Starting phenix.real_space_refine on Wed Jul 24 20:14:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/07_2024/7ole_12979_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/07_2024/7ole_12979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/07_2024/7ole_12979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/07_2024/7ole_12979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/07_2024/7ole_12979_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/07_2024/7ole_12979_neut.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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 10 5.49 5 S 88 5.16 5 C 16678 2.51 5 N 4879 2.21 5 O 5340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ASP 271": "OD1" <-> "OD2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A ASP 521": "OD1" <-> "OD2" Residue "A TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 550": "OD1" <-> "OD2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "B ASP 214": "OD1" <-> "OD2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ASP 424": "OD1" <-> "OD2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C ASP 173": "OD1" <-> "OD2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 214": "OD1" <-> "OD2" Residue "C ASP 273": "OD1" <-> "OD2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C ASP 356": "OD1" <-> "OD2" Residue "C PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D GLU 112": "OE1" <-> "OE2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D GLU 300": "OE1" <-> "OE2" Residue "D PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 352": "OD1" <-> "OD2" Residue "D ARG 353": "NH1" <-> "NH2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "E ASP 227": "OD1" <-> "OD2" Residue "E PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 333": "NH1" <-> "NH2" Residue "E GLU 396": "OE1" <-> "OE2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F GLU 136": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F ASP 148": "OD1" <-> "OD2" Residue "F ASP 185": "OD1" <-> "OD2" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F ASP 229": "OD1" <-> "OD2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F ARG 400": "NH1" <-> "NH2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 26995 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3328 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3209 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3281 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3224 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3156 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3232 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 3208 Classifications: {'peptide': 644} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 632} Link IDs: {'CIS': 1, 'TRANS': 642} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1282 Unresolved non-hydrogen angles: 1924 Unresolved non-hydrogen dihedrals: 638 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 638} Unresolved non-hydrogen planarities: 640 Chain: "J" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 2273 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 449} Link IDs: {'CIS': 2, 'TRANS': 453} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 901 Unresolved non-hydrogen angles: 1351 Unresolved non-hydrogen dihedrals: 450 Planarities with less than four sites: {'UNK:plan-1': 450} Unresolved non-hydrogen planarities: 451 Chain: "K" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 138 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "K" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 25} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 10, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 355 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 3, 'TRANS': 68} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'UNK:plan-1': 8, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 110 Chain: "K" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1316 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 231} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 253} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 759 Unresolved non-hydrogen angles: 975 Unresolved non-hydrogen dihedrals: 595 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 5, 'ASN:plan1': 5, 'TYR:plan': 2, 'UNK:plan-1': 18, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 15, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 382 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.87, per 1000 atoms: 0.55 Number of scatterers: 26995 At special positions: 0 Unit cell: (199.02, 190.46, 154.08, 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 88 16.00 P 10 15.00 O 5340 8.00 N 4879 7.00 C 16678 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 Atom "HETATM26882 O3A ADP B 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.28 Conformation dependent library (CDL) restraints added in 4.1 seconds 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7584 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 32 sheets defined 80.5% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 145 through 150 removed outlier: 4.151A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.851A pdb=" N SER A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.543A pdb=" N LEU A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.625A pdb=" N LYS A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 414 through 417 removed outlier: 3.581A pdb=" N LEU A 417 " --> pdb=" O HIS A 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 417' Processing helix chain 'A' and resid 445 through 448 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 485 through 499 removed outlier: 4.426A pdb=" N GLU A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 507 through 518 Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.793A pdb=" N VAL A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 550 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 49 through 65 removed outlier: 3.518A pdb=" N GLU B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 95 Processing helix chain 'B' and resid 104 through 109 removed outlier: 3.868A pdb=" N ILE B 108 " --> pdb=" O GLY B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 175 through 182 removed outlier: 3.739A pdb=" N GLU B 180 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 269 through 284 removed outlier: 3.792A pdb=" N ARG B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 305 through 318 removed outlier: 4.142A pdb=" N SER B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 373 through 376 