb=" C GLU e 538 " 0.114 2.00e-02 2.50e+03 pdb=" O GLU e 538 " -0.044 2.00e-02 2.50e+03 pdb=" N SER e 539 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 27 " -0.031 2.00e-02 2.50e+03 6.08e-02 3.69e+01 pdb=" C ALA Z 27 " 0.105 2.00e-02 2.50e+03 pdb=" O ALA Z 27 " -0.039 2.00e-02 2.50e+03 pdb=" N ARG Z 28 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA z 27 " -0.030 2.00e-02 2.50e+03 5.90e-02 3.48e+01 pdb=" C ALA z 27 " 0.102 2.00e-02 2.50e+03 pdb=" O ALA z 27 " -0.038 2.00e-02 2.50e+03 pdb=" N ARG z 28 " -0.034 2.00e-02 2.50e+03 ... (remaining 10489 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 11584 2.77 - 3.30: 60876 3.30 - 3.84: 108930 3.84 - 4.37: 125200 4.37 - 4.90: 199868 Nonbonded interactions: 506458 Sorted by model distance: nonbonded pdb=" O CYS H 158 " pdb=" OG1 THR H 161 " model vdw 2.238 2.440 nonbonded pdb=" OH TYR a 181 " pdb=" OG1 THR a 371 " model vdw 2.249 2.440 nonbonded pdb=" O MET H 160 " pdb=" OG SER H 164 " model vdw 2.270 2.440 nonbonded pdb=" OG SER a 222 " pdb=" O ALA a 305 " model vdw 2.276 2.440 nonbonded pdb=" O ALA d 433 " pdb=" OG1 THR d 437 " model vdw 2.284 2.440 ... (remaining 506453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 13 through 528) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 24 through 243 or resid 263 through 520)) selection = chain 'b' } ncs_group { reference = chain 'D' selection = (chain 'd' and (resid 30 through 256 or resid 280 through 539)) } ncs_group { reference = (chain 'E' and resid 25 through 540) selection = (chain 'e' and resid 25 through 540) } ncs_group { reference = (chain 'G' and (resid 17 through 241 or resid 274 through 525)) selection = chain 'g' } ncs_group { reference = chain 'H' selection = (chain 'h' and (resid 12 through 250 or resid 266 through 529)) } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = (chain 'Z' and resid 13 through 522) selection = (chain 'z' and (resid 13 through 240 or resid 255 through 522)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.340 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: 0.040 Extract box with map and model: 4.240 Check model and map are aligned: 0.660 Set scattering table: 0.400 Process input model: 117.650 Find NCS groups from input model: 5.340 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.005 0.077 60696 Z= 0.305 Angle : 0.959 18.710 81892 Z= 0.528 Chirality : 0.056 0.517 9848 Planarity : 0.007 0.117 10492 Dihedral : 15.671 134.831 22956 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.19 % Favored : 91.80 % Rotamer: Outliers : 0.76 % Allowed : 9.59 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.22 % 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: -4.47 (0.07), residues: 7802 helix: -2.81 (0.06), residues: 3757 sheet: -3.02 (0.22), residues: 399 loop : -3.08 (0.09), residues: 3646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 130 HIS 0.014 0.001 HIS b 285 PHE 0.028 0.002 PHE a 239 TYR 0.020 0.002 TYR B 299 ARG 0.021 0.001 ARG z 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 714 time to evaluate : 5.152 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 7 residues processed: 754 average time/residue: 0.6425 time to fit residues: 788.4059 Evaluate side-chains 495 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 488 time to evaluate : 5.151 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4094 time to fit residues: 12.5222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 657 optimal weight: 8.9990 chunk 590 optimal weight: 0.9990 chunk 327 optimal weight: 20.0000 chunk 201 optimal weight: 6.9990 chunk 398 optimal weight: 20.0000 chunk 315 optimal weight: 5.9990 chunk 610 optimal weight: 20.0000 chunk 236 optimal weight: 0.1980 chunk 371 optimal weight: 8.9990 chunk 454 optimal weight: 6.9990 chunk 707 optimal weight: 20.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 135 ASN a 164 ASN a 201 HIS a 393 HIS ** a 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 78 ASN b 174 HIS b 175 HIS ** b 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 298 ASN ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 453 ASN ** d 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 172 ASN d 231 GLN d 235 ASN ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 406 HIS d 472 ASN ** e 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 275 GLN g 300 GLN g 405 GLN g 433 GLN g 480 ASN h 195 GLN h 245 ASN h 363 ASN h 505 ASN q 41 GLN q 145 ASN q 172 GLN q 219 HIS q 274 ASN q 306 ASN q 316 ASN q 461 ASN z 68 GLN z 105 GLN z 346 HIS z 438 GLN z 460 GLN A 30 ASN A 135 