Starting phenix.real_space_refine on Tue Feb 20 11:59:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vom_21269/02_2024/6vom_21269_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vom_21269/02_2024/6vom_21269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vom_21269/02_2024/6vom_21269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vom_21269/02_2024/6vom_21269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vom_21269/02_2024/6vom_21269_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vom_21269/02_2024/6vom_21269_updated.pdb" } resolution = 3.6 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= 0.000 sd= 0.001 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 16 5.49 5 S 103 5.16 5 C 17261 2.51 5 N 4744 2.21 5 O 5368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 46": "OD1" <-> "OD2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ASP 326": "OD1" <-> "OD2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 402": "OD1" <-> "OD2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B ASP 404": "OD1" <-> "OD2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 171": "OD1" <-> "OD2" Residue "C TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C ASP 326": "OD1" <-> "OD2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C GLU 496": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D ASP 125": "OD1" <-> "OD2" Residue "D ARG 127": "NH1" <-> "NH2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 273": "OD1" <-> "OD2" Residue "D ASP 332": "OD1" <-> "OD2" Residue "D ASP 347": "OD1" <-> "OD2" Residue "D ASP 366": "OD1" <-> "OD2" Residue "D ASP 403": "OD1" <-> "OD2" Residue "D GLU 416": "OE1" <-> "OE2" Residue "D PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 481": "OD1" <-> "OD2" Residue "D GLU 491": "OE1" <-> "OE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 119": "OD1" <-> "OD2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "E TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 311": "OE1" <-> "OE2" Residue "E ASP 332": "OD1" <-> "OD2" Residue "E ASP 333": "OD1" <-> "OD2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 369": "OD1" <-> "OD2" Residue "E GLU 412": "OE1" <-> "OE2" Residue "E PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 481": "OD1" <-> "OD2" Residue "F ASP 32": "OD1" <-> "OD2" Residue "F ASP 53": "OD1" <-> "OD2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F ASP 125": "OD1" <-> "OD2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F GLU 204": "OE1" <-> "OE2" Residue "F GLU 215": "OE1" <-> "OE2" Residue "F TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 267": "OD1" <-> "OD2" Residue "F PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F GLU 311": "OE1" <-> "OE2" Residue "F ASP 333": "OD1" <-> "OD2" Residue "F ASP 403": "OD1" <-> "OD2" Residue "F TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 482": "OE1" <-> "OE2" Residue "d ASP 72": "OD1" <-> "OD2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d GLU 100": "OE1" <-> "OE2" Residue "d PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 130": "OD1" <-> "OD2" Residue "d GLU 153": "OE1" <-> "OE2" Residue "d ASP 167": "OD1" <-> "OD2" Residue "d PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 189": "OD1" <-> "OD2" Residue "d ARG 208": "NH1" <-> "NH2" Residue "d PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 228": "OE1" <-> "OE2" Residue "d GLU 243": "OE1" <-> "OE2" Residue "d GLU 249": "OE1" <-> "OE2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "g GLU 98": "OE1" <-> "OE2" Residue "g ARG 144": "NH1" <-> "NH2" Residue "g GLU 147": "OE1" <-> "OE2" Residue "g ARG 171": "NH1" <-> "NH2" Residue "g PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 206": "OE1" <-> "OE2" Residue "g ASP 248": "OD1" <-> "OD2" Residue "g PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 256": "NH1" <-> "NH2" Residue "g GLU 267": "OE1" <-> "OE2" Residue "g ASP 269": "OD1" <-> "OD2" Residue "g PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 287": "OD1" <-> "OD2" Residue "g ARG 306": "NH1" <-> "NH2" Residue "g GLU 352": "OE1" <-> "OE2" Residue "e ARG 12": "NH1" <-> "NH2" Residue "e ASP 45": "OD1" <-> "OD2" Residue "e PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e GLU 82": "OE1" <-> "OE2" Residue "e ASP 86": "OD1" <-> "OD2" Residue "e ARG 110": "NH1" <-> "NH2" Residue "e GLU 127": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27492 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3818 Classifications: {'peptide': 497} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 478} Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3851 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 481} Chain: "D" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3627 Classifications: {'peptide': 479} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 453} Chain: "F" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Chain: "d" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1383 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "g" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2497 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 308} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'ATP': 1, 'TTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.28, per 1000 atoms: 0.52 Number of scatterers: 27492 At special positions: 0 Unit cell: (170.586, 137.943, 132.678, 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 103 16.00 P 16 15.00 O 5368 8.00 N 4744 7.00 C 17261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 11.21 Conformation dependent library (CDL) restraints added in 5.4 seconds 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6554 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 30 sheets defined 41.8% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 233 through 252 Proline residue: A 240 - end of helix removed outlier: 3.724A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 4.108A pdb=" N LEU A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 removed outlier: 4.247A pdb=" N PHE A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 293 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 294 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 374 through 394 removed outlier: 3.556A pdb=" N LYS A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS A 382 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 400 No H-bonds generated for 'chain 'A' and resid 397 through 400' Processing helix chain 'A' and resid 407 through 421 Processing helix chain 'A' and resid 431 through 439 Processing helix chain 'A' and resid 451 through 467 removed outlier: 4.658A pdb=" N ARG A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 484 through 500 Processing helix chain 'B' and resid 12 through 18 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 176 through 188 removed outlier: 4.045A pdb=" N GLN