Processing helix chain 'B' and resid 384 through 397 removed outlier: 3.572A pdb=" N ILE B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 435 through 452 removed outlier: 3.571A pdb=" N GLN B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N MET B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR B 446 " --> pdb=" O TYR B 442 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 450 " --> pdb=" O TYR B 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.609A pdb=" N ALA C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.552A pdb=" N VAL C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 removed outlier: 4.145A pdb=" N LYS C 182 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU C 183 " --> pdb=" O LEU C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 183' Processing helix chain 'C' and resid 240 through 249 removed outlier: 4.249A pdb=" N ARG C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 290 removed outlier: 3.543A pdb=" N ARG C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 308 through 315 removed outlier: 3.821A pdb=" N PHE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 321 removed outlier: 4.017A pdb=" N SER C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 383 removed outlier: 4.160A pdb=" N GLN C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 removed outlier: 3.907A pdb=" N HIS C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 394 " --> pdb=" O ALA C 390 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 409 through 421 removed outlier: 3.601A pdb=" N ASN C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 434 removed outlier: 3.857A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 451 Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 49 through 65 Processing helix chain 'D' and resid 83 through 95 removed outlier: 3.586A pdb=" N ALA D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.627A pdb=" N PHE D 109 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 114 through 125 Processing helix chain 'D' and resid 177 through 185 removed outlier: 4.757A pdb=" N SER D 181 " --> pdb=" O LYS D 177 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D 182 " --> pdb=" O MET D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 251 removed outlier: 3.898A pdb=" N ASP D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.595A pdb=" N GLU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.585A pdb=" N PHE D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 353 removed outlier: 3.830A pdb=" N ARG D 353 " --> pdb=" O ASP D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 379 removed outlier: 3.921A pdb=" N THR D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 390 removed outlier: 3.539A pdb=" N VAL D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 395 Processing helix chain 'D' and resid 398 through 417 removed outlier: 3.894A pdb=" N GLN D 404 " --> pdb=" O ARG D 400 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 411 " --> pdb=" O THR D 407 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 440 Processing helix chain 'D' and resid 440 through 451 Processing helix chain 'E' and resid 11 through 15 Processing helix chain 'E' and resid 16 through 21 removed outlier: 4.123A pdb=" N HIS E 20 " --> pdb=" O SER E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 58 Processing helix chain 'E' and resid 75 through 88 Processing helix chain 'E' and resid 99 through 102 Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.636A pdb=" N VAL E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 184 Processing helix chain 'E' and resid 239 through 247 removed outlier: 3.849A pdb=" N LEU E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 289 removed outlier: 3.715A pdb=" N ARG E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN E 280 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS E 281 " --> pdb=" O GLY E 277 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 308 through 320 removed outlier: 3.550A pdb=" N PHE E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 357 removed outlier: 4.091A pdb=" N ARG E 357 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 383 removed outlier: 4.522A pdb=" N GLN E 373 " --> pdb=" O GLN E 369 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN E 380 " --> pdb=" O LYS E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 401 removed outlier: 4.198A pdb=" N LEU E 391 " --> pdb=" O SER E 387 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU E 396 " --> pdb=" O ASN E 392 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE E 397 " --> pdb=" O HIS E 393 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 407 Processing helix chain 'E' and resid 409 through 420 removed outlier: 3.956A pdb=" N LEU E 416 " --> pdb=" O PRO E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 437 removed outlier: 3.657A pdb=" N VAL E 430 " --> pdb=" O GLU E 426 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE E 433 " --> pdb=" O HIS E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 451 Processing helix chain 'F' and resid 49 through 65 Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.674A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 109 Processing helix chain 'F' and resid 114 through 126 Processing helix chain 'F' and resid 178 through 185 removed outlier: 4.107A pdb=" N ASP F 185 " --> pdb=" O SER F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 251 removed outlier: 3.648A pdb=" N ASN F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 287 removed outlier: 3.935A pdb=" N ARG F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA F 281 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU F 282 " --> pdb=" O ALA F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 378 removed outlier: 3.977A pdb=" N THR F 367 " --> pdb=" O SER F 363 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 removed outlier: 3.544A pdb=" N ILE F 393 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 396 " --> pdb=" O ARG F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 416 removed outlier: 4.031A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 435 through 452 Processing helix chain 'H' and resid 40 through 55 Processing helix chain 'H' and resid 63 through 82 Processing helix chain 'H' and resid 87 through 111 Processing helix chain 'H' and resid 113 through 135 removed outlier: 3.768A pdb=" N UNK H 133 " --> pdb=" O UNK H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 156 Processing helix chain 'H' and resid 156 through 161 Processing helix chain 'H' and resid 161 