ASN A 139 ASN A 193 ASN A 196 ASN A 242 GLN A 366 ASN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN B 91 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN B 391 HIS B 473 ASN B 502 GLN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN D 80 GLN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN D 231 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN D 472 ASN E 37 HIS ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN E 311 ASN ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 ASN E 515 GLN G 25 ASN G 300 GLN G 389 ASN G 433 GLN G 480 ASN H 25 ASN H 30 GLN H 241 ASN H 282 HIS Q 41 GLN Q 67 ASN Q 145 ASN Q 219 HIS Q 306 ASN Q 316 ASN Q 471 HIS ** Z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 HIS ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 218 HIS Z 497 ASN Z 514 ASN Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 60696 Z= 0.211 Angle : 0.665 11.842 81892 Z= 0.343 Chirality : 0.043 0.257 9848 Planarity : 0.005 0.105 10492 Dihedral : 6.680 125.600 8354 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.63 % Allowed : 15.70 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.02 (0.08), residues: 7802 helix: -1.23 (0.08), residues: 3830 sheet: -3.05 (0.24), residues: 372 loop : -2.76 (0.09), residues: 3600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 130 HIS 0.014 0.001 HIS a 201 PHE 0.030 0.002 PHE H 174 TYR 0.021 0.002 TYR h 236 ARG 0.008 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 523 time to evaluate : 5.514 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 50 residues processed: 594 average time/residue: 0.5925 time to fit residues: 596.9219 Evaluate side-chains 504 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 454 time to evaluate : 5.178 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.4440 time to fit residues: 48.8812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 393 optimal weight: 20.0000 chunk 219 optimal weight: 7.9990 chunk 588 optimal weight: 4.9990 chunk 481 optimal weight: 30.0000 chunk 195 optimal weight: 0.8980 chunk 708 optimal weight: 4.9990 chunk 765 optimal weight: 5.9990 chunk 631 optimal weight: 5.9990 chunk 702 optimal weight: 10.0000 chunk 241 optimal weight: 9.9990 chunk 568 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 473 ASN ** d 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 406 HIS d 482 ASN ** e 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 469 ASN ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 220 ASN ** h 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 452 GLN ** q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 294 GLN A 193 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 ASN E 411 ASN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 461 ASN ** Z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 60696 Z= 0.206 Angle : 0.649 11.764 81892 Z= 0.332 Chirality : 0.043 0.271 9848 Planarity : 0.004 0.099 10492 Dihedral : 6.336 122.256 8354 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 22.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.00 % Favored : 91.99 % Rotamer: Outliers : 1.80 % Allowed : 18.18 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.09), residues: 7802 helix: -0.51 (0.08), residues: 3839 sheet: -2.97 (0.23), residues: 424 loop : -2.62 (0.10), residues: 3539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Q 319 HIS 0.009 0.001 HIS E 403 PHE 0.040 0.002 PHE B 155 TYR 0.027 0.002 TYR G 246 ARG 0.007 0.000 ARG D 539 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 491 time to evaluate : 5.247 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 outliers start: 118 outliers final: 40 residues processed: 583 average time/residue: 0.5953 time to fit residues: 595.0887 Evaluate side-chains 483 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 443 time to evaluate : 5.240 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.4755 time to fit residues: 42.4550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 700 optimal weight: 9.9990 chunk 532 optimal weight: 30.0000 chunk 367 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 338 optimal weight: 8.9990 chunk 475 optimal weight: 0.7980 chunk 711 optimal weight: 1.9990 chunk 752 optimal weight: 8.9990 chunk 371 optimal weight: 5.9990 chunk 674 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 353 GLN ** a 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 406 HIS e 290 GLN ** e 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 60 ASN h 452 GLN ** q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 