B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 218 through 221 removed outlier: 3.790A pdb=" N TYR B 221 " --> pdb=" O ALA B 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 233 through 252 Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 289 through 300 removed outlier: 3.980A pdb=" N PHE B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 300 " --> pdb=" O ARG B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 368 through 371 Processing helix chain 'B' and resid 374 through 396 removed outlier: 4.360A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N PHE B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 421 Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 454 through 468 Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 484 through 503 Processing helix chain 'C' and resid 6 through 19 removed outlier: 3.732A pdb=" N GLY C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 176 through 189 removed outlier: 4.001A pdb=" N GLN C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLY C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 233 through 252 Proline residue: C 240 - end of helix removed outlier: 3.944A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 277 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 289 through 301 removed outlier: 3.974A pdb=" N PHE C 292 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG C 297 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU C 300 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 301 " --> pdb=" O LEU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 368 through 371 Processing helix chain 'C' and resid 374 through 380 Processing helix chain 'C' and resid 383 through 396 Processing helix chain 'C' and resid 405 through 420 Processing helix chain 'C' and resid 431 through 442 Processing helix chain 'C' and resid 453 through 468 Processing helix chain 'C' and resid 471 through 478 Processing helix chain 'C' and resid 484 through 503 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 243 through 262 removed outlier: 3.628A pdb=" N MET D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 289 Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.619A pdb=" N LEU D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 337 through 345 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 382 through 408 removed outlier: 4.845A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA D 406 " --> pdb=" O GLN D 402 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 430 Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 471 through 474 Processing helix chain 'D' and resid 480 through 495 Processing helix chain 'E' and resid 104 through 106 No H-bonds generated for 'chain 'E' and resid 104 through 106' Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 243 through 262 removed outlier: 5.212A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 289 removed outlier: 4.282A pdb=" N ALA E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 310 Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 337 through 345 removed outlier: 4.227A pdb=" N ALA E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 382 through 408 removed outlier: 4.590A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 430 Processing helix chain 'E' and resid 438 through 442 Processing helix chain 'E' and resid 451 through 463 Processing helix chain 'E' and resid 471 through 474 Processing helix chain 'E' and resid 481 through 495 Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 154 through 159 Processing helix chain 'F' and resid 178 through 189 Processing helix chain 'F' and resid 206 through 218 Processing helix chain 'F' and resid 243 through 246 No H-bonds generated for 'chain 'F' and resid 243 through 246' Processing helix chain 'F' and resid 249 through 264 Processing helix chain 'F' and resid 275 through 289 removed outlier: 3.530A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 312 removed outlier: 3.634A pdb=" N LEU F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG F 312 " --> pdb=" O SER F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 337 through 345 removed outlier: 4.447A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 382 through 408 removed outlier: 4.566A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 412 No H-bonds generated for 'chain 'F' and resid 410 through 412' Processing helix chain 'F' and resid 415 through 430 Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing helix chain 'F' and resid 451 through 463 removed outlier: 3.907A pdb=" N ARG F 456 " --> pdb=" O ALA F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 468 removed outlier: 4.459A pdb=" N SER F 468 " --> pdb=" O GLU F 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 465 through 468' Processing helix chain 'F' and resid 480 through 492 Processing helix chain 'd' and resid 74 through 89 Processing helix chain 'd' and resid 92 through 106 removed outlier: 3.547A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 116 Processing helix chain 'd' and resid 122 through 136 Processing helix chain 'd' and resid 140 through 152 Processing helix chain 'd' and resid 155 through 173 removed outlier: 3.631A pdb=" N VAL d 158 " --> pdb=" O ILE d 155 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS d 159 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE d 165 " --> pdb=" O LEU d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 202 Processing helix chain 'd' and resid 238 through 245 Processing helix chain 'g' and resid 44 through 99 removed outlier: 3.529A pdb=" N LEU g 66 " --> pdb=" O GLU g 62 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN g 81 " --> pdb=" O GLU g 77 " (cutoff:3.500A) Proline residue: g 84 - end of helix removed outlier: 3.594A pdb=" N ASN g 97 " --> pdb=" O LEU g 93 " (cutoff:3.500A) Processing helix chain 'g' and resid 133 through 148 removed outlier: 3.758A pdb=" N LEU g 137 " --> pdb=" O PHE g 133 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU g 142 " --> pdb=" O LEU g 138 " (cutoff:3.500A) Processing helix chain 'g' and resid 163 through 170 removed outlier: 3.742A pdb=" N ILE g 169 " --> pdb=" O ASN g 165 " (cutoff:3.500A) Processing helix chain 'g' and resid 189 through 203 Processing helix chain 'g' and resid 242 through 244 No H-bonds generated for 'chain 'g' and resid 242 through 244' Processing helix chain 'g' and resid 288 through 362 Proline residue: g 297 - end of helix removed outlier: 3.643A pdb=" N ILE g 304 " --> pdb=" O LEU g 300 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP g 328 " --> pdb=" O SER g 324 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY g 359 " --> pdb=" O GLU g 355 " (cutoff:3.500A) Processing helix chain 'e' and resid 89 through 104 Processing helix chain 'e' and resid 109 through 129 Processing sheet with id= A, first strand: chain 'A' and resid 32 through 36 