through 176 removed outlier: 4.160A pdb=" N UNK H 166 " --> pdb=" O UNK H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 191 Processing helix chain 'H' and resid 192 through 197 Processing helix chain 'H' and resid 198 through 219 removed outlier: 3.732A pdb=" N UNK H 218 " --> pdb=" O UNK H 214 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N UNK H 219 " --> pdb=" O UNK H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 239 Processing helix chain 'H' and resid 240 through 245 Processing helix chain 'H' and resid 245 through 256 Processing helix chain 'H' and resid 263 through 277 Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 296 through 309 Processing helix chain 'H' and resid 313 through 333 Processing helix chain 'H' and resid 339 through 360 removed outlier: 3.813A pdb=" N UNK H 343 " --> pdb=" O UNK H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 376 removed outlier: 3.590A pdb=" N UNK H 376 " --> pdb=" O UNK H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 390 removed outlier: 3.723A pdb=" N GLY H 383 " --> pdb=" O UNK H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 391 through 400 Processing helix chain 'H' and resid 401 through 414 Processing helix chain 'H' and resid 416 through 429 Processing helix chain 'H' and resid 434 through 450 Processing helix chain 'H' and resid 453 through 472 Processing helix chain 'H' and resid 473 through 475 No H-bonds generated for 'chain 'H' and resid 473 through 475' Processing helix chain 'H' and resid 476 through 495 removed outlier: 3.684A pdb=" N UNK H 495 " --> pdb=" O UNK H 491 " (cutoff:3.500A) Processing helix chain 'H' and resid 497 through 516 removed outlier: 3.827A pdb=" N UNK H 502 " --> pdb=" O UNK H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 520 through 540 Processing helix chain 'H' and resid 541 through 554 Processing helix chain 'H' and resid 560 through 572 Processing helix chain 'H' and resid 582 through 598 removed outlier: 4.388A pdb=" N UNK H 593 " --> pdb=" O UNK H 589 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N UNK H 594 " --> pdb=" O UNK H 590 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK H 598 " --> pdb=" O UNK H 594 " (cutoff:3.500A) Processing helix chain 'H' and resid 601 through 618 Processing helix chain 'H' and resid 621 through 636 removed outlier: 3.557A pdb=" N UNK H 635 " --> pdb=" O UNK H 631 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N UNK H 636 " --> pdb=" O UNK H 632 " (cutoff:3.500A) Processing helix chain 'H' and resid 637 through 647 Processing helix chain 'H' and resid 650 through 660 Processing helix chain 'H' and resid 669 through 682 Processing helix chain 'J' and resid 45 through 60 Processing helix chain 'J' and resid 71 through 83 Processing helix chain 'J' and resid 87 through 101 removed outlier: 3.590A pdb=" N UNK J 101 " --> pdb=" O UNK J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 122 Processing helix chain 'J' and resid 126 through 147 Processing helix chain 'J' and resid 152 through 170 WARNING: missing atoms! removed outlier: 4.277A pdb=" N UNK J 170 " --> pdb=" O GLY J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 191 removed outlier: 4.405A pdb=" N UNK J 191 " --> pdb=" O UNK J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 211 removed outlier: 3.672A pdb=" N UNK J 200 " --> pdb=" O UNK J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 231 Processing helix chain 'J' and resid 233 through 239 Processing helix chain 'J' and resid 243 through 263 Processing helix chain 'J' and resid 266 through 280 Processing helix chain 'J' and resid 287 through 304 removed outlier: 3.820A pdb=" N UNK J 295 " --> pdb=" O UNK J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 329 Processing helix chain 'J' and resid 331 through 349 Processing helix chain 'J' and resid 352 through 376 removed outlier: 4.016A pdb=" N UNK J 371 " --> pdb=" O UNK J 367 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N UNK J 374 " --> pdb=" O UNK J 370 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 395 removed outlier: 4.098A pdb=" N UNK J 381 " --> pdb=" O UNK J 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 396 through 420 Processing helix chain 'J' and resid 424 through 445 removed outlier: 4.037A pdb=" N UNK J 428 " --> pdb=" O UNK J 424 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N UNK J 429 " --> pdb=" O UNK J 425 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N UNK J 430 " --> pdb=" O UNK J 426 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N UNK J 433 " --> pdb=" O UNK J 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 451 Processing helix chain 'J' and resid 457 through 475 Processing helix chain 'J' and resid 479 through 494 Processing helix chain 'J' and resid 496 through 508 Processing helix chain 'K' and resid 12 through 22 Processing helix chain 'K' and resid 24 through 38 removed outlier: 4.054A pdb=" N LEU K 35 " --> pdb=" O THR K 31 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS K 36 " --> pdb=" O LEU K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 58 No H-bonds generated for 'chain 'K' and resid 40 through 58' Processing helix chain 'K' and resid 58 through 67 No H-bonds generated for 'chain 'K' and resid 58 through 67' Processing helix chain 'K' and resid 74 through 86 No H-bonds generated for 'chain 'K' and resid 74 through 86' Processing helix chain 'K' and resid 90 through 103 No H-bonds generated for 'chain 'K' and resid 90 through 103' Processing helix chain 'K' and resid 105 through 137 No H-bonds generated for 'chain 'K' and resid 105 through 137' Processing helix chain 'K' and resid 142 through 163 No H-bonds generated for 'chain 'K' and resid 142 through 163' Processing helix chain 'K' and resid 169 through 190 No H-bonds generated for 'chain 'K' and resid 169 through 190' Processing helix chain 'K' and resid 197 through 214 No H-bonds generated for 'chain 'K' and resid 197 through 214' Processing helix chain 'K' and resid 215 through 233 No H-bonds generated for 'chain 'K' and resid 215 through 233' Processing helix chain 'K' and resid 235 through 245 No H-bonds generated for 'chain 'K' and resid 235 through 245' Processing helix chain 'K' and resid 248 through 264 No H-bonds generated for 'chain 'K' and resid 248 through 264' Processing helix chain 'K' and resid 264 through 277 No H-bonds generated for 'chain 'K' and resid 264 through 277' Processing helix chain 'K' and resid 282 through 295 No H-bonds generated for 'chain 'K' and resid 282 through 295' Processing helix chain 'K' and