383 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 60696 Z= 0.181 Angle : 0.631 12.040 81892 Z= 0.321 Chirality : 0.043 0.252 9848 Planarity : 0.004 0.098 10492 Dihedral : 6.106 116.103 8354 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.63 % Favored : 92.36 % Rotamer: Outliers : 1.44 % Allowed : 19.78 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.04 (0.09), residues: 7802 helix: -0.19 (0.08), residues: 3842 sheet: -2.91 (0.23), residues: 467 loop : -2.49 (0.10), residues: 3493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Q 319 HIS 0.018 0.001 HIS Q 303 PHE 0.031 0.002 PHE d 316 TYR 0.024 0.001 TYR h 236 ARG 0.010 0.000 ARG a 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 472 time to evaluate : 5.218 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 outliers start: 94 outliers final: 46 residues processed: 539 average time/residue: 0.5690 time to fit residues: 527.2755 Evaluate side-chains 484 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 438 time to evaluate : 5.226 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.4479 time to fit residues: 45.9904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 627 optimal weight: 8.9990 chunk 427 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 560 optimal weight: 20.0000 chunk 310 optimal weight: 6.9990 chunk 642 optimal weight: 0.9990 chunk 520 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 384 optimal weight: 6.9990 chunk 675 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 406 HIS ** e 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 140 HIS ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 ASN ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 HIS ** Z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 60696 Z= 0.171 Angle : 0.627 10.768 81892 Z= 0.316 Chirality : 0.043 0.274 9848 Planarity : 0.004 0.099 10492 Dihedral : 5.888 109.989 8354 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.56 % Favored : 92.43 % Rotamer: Outliers : 1.10 % Allowed : 21.37 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.84 (0.09), residues: 7802 helix: -0.00 (0.08), residues: 3836 sheet: -2.79 (0.23), residues: 451 loop : -2.42 (0.10), residues: 3515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Q 319 HIS 0.012 0.001 HIS E 403 PHE 0.052 0.001 PHE b 304 TYR 0.022 0.001 TYR G 246 ARG 0.012 0.000 ARG a 480 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 456 time to evaluate : 5.239 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 outliers start: 72 outliers final: 29 residues processed: 514 average time/residue: 0.5797 time to fit residues: 515.0499 Evaluate side-chains 459 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 430 time to evaluate : 5.188 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4596 time to fit residues: 32.2587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 253 optimal weight: 20.0000 chunk 678 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 442 optimal weight: 30.0000 chunk 185 optimal weight: 5.9990 chunk 753 optimal weight: 7.9990 chunk 625 optimal weight: 3.9990 chunk 348 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 249 optimal weight: 5.9990 chunk 395 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 30 ASN ** a 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 91 GLN ** b 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 406 HIS e 37 HIS ** e 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 452 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 140 HIS ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 294 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 60696 Z= 0.257 Angle : 0.681 12.152 81892 Z= 0.346 Chirality : 0.044 0.303 9848 Planarity : 0.004 0.097 10492 Dihedral : 5.980 113.671 8354 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 26.33 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.66 % Favored : 91.32 % Rotamer: Outliers : 1.41 % Allowed : 22.98 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.79 (0.09), residues: 7802 helix: 0.04 (0.08), residues: 3852 sheet: -2.82 (0.23), residues: 471 loop : -2.40 (0.10), residues: 3479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Q 319 HIS 0.015 0.001 HIS E 403 PHE 0.036 0.002 PHE B 155 TYR 0.023 0.002 TYR h 236 ARG 0.016 0.001 ARG a 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 445 time to evaluate : 5.256 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 outliers start: 92 outliers final: 46 residues processed: 513 average time/residue: 0.5881 time to fit residues: 521.6992 Evaluate side-chains 475 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 429 time to evaluate : 5.219 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.4612 time to fit residues: 47.6210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 726 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 429 optimal weight: 8.9990 chunk 550 optimal weight: 30.0000 chunk 426 optimal weight: 6.9990 chunk 634 optimal weight: 1.9990 chunk 420 optimal weight: 6.9990 chunk 750 optimal weight: 7.9990 chunk 469 optimal weight: 0.7980 chunk 457 optimal weight: 0.0030 chunk 346 optimal weight: 30.0000 overall best weight: 3.