removed outlier: 6.753A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 54 through 56 Processing sheet with id= C, first strand: chain 'A' and resid 97 through 99 Processing sheet with id= D, first strand: chain 'A' and resid 107 through 109 Processing sheet with id= E, first strand: chain 'A' and resid 166 through 170 Processing sheet with id= F, first strand: chain 'B' and resid 32 through 36 removed outlier: 6.653A pdb=" N ARG B 41 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 66 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.071A pdb=" N GLU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 107 through 109 removed outlier: 3.730A pdb=" N ARG B 107 " --> pdb=" O THR B 222 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ILE B 223 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N CYS B 194 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLU B 227 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA B 198 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N HIS B 256 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL B 195 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 258 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL B 197 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE B 260 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE B 199 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP B 262 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLN B 201 " --> pdb=" O ASP B 262 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER B 313 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE B 259 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B 315 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N TYR B 261 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 341 through 344 Processing sheet with id= J, first strand: chain 'C' and resid 29 through 31 Processing sheet with id= K, first strand: chain 'C' and resid 32 through 36 removed outlier: 6.788A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 97 through 99 Processing sheet with id= M, first strand: chain 'C' and resid 342 through 345 removed outlier: 6.428A pdb=" N LEU C 167 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU C 345 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 169 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 170 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 257 through 262 removed outlier: 6.332A pdb=" N ILE C 193 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE C 260 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL C 195 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASP C 262 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL C 197 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 61 through 64 removed outlier: 4.538A pdb=" N ASN D 19 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= Q, first strand: chain 'D' and resid 348 through 352 removed outlier: 8.223A pdb=" N ILE D 168 " --> pdb=" O ILE D 321 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER D 323 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU D 170 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLN D 325 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLY D 172 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 272 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL D 196 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N PHE D 271 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL D 198 " --> pdb=" O PHE D 271 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 233 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 199 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 22 through 27 removed outlier: 6.394A pdb=" N ASP E 32 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE E 26 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL E 77 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL E 65 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= T, first strand: chain 'E' and resid 323 through 328 removed outlier: 3.597A pdb=" N GLN E 325 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA E 348 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N PHE E 171 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR E 350 " --> pdb=" O PHE E 171 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 268 through 273 removed outlier: 7.166A pdb=" N VAL E 196 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N PHE E 271 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL E 198 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ASP E 273 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY E 200 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E 233 " --> pdb=" O SER E 197 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 22 through 27 removed outlier: 6.381A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG F 75 " --> pdb=" O GLN F 67 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= X, first strand: chain 'F' and resid 168 through 172 removed outlier: 6.895A pdb=" N VAL F 268 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE F 324 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU F 270 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA F 326 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE F 272 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TYR F 328 " --> pdb=" O ILE F 272 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL F 196 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N PHE F 271 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL F 198 " --> pdb=" O PHE F 271 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'd' and resid 206 through 213 removed outlier: 3.963A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'g' and resid 154 through 160 removed outlier: 4.125A pdb=" N ALA g 119 " --> pdb=" O ASP g 208 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL g 210 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET g 121 " --> pdb=" O VAL g 210 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N MET g 212 " --> pdb=" O MET g 121 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL g 123 " --> pdb=" O MET g 212 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TYR g 214 " --> pdb=" O VAL g 123 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET g 212 " --> pdb=" O THR g 229 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR g 229 " --> pdb=" O MET g 212 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N TYR g 214 " --> pdb=" O ILE g 227 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ILE g 227 " --> pdb=" O TYR g 214 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'g' and resid 254 through 259 removed outlier: 3.557A pdb=" N LEU g 254 " --> pdb=" O ASP g 269 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'e' and resid 5 through 7 removed outlier: 3.597A pdb=" N TRP e 15 " --> pdb=" O VAL e 7 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'e' and resid 21 through 24 Processing sheet with id= AD, first strand: chain 'e' and resid 65 through 68 1105 hydrogen bonds defined for protein. 