resid 299 through 317 No H-bonds generated for 'chain 'K' and resid 299 through 317' Processing helix chain 'K' and resid 319 through 333 No H-bonds generated for 'chain 'K' and resid 319 through 333' Processing helix chain 'K' and resid 335 through 340 No H-bonds generated for 'chain 'K' and resid 335 through 340' Processing helix chain 'K' and resid 343 through 359 No H-bonds generated for 'chain 'K' and resid 343 through 359' Processing helix chain 'K' and resid 363 through 385 No H-bonds generated for 'chain 'K' and resid 363 through 385' Processing helix chain 'K' and resid 388 through 403 No H-bonds generated for 'chain 'K' and resid 388 through 403' Processing sheet with id=AA1, first strand: chain 'A' and resid 222 through 229 Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 259 Processing sheet with id=AA3, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.331A pdb=" N GLY A 395 " --> pdb=" O ILE A 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 434 through 435 removed outlier: 4.222A pdb=" N CYS A 434 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 444 " --> pdb=" O CYS A 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 484 removed outlier: 7.282A pdb=" N ASN A 483 " --> pdb=" O ILE A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.738A pdb=" N SER B 43 " --> pdb=" O MET B 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 72 through 76 removed outlier: 6.925A pdb=" N ALA B 72 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL B 357 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 74 " --> pdb=" O VAL B 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.585A pdb=" N THR B 101 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 243 Processing sheet with id=AB1, first strand: chain 'B' and resid 132 through 138 Processing sheet with id=AB2, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AB3, first strand: chain 'B' and resid 332 through 334 Processing sheet with id=AB4, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.612A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 236 through 239 Processing sheet with id=AB6, first strand: chain 'C' and resid 202 through 204 removed outlier: 4.682A pdb=" N ARG C 202 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR C 192 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY C 204 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 157 through 162 Processing sheet with id=AB8, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AB9, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.405A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AC2, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AC3, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AC4, first strand: chain 'E' and resid 96 through 97 removed outlier: 6.868A pdb=" N MET E 96 " --> pdb=" O ASP E 302 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL E 66 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N SER E 331 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU E 68 " --> pdb=" O SER E 331 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 230 through 237 Processing sheet with id=AC6, first strand: chain 'E' and resid 157 through 159 Processing sheet with id=AC7, first strand: chain 'E' and resid 162 through 163 Processing sheet with id=AC8, first strand: chain 'E' and resid 335 through 337 Processing sheet with id=AC9, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.188A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 239 through 243 Processing sheet with id=AD2, first strand: chain 'F' and resid 135 through 136 Processing sheet with id=AD3, first strand: chain 'F' and resid 141 through 142 Processing sheet with id=AD4, first strand: chain 'F' and resid 193 through 194 Processing sheet with id=AD5, first strand: chain 'F' and resid 332 through 334 1411 hydrogen bonds defined for protein. 4083 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: 8.85 Time building geometry restraints manager: 13.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 4832 1.26 - 1.40: 5695 1.40 - 1.54: 16338 1.54 - 1.68: 214 1.68 - 1.83: 151 Bond restraints: 27230 Sorted by residual: bond pdb=" C GLU K 268 " pdb=" O GLU K 268 " ideal model delta sigma weight residual 1.236 1.126 0.110 1.15e-02 7.56e+03 9.17e+01 bond pdb=" C GLN K 120 " pdb=" O GLN K 120 " ideal model delta sigma weight residual 1.236 1.118 0.118 1.29e-02 6.01e+03 8.33e+01 bond pdb=" CA VAL K 380 " pdb=" C VAL K 380 " ideal model delta sigma weight residual 1.524 1.421 0.103 1.16e-02 7.43e+03 7.92e+01 bond pdb=" C LYS K 280 " pdb=" O LYS K 280 " ideal model delta sigma weight residual 1.232 1.351 -0.118 1.38e-02 5.25e+03 7.33e+01 bond pdb=" C VAL K 380 " pdb=" O VAL K 380 " ideal model delta sigma weight residual 1.237 1.142 0.095 1.12e-02 7.97e+03 7.20e+01 ... (remaining 27225 not shown) Histogram of bond angle deviations from ideal: 81.57 - 96.12: 16 96.12 - 110.67: 9943 110.67 - 125.22: 26601 125.22 - 139.77: 526 139.77 - 154.32: 3 Bond angle restraints: 37089 Sorted by residual: angle pdb=" C ARG K 318 " pdb=" N PRO K 319 " pdb=" CA PRO K 319 " ideal model delta sigma weight residual 119.84 154.17 -34.33 1.25e+00 6.40e-01 7.54e+02 angle pdb=" N LEU K 273 " pdb=" CA LEU K 273 " pdb=" C LEU K 273 " ideal model delta sigma weight residual 111.03 91.22 19.81 1.11e+00 8.12e-01 3.18e+02 angle pdb=" C PHE K 169 " pdb=" N PRO K 170 " pdb=" CA PRO K 170 " ideal model delta sigma weight residual 119.19 134.97 -15.78 1.06e+00 8.90e-01 2.22e+02 angle pdb=" N VAL K 279 " pdb=" CA VAL K 279 " pdb=" C VAL K 279 " ideal model delta sigma weight residual 108.27 128.46 -20.19 1.37e+00 5.33e-01 2.17e+02 angle pdb=" N UNK H 311 " pdb=" CA UNK H 311 " pdb=" C UNK H 311 " ideal model delta sigma weight residual 110.74 154.32 -43.58 3.00e+00 1.11e-01 2.11e+02 ... (remaining 37084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 16315 35.01 - 70.03: 272 70.03 - 105.04: 30 105.04 - 140.05: 6 140.05 - 175.07: 2 Dihedral angle restraints: 16625 sinusoidal: 4978 harmonic: 11647 Sorted by residual: dihedral pdb=" CA UNK J 242 " pdb=" C UNK J 242 " pdb=" N UNK J 243 " pdb=" CA UNK J 243 " ideal model delta harmonic sigma weight residual 180.00 64.65 115.35 0 5.00e+00 4.00e-02 5.32e+02 dihedral pdb=" CA UNK J 349 " pdb=" C UNK J 349 " pdb=" N UNK J 350 " pdb=" CA UNK J 350 " ideal model delta harmonic sigma weight residual 180.00 87.76 92.24 0 5.00e+00 4.00e-02 3.40e+02 dihedral pdb=" CA UNK H 177 " pdb=" C UNK H 177 " pdb=" N UNK H 178 " pdb=" CA UNK H 178 " ideal model delta harmonic sigma weight residual 