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 30 ASN b 73 ASN ** b 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 406 HIS e 416 ASN ** e 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 245 ASN ** h 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN Q 303 HIS ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 60696 Z= 0.188 Angle : 0.655 12.550 81892 Z= 0.329 Chirality : 0.043 0.271 9848 Planarity : 0.004 0.097 10492 Dihedral : 5.809 104.302 8354 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 23.50 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.50 % Favored : 92.49 % Rotamer: Outliers : 0.92 % Allowed : 23.68 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.09), residues: 7802 helix: 0.15 (0.08), residues: 3849 sheet: -2.84 (0.22), residues: 480 loop : -2.38 (0.10), residues: 3473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Q 319 HIS 0.018 0.001 HIS E 403 PHE 0.030 0.002 PHE A 167 TYR 0.020 0.001 TYR h 236 ARG 0.010 0.000 ARG a 480 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 446 time to evaluate : 5.197 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 outliers start: 60 outliers final: 19 residues processed: 494 average time/residue: 0.5880 time to fit residues: 497.2378 Evaluate side-chains 446 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 427 time to evaluate : 5.188 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4602 time to fit residues: 23.1649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 464 optimal weight: 0.0070 chunk 299 optimal weight: 20.0000 chunk 448 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 477 optimal weight: 9.9990 chunk 511 optimal weight: 20.0000 chunk 371 optimal weight: 5.9990 chunk 69 optimal weight: 0.0070 chunk 590 optimal weight: 0.8980 overall best weight: 1.3820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 73 ASN ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 122 GLN ** e 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 245 ASN ** h 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 405 GLN G 469 HIS ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 60696 Z= 0.160 Angle : 0.641 11.922 81892 Z= 0.320 Chirality : 0.043 0.256 9848 Planarity : 0.004 0.096 10492 Dihedral : 5.524 86.930 8354 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.36 % Favored : 92.63 % Rotamer: Outliers : 0.75 % Allowed : 24.05 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.09), residues: 7802 helix: 0.25 (0.08), residues: 3836 sheet: -2.60 (0.23), residues: 486 loop : -2.33 (0.10), residues: 3480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Q 319 HIS 0.017 0.001 HIS E 403 PHE 0.025 0.001 PHE B 155 TYR 0.019 0.001 TYR G 246 ARG 0.012 0.000 ARG b 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 469 time to evaluate : 5.155 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 outliers start: 49 outliers final: 19 residues processed: 507 average time/residue: 0.5965 time to fit residues: 512.3248 Evaluate side-chains 444 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 425 time to evaluate : 5.245 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4344 time to fit residues: 22.7914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 683 optimal weight: 6.9990 chunk 719 optimal weight: 6.9990 chunk 656 optimal weight: 9.9990 chunk 699 optimal weight: 5.9990 chunk 421 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 chunk 549 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 632 optimal weight: 6.9990 chunk 661 optimal weight: 40.0000 chunk 697 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 30 ASN b 161 ASN ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 184 GLN ** e 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 60696 Z= 0.250 Angle : 0.711 13.515 81892 Z= 0.356 Chirality : 0.045 0.338 9848 Planarity : 0.004 0.095 10492 Dihedral : 5.653 84.949 8354 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 