3171 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: 8.73 Time building geometry restraints manager: 11.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9102 1.34 - 1.46: 3722 1.46 - 1.58: 14832 1.58 - 1.70: 26 1.70 - 1.82: 195 Bond restraints: 27877 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.27e+01 bond pdb=" C4 ATP F 502 " pdb=" C5 ATP F 502 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.15e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.02e+01 bond pdb=" C5 ATP C 601 " pdb=" C6 ATP C 601 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.01e+01 ... (remaining 27872 not shown) Histogram of bond angle deviations from ideal: 98.68 - 106.26: 704 106.26 - 113.83: 16145 113.83 - 121.41: 14475 121.41 - 128.98: 6401 128.98 - 136.56: 62 Bond angle restraints: 37787 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 120.25 19.62 1.00e+00 1.00e+00 3.85e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 120.54 19.33 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 121.96 17.91 1.00e+00 1.00e+00 3.21e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 118.96 17.87 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 119.12 17.71 1.00e+00 1.00e+00 3.14e+02 ... (remaining 37782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.16: 16602 33.16 - 66.31: 508 66.31 - 99.47: 51 99.47 - 132.63: 3 132.63 - 165.79: 2 Dihedral angle restraints: 17166 sinusoidal: 6954 harmonic: 10212 Sorted by residual: dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual -180.00 -132.03 -47.97 0 5.00e+00 4.00e-02 9.20e+01 dihedral pdb=" CA ALA E 295 " pdb=" C ALA E 295 " pdb=" N VAL E 296 " pdb=" CA VAL E 296 " ideal model delta harmonic sigma weight residual -180.00 -134.11 -45.89 0 5.00e+00 4.00e-02 8.42e+01 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -143.76 -36.24 0 5.00e+00 4.00e-02 5.25e+01 ... (remaining 17163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3374 0.052 - 0.105: 855 0.105 - 0.157: 197 0.157 - 0.209: 14 0.209 - 0.262: 3 Chirality restraints: 4443 Sorted by residual: chirality pdb=" CB ILE F 27 " pdb=" CA ILE F 27 " pdb=" CG1 ILE F 27 " pdb=" CG2 ILE F 27 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE g 112 " pdb=" CA ILE g 112 " pdb=" CG1 ILE g 112 " pdb=" CG2 ILE g 112 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL A 367 " pdb=" CA VAL A 367 " pdb=" CG1 VAL A 367 " pdb=" CG2 VAL A 367 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 4440 not shown) Planarity restraints: 4907 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 TTX F 501 " 0.684 2.00e-02 2.50e+03 6.32e-01 5.99e+03 pdb=" C12 TTX F 501 " -0.071 2.00e-02 2.50e+03 pdb=" C13 TTX F 501 " 0.880 2.00e-02 2.50e+03 pdb=" C9 TTX F 501 " -0.627 2.00e-02 2.50e+03 pdb=" N3 TTX F 501 " 0.005 2.00e-02 2.50e+03 pdb=" O3 TTX F 501 " -0.870 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 TTX F 501 " 0.332 2.00e-02 2.50e+03 3.97e-01 2.36e+03 pdb=" C5 TTX F 501 " -0.514 2.00e-02 2.50e+03 pdb=" C6 TTX F 501 " 0.079 2.00e-02 2.50e+03 pdb=" C7 TTX F 501 " -0.576 2.00e-02 2.50e+03 pdb=" N1 TTX F 501 " 0.325 2.00e-02 2.50e+03 pdb=" O1 TTX F 501 " 0.354 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 TTX F 501 " -0.544 2.00e-02 2.50e+03 2.72e-01 1.48e+03 pdb=" C14 TTX F 501 " 0.138 2.00e-02 2.50e+03 pdb=" C15 TTX F 501 " 0.094 2.00e-02 2.50e+03 pdb=" C16 TTX F 501 " -0.083 2.00e-02 2.50e+03 pdb=" C17 TTX F 501 " -0.175 2.00e-02 2.50e+03 pdb=" N1 TTX F 501 " 0.236 2.00e-02 2.50e+03 pdb=" N4 TTX F 501 " 0.412 2.00e-02 2.50e+03 pdb=" O4 TTX F 501 " -0.079 2.00e-02 2.50e+03 ... (remaining 4904 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1081 2.71 - 3.25: 28962 3.25 - 3.80: 46138 3.80 - 4.35: 59477 4.35 - 4.90: 97891 Nonbonded interactions: 233549 Sorted by model distance: nonbonded pdb=" O ALA D 295 " pdb=" N GLY D 297 " model vdw 2.157 2.520 nonbonded pdb=" O GLY F 450 " pdb=" OG1 THR F 454 " model vdw 2.157 2.440 nonbonded pdb=" O ALA E 295 " pdb=" N GLY E 297 " model vdw 2.165 2.520 nonbonded pdb=" OE1 GLU C 58 " pdb=" OG1 THR C 60 " model vdw 2.175 2.440 nonbonded pdb=" OD1 ASP C 404 " pdb=" OG1 THR C 407 " model vdw 2.192 2.440 ... (remaining 233544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 7 through 503 or resid 601)) selection = (chain 'C' and (resid 7 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and resid 18 through 494) selection = (chain 'E' and resid 18 through 494) selection = (chain 'F' and resid 18 through 494) } 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: 6.850 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: 0.020 Extract box with map and model: 16.320 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 72.530 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.140 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.006 0.079 27877 Z= 0.374 Angle : 0.917 19.617 37787 Z= 0.585 Chirality : 0.049 0.262 4443 Planarity : 0.013 0.632 4907 Dihedral : 15.877 165.787 10612 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 0.10 % Allowed : 7.66 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.19 (0.12), residues: 3548 helix: -1.52 (0.11), residues: 1495 sheet: -2.52 (0.18), residues: 569 loop : -2.44 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP e 57 HIS 0.010 0.001 HIS d 141 PHE 0.016 0.002 PHE A 396 TYR 0.029 0.002 TYR C 20 ARG 0.010 0.000 ARG D 261 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 832 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 SER cc_start: 0.8469 (m) cc_final: 0.8170 (p) REVERT: A 405 LYS cc_start: 0.6244 (pttt) cc_final: 0.6022 (ptmt) REVERT: B 215 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7160 (pt0) REVERT: B 384 LYS cc_start: 0.8049 (mttt) cc_final: 0.7708 (mtmt) REVERT: C 197 VAL cc_start: 0.9067 (t) cc_final: 0.8837 (m) REVERT: C 327 VAL cc_start: 0.7274 (t) cc_final: 0.6976 (t) REVERT: D 379 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8386 (mp) REVERT: D 416 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6883 (mp0) REVERT: E 106 THR cc_start: 0.8377 (p) cc_final: 0.7444 (p) REVERT: E 217 LYS cc_start: 0.8507 (mttt) cc_final: 0.8269 (ttmm) REVERT: E 336 ASP cc_start: 0.7236 (t0) cc_final: 0.6984 (t0) REVERT: F 213 TYR cc_start: 0.7545 (t80) cc_final: 0.7313 (t80) REVERT: d 196 LYS cc_start: 0.7606 (mmmm) cc_final: 0.7252 (pttt) REVERT: g 92 VAL cc_start: 0.7730 (t) cc_final: 0.7493 (t) REVERT: g 126 ASP cc_start: 0.4999 (m-30) cc_final: 0.4703 (m-30) REVERT: g 286 GLN cc_start: 0.7189 (tt0) cc_final: 0.6957 (tt0) REVERT: e 9 THR cc_start: 0.8175 (t) cc_final: 0.7708 (m) REVERT: e 21 GLU cc_start: 0.4611 (tt0) cc_final: 0.4205 (tp30) REVERT: e 58 LEU cc_start: 0.5214 (tp) cc_final: 0.4979 (mt) REVERT: e 72 ASN cc_start: 0.6737 (m-40) cc_final: 0.6496 (m110) REVERT: e 110 ARG cc_start: 0.4772 (mtt180) cc_final: 0.4125 (ptp90) outliers start: 3 outliers final: 0 residues processed: 835 average time/residue: 0.4445 time to fit residues: 554.9587 Evaluate side-chains 492 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 490 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain D residue 379 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 0.8980 chunk 267 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 180 optimal weight: 0.0670 chunk 142 optimal weight: 0.6980 chunk 276 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 205 optimal weight: 0.5980 chunk 320 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS A 351 ASN A 389 GLN A 443 ASN B 34 GLN B 97 GLN B 187 GLN B 236 GLN B 256 HIS B 295 HIS B 409 ASN B 415 GLN B 453 GLN C 43 HIS C 187 GLN C 201 GLN C 208 GLN C 214 GLN C 351 ASN C 389 GLN C 409 ASN D 19 ASN D 112 ASN D 133 HIS ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN E 25 GLN E 72 ASN E 120 ASN E 188 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 ASN F 45 ASN F 66 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 GLN F 223 ASN F 238 GLN ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 HIS d 170 ASN d 193 GLN g 81 ASN g 243 ASN e 16 ASN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN e 116 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27877 Z= 0.201 Angle : 0.647 12.040 37787 Z= 0.325 Chirality : 0.045 0.271 4443 Planarity : 0.005 0.054 4907 Dihedral : 8.494 168.586 4050 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.45 % Favored : 95.41 % Rotamer: Outliers : 2.55 % Allowed : 16.17 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.65 (0.13), residues: 3548 helix: 0.00 (0.12), residues: 1508 sheet: -2.02 (0.19), residues: 583 loop : -1.78 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP e 57 HIS 0.007 0.001 HIS d 141 PHE 0.019 0.002 PHE e 66 TYR 0.026 0.001 TYR D 259 ARG 0.008 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 545 time to evaluate : 3.277 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: A 363 SER cc_start: 0.8430 (m) cc_final: 0.8157 (p) REVERT: A 376 MET cc_start: 0.8447 (mmm) cc_final: 0.8183 (mmm) REVERT: A 405 LYS cc_start: 0.6374 (pttt) cc_final: 0.6130 (ptmt) REVERT: B 9 ILE cc_start: 0.7401 (mm) cc_final: 0.7134 (mm) REVERT: B 215 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7429 (pt0) REVERT: B 384 LYS cc_start: 0.8202 (mttt) cc_final: 0.7798 (mtmt) REVERT: D 362 TYR cc_start: 0.7997 (m-80) cc_final: 0.7535 (m-10) REVERT: D 385 TYR cc_start: 0.7968 (t80) cc_final: 0.7702 (t80) REVERT: E 247 MET cc_start: 0.6647 (mtm) cc_final: 0.6321 (mtm) REVERT: F 79 MET cc_start: 0.8228 (mmm) cc_final: 0.7966 (mmp) REVERT: F 361 ILE cc_start: 0.8640 (mp) cc_final: 0.8083 (mp) REVERT: d 196 LYS cc_start: 0.7773 (mmmm) cc_final: 0.7307 (pttt) REVERT: d 208 ARG cc_start: 0.7508 (ttm170) cc_final: 0.7191 (mtm110) REVERT: g 341 TYR cc_start: 0.8384 (t80) cc_final: 0.8154 (t80) REVERT: e 58 LEU cc_start: 0.5543 (tp) cc_final: 0.5205 (mt) REVERT: e 63 MET cc_start: 0.4739 (mmt) cc_final: 0.4275 (mmt) REVERT: e 110 ARG cc_start: 0.5123 (mtt180) cc_final: 0.4135 (ptp90) outliers start: 75 outliers final: 40 residues processed: 594 average time/residue: 0.4180 time to fit residues: 379.3875 Evaluate side-chains 488 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 447 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 247 VAL Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain e residue 16 ASN Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 130 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 0.4980 chunk 99 optimal weight: 0.6980 chunk 266 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 88 optimal weight: 0.0770 chunk 321 optimal weight: 0.9980 chunk 346 optimal weight: 4.9990 chunk 286 optimal weight: 2.9990 chunk 318 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 257 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 295 HIS A 415 GLN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN F 45 ASN F 57 GLN g 58 GLN g 134 ASN g 286 GLN ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 16 ASN e 94 GLN e 111 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27877 Z= 0.195 Angle : 0.617 10.394 37787 Z= 0.307 Chirality : 0.044 0.274 4443 Planarity : 0.004 0.053 4907 Dihedral : 8.053 165.172 4048 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.03 % Favored : 95.86 % Rotamer: Outliers : 3.10 % Allowed : 17.74 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3548 helix: 0.60 (0.13), residues: 1504 sheet: -1.63 (0.20), residues: 589 loop : -1.44 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP e 15 HIS 0.004 0.001 HIS F 133 PHE 0.035 0.001 PHE A 390 TYR 0.022 0.001 TYR D 259 ARG 0.008 0.000 ARG F 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 474 time to evaluate : 3.374 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: A 363 SER cc_start: 0.8388 (m) cc_final: 0.8095 (p) REVERT: A 405 LYS cc_start: 0.6224 (pttt) cc_final: 0.5952 (ptmt) REVERT: B 384 LYS cc_start: 0.8127 (mttt) cc_final: 0.7873 (mtmt) REVERT: D 79 MET cc_start: 0.8524 (mmt) cc_final: 0.7569 (mmt) REVERT: D 362 TYR cc_start: 0.8101 (m-80) cc_final: 0.7751 (m-10) REVERT: E 247 MET cc_start: 0.6572 (mtm) cc_final: 0.6371 (mtm) REVERT: E 408 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7767 (tp) REVERT: d 113 TYR cc_start: 0.7466 (t80) cc_final: 0.7260 (t80) REVERT: d 208 ARG cc_start: 0.7630 (ttm170) cc_final: 0.7224 (mtm110) REVERT: g 47 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8475 (mt) REVERT: g 103 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6507 (pm20) REVERT: g 192 GLN cc_start: 0.8122 (tp40) cc_final: 0.7763 (tp40) REVERT: g 224 ASP cc_start: 0.8026 (t0) cc_final: 0.7814 (m-30) REVERT: e 11 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.8039 (p0) REVERT: e 58 LEU cc_start: 0.5610 (tp) cc_final: 0.5253 (mt) REVERT: e 68 ARG cc_start: 0.5911 (ttt90) cc_final: 0.4618 (tpt170) REVERT: e 110 ARG cc_start: 0.5155 (mtt180) cc_final: 0.4008 (ptp90) outliers start: 91 outliers final: 52 residues processed: 524 average time/residue: 0.4026 time to fit residues: 326.2340 Evaluate side-chains 475 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 419 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 211 THR Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 103 GLU Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 259 THR Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 363 CYS Chi-restraints excluded: chain e residue 11 ASN Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 130 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 317 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 322 optimal weight: 6.9990 chunk 341 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 