180.00 89.23 90.77 0 5.00e+00 4.00e-02 3.30e+02 ... (remaining 16622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.337: 4556 0.337 - 0.675: 40 0.675 - 1.012: 12 1.012 - 1.350: 1 1.350 - 1.687: 1 Chirality restraints: 4610 Sorted by residual: chirality pdb=" CA UNK J 241 " pdb=" N UNK J 241 " pdb=" C UNK J 241 " pdb=" CB UNK J 241 " both_signs ideal model delta sigma weight residual False 2.52 0.83 1.69 2.00e-01 2.50e+01 7.12e+01 chirality pdb=" CA UNK H 311 " pdb=" N UNK H 311 " pdb=" C UNK H 311 " pdb=" CB UNK H 311 " both_signs ideal model delta sigma weight residual False 2.52 1.21 1.32 2.00e-01 2.50e+01 4.32e+01 chirality pdb=" CA UNK J 287 " pdb=" N UNK J 287 " pdb=" C UNK J 287 " pdb=" CB UNK J 287 " both_signs ideal model delta sigma weight residual False 2.52 1.54 0.98 2.00e-01 2.50e+01 2.40e+01 ... (remaining 4607 not shown) Planarity restraints: 4903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY K 214 " -0.075 2.00e-02 2.50e+03 1.39e-01 1.94e+02 pdb=" C GLY K 214 " 0.241 2.00e-02 2.50e+03 pdb=" O GLY K 214 " -0.089 2.00e-02 2.50e+03 pdb=" N ARG K 215 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK J 59 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C UNK J 59 " 0.216 2.00e-02 2.50e+03 pdb=" O UNK J 59 " -0.080 2.00e-02 2.50e+03 pdb=" N UNK J 60 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK H 497 " -0.063 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C UNK H 497 " 0.193 2.00e-02 2.50e+03 pdb=" O UNK H 497 " -0.067 2.00e-02 2.50e+03 pdb=" N UNK H 498 " -0.063 2.00e-02 2.50e+03 ... (remaining 4900 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 32 2.05 - 2.76: 6377 2.76 - 3.47: 47517 3.47 - 4.19: 65127 4.19 - 4.90: 106981 Nonbonded interactions: 226034 Sorted by model distance: nonbonded pdb=" C GLY K 138 " pdb=" N UNK K 139 " model vdw 1.337 3.350 nonbonded pdb=" C LEU K 66 " pdb=" N UNK K 67 " model vdw 1.337 3.350 nonbonded pdb=" C TYR K 38 " pdb=" N UNK K 39 " model vdw 1.338 3.350 nonbonded pdb=" O PRO K 302 " pdb=" N SER K 306 " model vdw 1.371 2.520 nonbonded pdb=" O UNK H 376 " pdb=" CB UNK H 381 " model vdw 1.448 3.440 ... (remaining 226029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 103 through 238 or resid 254 through 346 or (resid 369 thr \ ough 370 and (name N or name CA or name C or name O or name CB )) or resid 371 o \ r (resid 372 through 374 and (name N or name CA or name C or name O or name CB ) \ ) or resid 375 through 501 or (resid 502 and (name N or name CA or name C or nam \ e O or name CB )) or resid 503 through 550)) selection = (chain 'C' and (resid 5 through 140 or resid 156 through 248 or (resid 271 throu \ gh 272 and (name N or name CA or name C or name O or name CB )) or resid 273 or \ (resid 274 through 276 and (name N or name CA or name C or name O or name CB )) \ or resid 277 through 403 or (resid 404 and (name N or name CA or name C or name \ O or name CB )) or resid 405 through 452)) selection = (chain 'E' and (resid 5 through 248 or resid 271 through 452)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 23 through 253 or resid 267 through 269 or (resid 270 and \ (name N or name CA or name C or name O or name CB )) or resid 271 through 451 or \ (resid 452 through 453 and (name N or name CA or name C or name O or name CB )) \ or resid 501)) selection = (chain 'F' and (resid 23 through 252 or (resid 253 through 267 and (name N or na \ me CA or name C or name O or name CB )) or resid 268 through 451 or (resid 452 t \ hrough 453 and (name N or name CA or name C or name O or name CB )) or resid 501 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 1.140 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 70.700 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2731 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 : 0.013 0.171 27230 Z= 0.772 Angle : 1.742 43.583 37089 Z= 0.969 Chirality : 0.099 1.687 4610 Planarity : 0.009 0.139 4903 Dihedral : 15.119 175.065 9041 Min Nonbonded Distance : 1.337 Molprobity Statistics. All-atom Clashscore : 42.05 Ramachandran Plot: Outliers : 0.84 % Allowed : 17.25 % Favored : 81.91 % Rotamer: Outliers : 0.38 % Allowed : 13.07 % Favored : 86.55 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.68 % 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: -5.68 (0.11), residues: 2853 helix: -3.72 (0.10), residues: 1119 sheet: -2.69 (0.28), residues: 258 loop : -4.12 (0.13), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 283 HIS 0.012 0.002 HIS B 27 PHE 0.033 0.002 PHE A 398 TYR 0.023 0.003 TYR E 209 ARG 0.009 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 349 time to evaluate : 2.780 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: A 212 GLU cc_start: 0.6714 (tp30) cc_final: 0.6310 (tp30) REVERT: A 216 ARG cc_start: 0.4324 (tpm170) cc_final: 0.3246 (ptm160) REVERT: A 330 LYS cc_start: 0.7812 (tptp) cc_final: 0.7592 (ptpt) REVERT: A 392 LEU cc_start: 0.8792 (pp) cc_final: 0.8580 (mt) REVERT: A 403 HIS cc_start: 0.3952 (t70) cc_final: 0.3138 (t-90) REVERT: A 404 MET cc_start: 0.4137 (ttm) cc_final: 0.3930 (ttp) REVERT: A 425 VAL cc_start: 0.1041 (p) cc_final: 0.0769 (p) REVERT: A 448 ILE cc_start: 0.2709 (pt) cc_final: 0.2277 (pt) REVERT: A 456 VAL cc_start: 0.3238 (m) cc_final: 0.2195 (m) REVERT: A 469 MET cc_start: 0.7468 (mtp) cc_final: 0.6773 (mmm) REVERT: A 473 ILE cc_start: 0.7302 (mp) cc_final: 0.6938 (mt) REVERT: A 476 ARG cc_start: 0.2922 (mmt180) cc_final: 0.1892 (ptp-170) REVERT: B 46 MET cc_start: -0.2700 (ptt) cc_final: -0.2953 (ptt) REVERT: B 62 MET cc_start: 0.5981 (mtp) cc_final: 0.5713 (mmt) REVERT: B 67 LYS cc_start: 0.5770 (mttt) cc_final: 0.5429 (ttpt) REVERT: B 94 LEU cc_start: 0.3009 (tp) cc_final: 0.2559 (tt) REVERT: B 168 MET cc_start: 0.2637 (ptp) cc_final: 0.2429 (ttp) REVERT: B 250 ILE cc_start: 0.5199 (mt) cc_final: 0.4409 (mt) REVERT: C 315 LEU cc_start: 0.7484 (mt) cc_final: 0.7226 (mt) REVERT: D 382 MET cc_start: 0.7197 (ttt) cc_final: 0.6975 (ttt) REVERT: F 297 PHE cc_start: 0.5288 (t80) cc_final: 0.4974 (t80) outliers start: 8 outliers final: 1 residues processed: 356 average time/residue: 0.3970 time to fit residues: 220.1038 Evaluate side-chains 212 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 145 optimal weight: 20.0000 chunk 115 optimal weight: 0.9990 chunk 222 optimal weight: 0.2980 chunk 86 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 257 optimal weight: 50.