25.89 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.42 % Favored : 91.57 % Rotamer: Outliers : 0.61 % Allowed : 24.63 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.09), residues: 7802 helix: 0.25 (0.08), residues: 3841 sheet: -2.67 (0.22), residues: 502 loop : -2.31 (0.10), residues: 3459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 474 HIS 0.015 0.001 HIS d 129 PHE 0.062 0.002 PHE B 218 TYR 0.029 0.002 TYR H 275 ARG 0.010 0.000 ARG Z 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 441 time to evaluate : 5.213 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 outliers start: 40 outliers final: 18 residues processed: 464 average time/residue: 0.5869 time to fit residues: 466.3348 Evaluate side-chains 445 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 427 time to evaluate : 5.140 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4579 time to fit residues: 22.5879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 459 optimal weight: 7.9990 chunk 739 optimal weight: 7.9990 chunk 451 optimal weight: 6.9990 chunk 350 optimal weight: 8.9990 chunk 514 optimal weight: 3.9990 chunk 776 optimal weight: 20.0000 chunk 714 optimal weight: 20.0000 chunk 618 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 477 optimal weight: 6.9990 chunk 378 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 178 HIS b 298 ASN b 426 ASN ** d 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 245 ASN ** h 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 60696 Z= 0.239 Angle : 0.715 12.658 81892 Z= 0.358 Chirality : 0.045 0.320 9848 Planarity : 0.004 0.094 10492 Dihedral : 5.725 80.105 8354 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 26.32 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.23 % Favored : 91.76 % Rotamer: Outliers : 0.37 % Allowed : 24.84 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.09), residues: 7802 helix: 0.21 (0.08), residues: 3844 sheet: -2.69 (0.23), residues: 465 loop : -2.32 (0.10), residues: 3493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 474 HIS 0.016 0.001 HIS d 129 PHE 0.031 0.002 PHE B 155 TYR 0.030 0.002 TYR H 275 ARG 0.009 0.000 ARG Z 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15604 Ramachandran restraints generated. 7802 Oldfield, 0 Emsley, 7802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 437 time to evaluate : 5.197 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 outliers start: 24 outliers final: 15 residues processed: 453 average time/residue: 0.5843 time to fit residues: 451.0562 Evaluate side-chains 432 residues out of total 6546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 417 time to evaluate : 5.197 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4406 time to fit residues: 19.6547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 490 optimal weight: 7.9990 chunk 658 optimal weight: 8.9990 chunk 189 optimal weight: 0.5980 chunk 569 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 618 optimal weight: 30.0000 chunk 259 optimal weight: 8.9990 chunk 635 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 242 GLN ** a 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 298 ASN ** d 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 30 GLN ** h 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 245 ASN ** h 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 67 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.061647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.050655 restraints weight = 500615.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.051854 restraints weight = 346162.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.052655 restraints weight = 262221.455| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 60696 Z= 0.263 Angle : 0.738 16.014 81892 Z= 0.370 Chirality : 0.045 0.291 9848 Planarity : 0.004 0.094 10492 Dihedral : 5.810 77.477 8354 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 28.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.98 % Favored : 91.00 % Rotamer: Outliers : 0.35 % Allowed : 25.08 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.09), residues: 7802 helix: 0.19 (0.08), residues: 3831 sheet: -2.73 (0.22), residues: 490 loop : -2.34 (0.10), residues: 3481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 474 HIS 0.016 0.001 HIS d 129 PHE 0.031 0.002 PHE B 155 TYR 0.025 0.002 TYR H 275 ARG 0.009 0.001 ARG a 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10245.93 seconds wall clock time: 184 minutes 45.73 seconds (11085.73 seconds total)