305 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN B 97 GLN B 443 ASN B 473 GLN C 208 GLN C 256 HIS ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 303 GLN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27877 Z= 0.294 Angle : 0.651 10.313 37787 Z= 0.327 Chirality : 0.045 0.308 4443 Planarity : 0.005 0.086 4907 Dihedral : 8.094 161.310 4045 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.68 % Favored : 95.21 % Rotamer: Outliers : 4.43 % Allowed : 18.25 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3548 helix: 0.77 (0.13), residues: 1505 sheet: -1.36 (0.20), residues: 568 loop : -1.33 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP e 15 HIS 0.005 0.001 HIS E 133 PHE 0.024 0.002 PHE A 390 TYR 0.027 0.002 TYR D 259 ARG 0.014 0.001 ARG e 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 454 time to evaluate : 3.091 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: A 405 LYS cc_start: 0.6389 (pttt) cc_final: 0.6087 (ptmt) REVERT: B 387 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8374 (mm) REVERT: D 362 TYR cc_start: 0.8374 (m-80) cc_final: 0.8168 (m-80) REVERT: E 214 MET cc_start: 0.7407 (mmm) cc_final: 0.7190 (mmm) REVERT: E 346 LEU cc_start: 0.8760 (mm) cc_final: 0.8483 (mt) REVERT: E 402 GLN cc_start: 0.7234 (tp40) cc_final: 0.6936 (tp40) REVERT: F 311 GLU cc_start: 0.7087 (tp30) cc_final: 0.6857 (tp30) REVERT: F 379 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8530 (mt) REVERT: F 488 MET cc_start: 0.7250 (mmm) cc_final: 0.6856 (tmm) REVERT: d 113 TYR cc_start: 0.7661 (t80) cc_final: 0.7421 (t80) REVERT: d 145 PHE cc_start: 0.8100 (t80) cc_final: 0.7858 (t80) REVERT: d 150 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8391 (pt) REVERT: d 208 ARG cc_start: 0.7710 (ttm170) cc_final: 0.7278 (mtm110) REVERT: g 47 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8304 (mt) REVERT: g 103 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6619 (pm20) REVERT: g 224 ASP cc_start: 0.8060 (t0) cc_final: 0.7823 (m-30) REVERT: g 299 TYR cc_start: 0.7114 (t80) cc_final: 0.6751 (t80) REVERT: e 110 ARG cc_start: 0.4925 (mtt180) cc_final: 0.4075 (ptp90) outliers start: 130 outliers final: 69 residues processed: 546 average time/residue: 0.4087 time to fit residues: 345.1637 Evaluate side-chains 472 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 398 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 441 PHE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 441 PHE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain d residue 142 THR Chi-restraints excluded: chain d residue 150 ILE Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 211 THR Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 103 GLU Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 303 GLN Chi-restraints excluded: chain g residue 363 CYS Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 130 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 284 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 254 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 291 optimal weight: 0.0980 chunk 235 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 306 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 ASN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN g 101 GLN g 303 GLN ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27877 Z= 0.178 Angle : 0.610 11.644 37787 Z= 0.301 Chirality : 0.043 0.291 4443 Planarity : 0.004 0.053 4907 Dihedral : 7.676 164.257 4045 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.03 % Favored : 95.86 % Rotamer: Outliers : 3.58 % Allowed : 20.53 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3548 helix: 1.01 (0.13), residues: 1506 sheet: -1.19 (0.21), residues: 570 loop : -1.14 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP e 15 HIS 0.003 0.001 HIS E 133 PHE 0.022 0.001 PHE A 390 TYR 0.019 0.001 TYR D 259 ARG 0.008 0.000 ARG e 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 446 time to evaluate : 3.255 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: A 405 LYS cc_start: 0.6289 (pttt) cc_final: 0.6002 (ptmt) REVERT: B 387 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8320 (mm) REVERT: D 259 TYR cc_start: 0.8020 (t80) cc_final: 0.7816 (t80) REVERT: E 346 LEU cc_start: 0.8788 (mm) cc_final: 0.8507 (mt) REVERT: E 402 GLN cc_start: 0.7165 (tp40) cc_final: 0.6867 (tp40) REVERT: F 379 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8368 (mt) REVERT: F 488 MET cc_start: 0.7210 (mmm) cc_final: 0.6929 (tmm) REVERT: d 150 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8316 (pt) REVERT: d 208 ARG cc_start: 0.7660 (ttm170) cc_final: 0.7249 (mtm110) REVERT: d 239 LYS cc_start: 0.5881 (ptpp) cc_final: 0.5279 (mtmm) REVERT: d 243 GLU cc_start: 0.7465 (pt0) cc_final: 0.7082 (pt0) REVERT: g 47 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8110 (mp) REVERT: g 103 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6559 (pm20) REVERT: g 224 ASP cc_start: 0.8017 (t0) cc_final: 0.7761 (m-30) REVERT: e 110 ARG cc_start: 0.4912 (mtt180) cc_final: 0.3929 (ptp90) outliers start: 105 outliers final: 63 residues processed: 517 average time/residue: 0.4112 time to fit residues: 331.1139 Evaluate side-chains 470 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 402 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 441 PHE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain d residue 150 ILE Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 103 GLU Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 363 CYS Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 27 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 114 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 200 optimal weight: 0.0770 chunk 84 optimal weight: 0.7980 chunk 341 optimal weight: 0.9980 chunk 283 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27877 Z= 0.210 Angle : 0.614 12.120 37787 Z= 0.303 Chirality : 0.043 0.245 4443 Planarity : 0.004 0.052 4907 Dihedral : 7.517 166.068 4045 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.57 % Favored : 95.32 % Rotamer: Outliers : 3.75 % Allowed : 21.48 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3548 helix: 1.08 (0.13), residues: 1510 sheet: -1.02 (0.21), residues: 582 loop : -1.09 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP e 15 HIS 0.002 0.001 HIS E 133 PHE 0.021 0.001 PHE d 145 TYR 0.035 0.001 TYR F 259 ARG 0.018 0.000 ARG e 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 427 time to evaluate : 3.293 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: A 405 LYS cc_start: 0.6259 (pttt) cc_final: 0.5988 (ptmt) REVERT: B 387 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8249 (mm) REVERT: D 399 LYS cc_start: 0.8224 (ttmt) cc_final: 0.8013 (mtmt) REVERT: E 346 LEU cc_start: 0.8768 (mm) cc_final: 0.8547 (mt) REVERT: E 402 GLN cc_start: 0.7034 (tp40) cc_final: 0.6787 (tp40) REVERT: F 379 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8368 (mt) REVERT: F 488 MET cc_start: 0.7258 (mmm) cc_final: 0.6969 (tmm) REVERT: d 145 PHE cc_start: 0.8038 (t80) cc_final: 0.7772 (t80) REVERT: d 150 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8367 (pt) REVERT: d 208 ARG cc_start: 0.7691 (ttm170) cc_final: 0.7241 (mtm110) REVERT: d 243 GLU cc_start: 0.7500 (pt0) cc_final: 0.7103 (pt0) REVERT: g 103 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6600 (pm20) REVERT: g 224 ASP cc_start: 0.7974 (t0) cc_final: 0.7721 (m-30) REVERT: e 110 ARG cc_start: 0.4898 (mtt180) cc_final: 0.3931 (ptp90) outliers start: 110 outliers final: 75 residues processed: 502 average time/residue: 0.4367 time to fit residues: 340.3071 Evaluate side-chains 470 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 391 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 248 ARG Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain d residue 150 ILE Chi-restraints excluded: chain d residue 151 ASP Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain g residue 103 GLU Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 226 VAL Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 363 CYS Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 130 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 329 optimal weight: 0.0670 chunk 38 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 249 optimal weight: 0.5980 chunk 193 optimal weight: 0.9990 chunk 287 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 chunk 340 optimal weight: 0.6980 chunk 212 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27877 Z= 0.191 Angle : 0.610 10.834 37787 Z= 0.299 Chirality : 0.043 0.197 4443 Planarity : 0.004 0.052 4907 Dihedral : 7.331 168.001 4045 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 3.71 % Allowed : 21.76 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3548 helix: 1.16 (0.13), residues: 1508 sheet: -0.97 (0.21), residues: 597 loop : -1.03 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP e 15 HIS 0.002 0.001 HIS F 133 PHE 0.019 0.001 PHE A 390 TYR 0.032 0.001 TYR F 259 ARG 0.011 0.000 ARG e 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 423 time to evaluate : 3.220 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: A 405 LYS cc_start: 0.6449 (pttt) cc_final: 0.6230 (ptmt) REVERT: B 131 GLU cc_start: 0.7577 (mp0) cc_final: 0.7356 (mp0) REVERT: B 384 LYS cc_start: 0.7416 (mtmt) cc_final: 0.7115 (mtmm) REVERT: B 387 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8244 (mm) REVERT: B 394 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5469 (pm20) REVERT: B 408 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.6333 (tt0) REVERT: E 346 LEU cc_start: 0.8815 (mm) cc_final: 0.8580 (mt) REVERT: E 402 GLN cc_start: 0.7077 (tp40) cc_final: 0.6863 (tp40) REVERT: F 79 MET cc_start: 0.7999 (mmm) cc_final: 0.7579 (mmp) REVERT: F 89 MET cc_start: 0.8252 (mmt) cc_final: 0.8010 (mmm) REVERT: F 379 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8361 (mt) REVERT: F 488 MET cc_start: 0.7233 (mmm) cc_final: 0.6986 (tmm) REVERT: d 150 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8341 (pt) REVERT: d 208 ARG cc_start: 0.7682 (ttm170) cc_final: 0.7335 (mtm110) REVERT: d 239 LYS cc_start: 0.5814 (ptpp) cc_final: 0.5568 (mtmm) REVERT: g 103 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6559 (pm20) REVERT: e 68 ARG cc_start: 0.5931 (ttt90) cc_final: 0.4997 (tpt170) REVERT: e 110 ARG cc_start: 0.4882 (mtt180) cc_final: 0.3757 (ptp90) outliers start: 109 outliers final: 78 residues processed: 500 average time/residue: 0.4154 time to fit residues: 319.3232 Evaluate side-chains 477 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 393 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 248 ARG Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain d residue 150 ILE Chi-restraints excluded: chain d residue 151 ASP Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 211 THR Chi-restraints excluded: chain g residue 103 GLU Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 226 VAL Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 363 CYS Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 130 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 210 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 216 optimal weight: 0.9990 chunk 231 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 chunk 31 optimal weight: 0.0020 chunk 267 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 303 GLN ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27877 Z= 0.207 Angle : 0.628 16.181 37787 Z= 0.307 Chirality : 0.044 0.346 4443 Planarity : 0.004 0.051 4907 Dihedral : 7.294 170.046 4045 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.43 % Rotamer: Outliers : 3.71 % Allowed : 22.13 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3548 helix: 1.18 (0.13), residues: 1507 sheet: -0.96 (0.21), residues: 619 loop : -0.95 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 15 HIS 0.002 0.001 HIS F 384 PHE 0.027 0.001 PHE d 145 TYR 0.034 0.001 TYR F 259 ARG 0.013 0.000 ARG e 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 405 time to evaluate : 3.180 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: A 405 LYS cc_start: 0.6457 (pttt) cc_final: 0.6233 (ptmt) REVERT: B 387 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8280 (mm) REVERT: B 394 GLU cc_start: 0.6101 (OUTLIER) cc_final: 0.5437 (pm20) REVERT: B 408 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.6457 (tt0) REVERT: E 346 LEU cc_start: 0.8791 (mm) cc_final: 0.8529 (mt) REVERT: E 402 GLN cc_start: 0.7041 (tp40) cc_final: 0.6819 (tp40) REVERT: F 79 MET cc_start: 0.8009 (mmm) cc_final: 0.7670 (mmp) REVERT: F 89 MET cc_start: 0.8241 (mmt) cc_final: 0.8001 (mmm) REVERT: F 379 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8366 (mt) REVERT: F 488 MET cc_start: 0.7339 (mmm) cc_final: 0.7029 (tmm) REVERT: d 150 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8423 (pt) REVERT: d 208 ARG cc_start: 0.7697 (ttm170) cc_final: 0.7380 (mtm110) REVERT: d 239 LYS cc_start: 0.5828 (ptpp) cc_final: 0.5372 (ptpp) REVERT: g 103 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6614 (pm20) REVERT: e 110 ARG cc_start: 0.4796 (mtt180) cc_final: 0.3802 (ptp90) outliers start: 109 outliers final: 82 residues processed: 482 average time/residue: 0.4165 time to fit residues: 311.2366 Evaluate side-chains 477 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 389 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 248 ARG Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain d residue 150 ILE Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 211 THR Chi-restraints excluded: chain g residue 103 GLU Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 226 VAL Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 