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 483 ASN A 548 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN B 422 GLN B 441 GLN C 18 HIS ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 284 ASN C 305 HIS ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 341 GLN D 369 GLN E 18 HIS E 42 GLN E 156 HIS E 181 GLN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 GLN ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN F 341 GLN F 344 HIS F 447 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2936 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27230 Z= 0.251 Angle : 0.884 15.959 37089 Z= 0.430 Chirality : 0.044 0.273 4610 Planarity : 0.005 0.086 4903 Dihedral : 8.708 145.693 4257 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.69 % Favored : 88.85 % Rotamer: Outliers : 3.28 % Allowed : 19.77 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.40 % 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: -3.71 (0.14), residues: 2853 helix: -1.46 (0.13), residues: 1206 sheet: -2.00 (0.29), residues: 283 loop : -3.59 (0.14), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 283 HIS 0.014 0.002 HIS B 27 PHE 0.023 0.002 PHE F 297 TYR 0.025 0.002 TYR E 192 ARG 0.010 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 227 time to evaluate : 2.572 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 159 MET cc_start: 0.6532 (ptm) cc_final: 0.5997 (ppp) REVERT: A 212 GLU cc_start: 0.6842 (tp30) cc_final: 0.6397 (tp30) REVERT: A 216 ARG cc_start: 0.4537 (tpm170) cc_final: 0.3579 (ptm160) REVERT: B 60 LEU cc_start: 0.8705 (mt) cc_final: 0.8488 (tp) REVERT: B 125 ARG cc_start: 0.6924 (tpp80) cc_final: 0.6177 (tpt90) REVERT: B 168 MET cc_start: 0.2256 (ptp) cc_final: 0.2036 (ttp) REVERT: B 170 THR cc_start: 0.3231 (OUTLIER) cc_final: 0.2905 (p) REVERT: C 96 MET cc_start: 0.3609 (mmt) cc_final: 0.2893 (mmm) REVERT: C 359 MET cc_start: 0.6077 (ttm) cc_final: 0.5822 (mtp) REVERT: D 113 MET cc_start: 0.6361 (mmt) cc_final: 0.5774 (mtm) REVERT: F 172 TYR cc_start: 0.1907 (p90) cc_final: 0.1610 (p90) outliers start: 69 outliers final: 22 residues processed: 281 average time/residue: 0.3550 time to fit residues: 163.0715 Evaluate side-chains 204 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 431 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 214 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 258 optimal weight: 50.0000 chunk 279 optimal weight: 50.0000 chunk 230 optimal weight: 5.9990 chunk 256 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS F 78 GLN F 226 GLN ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3308 moved from start: 0.7145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27230 Z= 0.300 Angle : 0.891 16.984 37089 Z= 0.435 Chirality : 0.045 0.303 4610 Planarity : 0.005 0.081 4903 Dihedral : 7.736 153.180 4255 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 25.40 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.71 % Favored : 87.91 % Rotamer: Outliers : 6.42 % Allowed : 20.96 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.14), residues: 2853 helix: -0.52 (0.14), residues: 1164 sheet: -1.78 (0.29), residues: 292 loop : -3.31 (0.15), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 283 HIS 0.011 0.002 HIS B 245 PHE 0.024 0.003 PHE F 109 TYR 0.032 0.002 TYR F 442 ARG 0.011 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 197 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.7484 (ptm) cc_final: 0.6989 (ppp) REVERT: A 212 GLU cc_start: 0.6910 (tp30) cc_final: 0.6459 (tp30) REVERT: B 88 MET cc_start: 0.6546 (tpt) cc_final: 0.6309 (tpp) REVERT: B 168 MET cc_start: 0.2368 (ptp) cc_final: 0.2093 (ttp) REVERT: B 232 LEU cc_start: 0.0984 (OUTLIER) cc_final: 0.0356 (tp) REVERT: B 297 PHE cc_start: 0.5702 (t80) cc_final: 0.5439 (t80) REVERT: B 316 LEU cc_start: 0.8923 (tt) cc_final: 0.8540 (pp) REVERT: B 317 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: B 382 MET cc_start: 0.3588 (tpt) cc_final: 0.2993 (ttm) REVERT: B 406 ILE cc_start: 0.5893 (tt) cc_final: 0.5669 (tt) REVERT: C 359 MET cc_start: 0.6262 (ttm) cc_final: 0.5959 (mtp) REVERT: D 113 MET cc_start: 0.5982 (mmt) cc_final: 0.5617 (mtm) REVERT: D 178 MET cc_start: 0.6758 (tpp) cc_final: 0.6481 (tpp) REVERT: E 359 MET cc_start: 0.8235 (mpp) cc_final: 0.7764 (mtt) REVERT: F 98 THR cc_start: 0.5881 (m) cc_final: 0.5642 (p) REVERT: F 218 MET cc_start: 0.1422 (ppp) cc_final: -0.0198 (tmm) outliers start: 135 outliers final: 52 residues processed: 319 average time/residue: 0.3218 time to fit residues: 169.6188 Evaluate side-chains 203 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 149 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 123 optimal weight: 0.4980 chunk 173 optimal weight: 8.9990 chunk 259 optimal weight: 50.0000 chunk 274 optimal weight: 50.0000 chunk 135 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 HIS ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3403 moved from start: 0.8375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 27230 Z= 0.244 Angle : 0.766 11.934 37089 Z= 0.373 Chirality : 0.043 0.252 4610 Planarity : 0.004 0.102 4903 Dihedral : 7.272 179.777 4255 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.02 % Favored : 89.62 % Rotamer: Outliers : 4.13 % Allowed : 24.33 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.15), residues: 2853 helix: 0.03 (0.15), residues: 1187 sheet: -1.52 (0.29), residues: 289 loop : -3.12 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 283 HIS 0.009 0.002 HIS A 403 PHE 0.023 0.002 PHE F 123 TYR 0.019 0.002 TYR B 442 ARG 0.013 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 150 time to evaluate : 2.926 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: A 159 MET cc_start: 0.6733 (ptm) cc_final: 0.6110 (ppp) REVERT: A 212 GLU cc_start: 0.7124 (tp30) cc_final: 0.6753 (tp30) REVERT: A 216 ARG cc_start: 0.5830 (tpm170) cc_final: 0.5275 (ttp-170) REVERT: A 507 LEU cc_start: 0.7181 (mt) cc_final: 0.6839 (tt) REVERT: B 113 MET cc_start: 0.4262 (mpp) cc_final: 0.3888 (mpp) REVERT: B 168 MET cc_start: 0.2337 (ptp) cc_final: 0.2031 (ttp) REVERT: B 232 LEU cc_start: 0.1063 (OUTLIER) cc_final: 0.0503 (tp) REVERT: B 243 SER cc_start: 0.4253 (OUTLIER) cc_final: 0.3870 (t) REVERT: B 316 LEU cc_start: 0.9036 (tt) cc_final: 0.8635 (pp) REVERT: B 317 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8255 (mm-30) REVERT: B 382 MET cc_start: 0.3887 (tpt) cc_final: 0.2605 (ttm) REVERT: C 359 MET cc_start: 0.6442 (ttm) cc_final: 0.6032 (mtp) REVERT: D 113 MET cc_start: 0.6295 (mmt) cc_final: 0.5923 (mtm) REVERT: E 359 MET cc_start: 0.8270 (mpp) cc_final: 0.7598 (mtt) REVERT: F 97 ASP cc_start: 0.6604 (OUTLIER) cc_final: 0.6039 (p0) REVERT: F 325 ILE cc_start: 0.8219 (pt) cc_final: 0.7996 (mt) outliers start: 87 outliers final: 36 residues processed: 232 average time/residue: 0.3445 time to fit residues: 132.7638 Evaluate side-chains 164 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 140 optimal weight: 40.0000 chunk 246 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 145 ASN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3439 moved from start: 0.9293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27230 Z= 0.210 Angle : 0.730 14.557 37089 Z= 0.351 Chirality : 0.041 0.241 4610 Planarity : 0.004 0.062 4903 Dihedral : 6.887 171.205 4255 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.41 % Favored : 89.34 % Rotamer: Outliers : 3.80 % Allowed : 24.95 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.18 % 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: -1.92 (0.16), residues: 2853 helix: 0.32 (0.15), residues: 1208 sheet: -1.22 (0.30), residues: 281 loop : -2.88 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 283 HIS 0.012 0.001 HIS A 446 PHE 0.022 0.001 PHE D 433 TYR 0.015 0.001 TYR B 362 ARG 0.010 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 130 time to evaluate : 2.606 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 159 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6431 (ppp) REVERT: A 194 MET cc_start: 0.1229 (tmm) cc_final: 0.0909 (tmm) REVERT: A 216 ARG cc_start: 0.5843 (tpm170) cc_final: 0.5454 (ttp-170) REVERT: A 507 LEU cc_start: 0.7724 (mt) cc_final: 0.7472 (tt) REVERT: B 168 MET cc_start: 0.1429 (ptp) cc_final: 0.1000 (ttp) REVERT: B 232 LEU cc_start: 0.0728 (OUTLIER) cc_final: 0.0071 (tp) REVERT: B 243 SER cc_start: 0.4233 (p) cc_final: 0.4021 (t) REVERT: B 316 LEU cc_start: 0.9017 (tt) cc_final: 0.8674 (pp) REVERT: B 317 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8286 (mm-30) REVERT: C 61 MET cc_start: 0.4437 (tpp) cc_final: 0.2325 (mmm) REVERT: C 173 ASP cc_start: 0.2560 (OUTLIER) cc_final: 0.2228 (t70) REVERT: D 46 MET cc_start: 0.6665 (tpp) cc_final: 0.6009 (ttm) REVERT: D 113 MET cc_start: 0.6060 (mmt) cc_final: 0.5705 (mtp) REVERT: D 204 LYS cc_start: 0.5466 (tptt) cc_final: 0.5117 (tptt) REVERT: E 359 MET cc_start: 0.8245 (mpp) cc_final: 0.7598 (mtt) REVERT: F 97 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6838 (p0) REVERT: F 226 GLN cc_start: 0.0660 (OUTLIER) cc_final: -0.0997 (mt0) outliers start: 80 outliers final: 46 residues processed: 204 average time/residue: 0.3297 time to fit residues: 113.0293 Evaluate side-chains 175 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 124 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 6.9990 chunk 247 optimal weight: 0.9990 chunk 54 optimal weight: 40.0000 chunk 161 optimal weight: 0.0670 chunk 67 optimal weight: 20.0000 chunk 274 optimal weight: 40.0000 chunk 228 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 HIS E 34 GLN E 229 HIS ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3579 moved from start: 1.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 27230 Z= 0.339 Angle : 0.833 15.366 37089 Z= 0.407 Chirality : 0.044 0.255 4610 Planarity : 0.005 0.062 4903 Dihedral : 7.369 178.327 4255 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.15 % Favored : 88.64 % Rotamer: Outliers : 4.42 % Allowed : 24.90 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.15), residues: 2853 helix: 0.01 (0.15), residues: 1219 sheet: -1.16 (0.31), residues: 274 loop : -2.98 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 283 HIS 0.010 0.002 HIS B 27 PHE 0.034 0.002 PHE B 433 TYR 0.020 0.002 TYR B 362 ARG 0.011 0.001 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 127 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.5732 (OUTLIER) cc_final: 0.4751 (tm-30) REVERT: A 159 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.5913 (ppp) REVERT: A 304 CYS cc_start: 0.7876 (m) cc_final: 0.7566 (p) REVERT: B 28 ILE cc_start: 0.2508 (tp) cc_final: 0.0796 (pt) REVERT: B 236 LYS cc_start: 0.8988 (tptt) cc_final: 0.8759 (mtmm) REVERT: B 243 SER cc_start: 0.4734 (OUTLIER) cc_final: 0.4526 (t) REVERT: B 316 LEU cc_start: 0.9008 (tt) cc_final: 0.8734 (pp) REVERT: B 317 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8399 (mm-30) REVERT: D 46 MET cc_start: 0.6238 (tpp) cc_final: 0.5400 (ttp) REVERT: D 113 MET cc_start: 0.6157 (mmt) cc_final: 0.5838 (mtm) REVERT: D 204 LYS cc_start: 0.6147 (tptt) cc_final: 0.5809 (tptt) REVERT: E 316 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7765 (t70) REVERT: F 226 GLN cc_start: 0.0598 (OUTLIER) cc_final: -0.0746 (mt0) REVERT: F 325 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8816 (mm) outliers start: 93 outliers final: 61 residues processed: 213 average time/residue: 0.3332 time to fit residues: 118.6021 Evaluate side-chains 170 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 103 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 220 TYR Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 156 optimal weight: 0.4980 chunk 200 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 273 optimal weight: 50.0000 chunk 171 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3528 moved from start: 1.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27230 Z= 0.187 Angle : 0.718 13.631 37089 Z= 0.345 Chirality : 0.041 0.272 4610 Planarity : 0.004 0.084 4903 Dihedral : 6.800 168.493 4255 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.85 % Favored : 89.98 % Rotamer: Outliers : 3.52 % Allowed : 25.86 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.18 % 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: -1.87 (0.16), residues: 2853 helix: 0.30 (0.15), residues: 1212 sheet: -1.14 (0.31), residues: 279 loop : -2.82 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 283 HIS 0.007 0.001 HIS A 327 PHE 0.016 0.001 PHE E 300 TYR 0.024 0.001 TYR B 446 ARG 0.007 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 122 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7010 (tp30) REVERT: A 159 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.6077 (ppp) REVERT: A 469 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7683 (tpp) REVERT: B 28 ILE cc_start: 0.0091 (tp) cc_final: -0.0145 (tt) REVERT: B 136 GLU cc_start: -0.3529 (OUTLIER) cc_final: -0.4200 (mt-10) REVERT: B 236 LYS cc_start: 0.8992 (tptt) cc_final: 0.8778 (mtmm) REVERT: B 316 LEU cc_start: 0.9014 (tt) cc_final: 0.8776 (pp) REVERT: B 317 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8410 (mm-30) REVERT: B 320 MET cc_start: 0.7170 (mmp) cc_final: 0.6434 (tpp) REVERT: D 46 MET cc_start: 0.6877 (tpp) cc_final: 0.6182 (ttm) REVERT: D 113 MET cc_start: 0.6366 (mmt) cc_final: 0.6038 (mtm) REVERT: D 204 LYS cc_start: 0.5756 (tptt) cc_final: 0.5368 (tptt) REVERT: F 226 GLN cc_start: 0.0632 (OUTLIER) cc_final: -0.0797 (mt0) REVERT: F 326 MET cc_start: 0.7954 (mpp) cc_final: 0.7683 (mtm) outliers start: 74 outliers final: 47 residues processed: 189 average time/residue: 0.3277 time to fit residues: 104.7790 Evaluate side-chains 164 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 113 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 220 TYR Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 0.0770 chunk 109 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 overall best weight: 2.