303 GLN Chi-restraints excluded: chain g residue 363 CYS Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 130 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 309 optimal weight: 0.6980 chunk 325 optimal weight: 3.9990 chunk 297 optimal weight: 1.9990 chunk 317 optimal weight: 0.5980 chunk 190 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 299 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 HIS ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27877 Z= 0.262 Angle : 0.655 15.417 37787 Z= 0.323 Chirality : 0.045 0.362 4443 Planarity : 0.004 0.051 4907 Dihedral : 7.382 174.464 4045 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.98 % Rotamer: Outliers : 3.51 % Allowed : 22.71 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3548 helix: 1.16 (0.13), residues: 1499 sheet: -0.92 (0.21), residues: 614 loop : -1.00 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP e 15 HIS 0.003 0.001 HIS D 384 PHE 0.020 0.001 PHE A 390 TYR 0.032 0.002 TYR F 259 ARG 0.006 0.000 ARG e 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 395 time to evaluate : 3.203 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: B 5 ARG cc_start: 0.6934 (mmt-90) cc_final: 0.6677 (mmt-90) REVERT: B 387 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8329 (mm) REVERT: B 408 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.6465 (tt0) REVERT: C 95 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8046 (pt) REVERT: E 346 LEU cc_start: 0.8818 (mm) cc_final: 0.8546 (mt) REVERT: E 402 GLN cc_start: 0.7142 (tp40) cc_final: 0.6875 (tp40) REVERT: F 89 MET cc_start: 0.8254 (mmt) cc_final: 0.8037 (mmm) REVERT: F 379 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8505 (mt) REVERT: F 488 MET cc_start: 0.7307 (mmm) cc_final: 0.7013 (tmm) REVERT: d 150 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8519 (pt) REVERT: d 208 ARG cc_start: 0.7697 (ttm170) cc_final: 0.7380 (mtm110) REVERT: g 103 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6596 (pm20) REVERT: e 110 ARG cc_start: 0.4875 (mtt180) cc_final: 0.3758 (ptp90) outliers start: 103 outliers final: 83 residues processed: 468 average time/residue: 0.4232 time to fit residues: 306.3637 Evaluate side-chains 466 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 377 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 248 ARG Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain d residue 150 ILE Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 211 THR Chi-restraints excluded: chain g residue 103 GLU Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain g residue 226 VAL Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 363 CYS Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 130 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 208 optimal weight: 0.0670 chunk 335 optimal weight: 0.9980 chunk 204 optimal weight: 0.9990 chunk 159 optimal weight: 0.0270 chunk 233 optimal weight: 2.9990 chunk 351 optimal weight: 1.9990 chunk 323 optimal weight: 0.3980 chunk 280 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 216 optimal weight: 0.7980 chunk 171 optimal weight: 0.0770 overall best weight: 0.1934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN E 396 GLN ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27877 Z= 0.158 Angle : 0.632 15.170 37787 Z= 0.309 Chirality : 0.043 0.327 4443 Planarity : 0.004 0.063 4907 Dihedral : 7.051 177.240 4045 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.64 % Favored : 96.25 % Rotamer: Outliers : 2.28 % Allowed : 24.17 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3548 helix: 1.31 (0.13), residues: 1506 sheet: -0.83 (0.21), residues: 622 loop : -0.86 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP e 15 HIS 0.002 0.000 HIS E 133 PHE 0.018 0.001 PHE d 145 TYR 0.027 0.001 TYR F 259 ARG 0.006 0.000 ARG e 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 431 time to evaluate : 3.405 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: A 22 ARG cc_start: 0.7793 (mmm-85) cc_final: 0.7137 (mmm160) REVERT: A 228 THR cc_start: 0.7814 (t) cc_final: 0.7593 (p) REVERT: B 5 ARG cc_start: 0.7004 (mmt-90) cc_final: 0.6483 (mmt-90) REVERT: C 95 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7987 (pt) REVERT: E 346 LEU cc_start: 0.8779 (mm) cc_final: 0.8528 (mt) REVERT: F 89 MET cc_start: 0.8156 (mmt) cc_final: 0.7954 (mmm) REVERT: d 113 TYR cc_start: 0.7765 (t80) cc_final: 0.7485 (t80) REVERT: d 145 PHE cc_start: 0.7570 (t80) cc_final: 0.7357 (t80) REVERT: d 150 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8397 (pt) REVERT: d 208 ARG cc_start: 0.7698 (ttm170) cc_final: 0.7403 (mtm110) REVERT: g 96 MET cc_start: 0.6690 (ptt) cc_final: 0.5451 (mmp) REVERT: g 103 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6501 (pm20) REVERT: e 110 ARG cc_start: 0.4813 (mtt180) cc_final: 0.3750 (ptp90) outliers start: 67 outliers final: 50 residues processed: 472 average time/residue: 0.4430 time to fit residues: 324.8766 Evaluate side-chains 444 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 391 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 248 ARG Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain d residue 150 ILE Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 211 THR Chi-restraints excluded: chain g residue 103 GLU Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain g residue 292 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 222 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 chunk 85 optimal weight: 0.0470 chunk 258 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 77 optimal weight: 0.0030 chunk 280 optimal weight: 0.0670 chunk 117 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 0.0270 overall best weight: 0.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 345 HIS ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.108685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.092809 restraints weight = 64775.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.095495 restraints weight = 31067.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.097222 restraints weight = 18001.866| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27877 Z= 0.159 Angle : 0.637 15.255 37787 Z= 0.307 Chirality : 0.043 0.313 4443 Planarity : 0.004 0.050 4907 Dihedral : 6.869 173.669 4045 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.92 % Favored : 95.97 % Rotamer: Outliers : 1.91 % Allowed : 24.92 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3548 helix: 1.39 (0.14), residues: 1506 sheet: -0.64 (0.21), residues: 595 loop : -0.81 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP e 15 HIS 0.002 0.000 HIS E 193 PHE 0.017 0.001 PHE A 390 TYR 0.021 0.001 TYR F 259 ARG 0.007 0.000 ARG C 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6680.92 seconds wall clock time: 121 minutes 17.36 seconds (7277.36 seconds total)