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3546 moved from start: 1.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27230 Z= 0.198 Angle : 0.713 14.308 37089 Z= 0.342 Chirality : 0.041 0.264 4610 Planarity : 0.004 0.073 4903 Dihedral : 6.623 153.285 4255 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.34 % Favored : 89.48 % Rotamer: Outliers : 3.71 % Allowed : 26.28 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.14 % 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: -1.75 (0.16), residues: 2853 helix: 0.41 (0.15), residues: 1216 sheet: -1.02 (0.31), residues: 279 loop : -2.79 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 283 HIS 0.012 0.001 HIS A 403 PHE 0.066 0.002 PHE F 309 TYR 0.022 0.001 TYR B 446 ARG 0.005 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 118 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7478 (mm-30) cc_final: 0.6908 (tp30) REVERT: A 159 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.5953 (ppp) REVERT: A 220 LEU cc_start: 0.5100 (mt) cc_final: 0.4546 (tt) REVERT: B 136 GLU cc_start: -0.3472 (OUTLIER) cc_final: -0.4152 (mt-10) REVERT: B 236 LYS cc_start: 0.8994 (tptt) cc_final: 0.8781 (mtmm) REVERT: B 243 SER cc_start: 0.4254 (OUTLIER) cc_final: 0.4016 (t) REVERT: B 316 LEU cc_start: 0.9007 (tt) cc_final: 0.8779 (pp) REVERT: B 317 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8449 (mm-30) REVERT: B 320 MET cc_start: 0.6956 (mmp) cc_final: 0.6255 (mmm) REVERT: C 357 ARG cc_start: 0.6042 (mtm-85) cc_final: 0.5683 (mtm-85) REVERT: D 46 MET cc_start: 0.6903 (tpp) cc_final: 0.6102 (ttp) REVERT: D 113 MET cc_start: 0.6398 (mmt) cc_final: 0.6049 (mtm) REVERT: D 193 ILE cc_start: 0.0363 (OUTLIER) cc_final: -0.0266 (pt) REVERT: D 204 LYS cc_start: 0.5855 (tptt) cc_final: 0.5507 (tptt) REVERT: F 226 GLN cc_start: 0.0763 (OUTLIER) cc_final: -0.0574 (mt0) REVERT: F 326 MET cc_start: 0.7905 (mpp) cc_final: 0.7618 (mtm) outliers start: 78 outliers final: 46 residues processed: 186 average time/residue: 0.3400 time to fit residues: 107.1118 Evaluate side-chains 161 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 110 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 50.0000 chunk 239 optimal weight: 7.9990 chunk 255 optimal weight: 50.0000 chunk 153 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 chunk 254 optimal weight: 50.0000 chunk 167 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 ASN C 451 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3569 moved from start: 1.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27230 Z= 0.214 Angle : 0.726 12.490 37089 Z= 0.350 Chirality : 0.041 0.266 4610 Planarity : 0.004 0.063 4903 Dihedral : 6.563 135.652 4255 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.59 % Favored : 89.24 % Rotamer: Outliers : 2.99 % Allowed : 26.85 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.11 % 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: -1.72 (0.16), residues: 2853 helix: 0.38 (0.15), residues: 1230 sheet: -0.94 (0.32), residues: 279 loop : -2.76 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 283 HIS 0.017 0.001 HIS A 403 PHE 0.019 0.002 PHE F 100 TYR 0.019 0.002 TYR B 446 ARG 0.012 0.001 ARG D 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 112 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6933 (tp30) REVERT: A 159 MET cc_start: 0.6245 (OUTLIER) cc_final: 0.5616 (ppp) REVERT: B 46 MET cc_start: 0.0496 (mmm) cc_final: -0.0555 (mmt) REVERT: B 113 MET cc_start: 0.4994 (mmm) cc_final: 0.4704 (mtt) REVERT: B 317 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8487 (mm-30) REVERT: B 320 MET cc_start: 0.6965 (mmp) cc_final: 0.6296 (mmm) REVERT: C 357 ARG cc_start: 0.5990 (mtm-85) cc_final: 0.5712 (mtm-85) REVERT: D 46 MET cc_start: 0.6949 (tpp) cc_final: 0.6166 (ttp) REVERT: D 113 MET cc_start: 0.6145 (mmt) cc_final: 0.5769 (mtm) REVERT: D 204 LYS cc_start: 0.5755 (tptt) cc_final: 0.5343 (tptt) REVERT: E 306 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7069 (mpp) REVERT: F 226 GLN cc_start: 0.0690 (OUTLIER) cc_final: -0.0677 (mt0) REVERT: F 326 MET cc_start: 0.7999 (mpp) cc_final: 0.7525 (mtm) outliers start: 63 outliers final: 44 residues processed: 170 average time/residue: 0.3272 time to fit residues: 95.4015 Evaluate side-chains 157 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 110 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 220 TYR Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.4398 > 50: distance: 5 - 11: 26.348 distance: 11 - 12: 14.308 distance: 12 - 13: 11.640 distance: 13 - 14: 6.920 distance: 13 - 15: 7.416 distance: 15 - 16: 10.964 distance: 16 - 19: 9.193 distance: 17 - 18: 36.064 distance: 17 - 23: 26.675 distance: 19 - 20: 12.305 distance: 20 - 21: 11.447 distance: 20 - 22: 8.380 distance: 23 - 24: 19.902 distance: 24 - 25: 40.363 distance: 24 - 27: 17.229 distance: 25 - 26: 22.430 distance: 25 - 31: 39.419 distance: 27 - 28: 16.764 distance: 28 - 29: 18.497 distance: 28 - 30: 20.404 distance: 31 - 32: 39.839 distance: 32 - 33: 31.685 distance: 32 - 35: 8.817 distance: 33 - 34: 15.109 distance: 33 - 39: 38.563 distance: 35 - 36: 7.205 distance: 36 - 37: 26.361 distance: 36 - 38: 31.861 distance: 39 - 40: 27.781 distance: 40 - 41: 48.559 distance: 40 - 43: 39.874 distance: 41 - 42: 53.798 distance: 41 - 44: 26.976 distance: 44 - 45: 17.883 distance: 45 - 46: 40.222 distance: 45 - 48: 56.770 distance: 46 - 47: 21.018 distance: 46 - 52: 45.796 distance: 48 - 49: 46.741 distance: 49 - 50: 35.911 distance: 49 - 51: 44.941 distance: 52 - 53: 50.060 distance: 53 - 54: 25.953 distance: 53 - 56: 43.634 distance: 54 - 55: 47.376 distance: 54 - 61: 57.107 distance: 56 - 57: 50.962 distance: 57 - 58: 56.465 distance: 58 - 59: 41.477 distance: 58 - 60: 29.457 distance: 61 - 62: 38.942 distance: 61 - 67: 30.769 distance: 62 - 63: 12.320 distance: 62 - 65: 25.592 distance: 63 - 64: 22.876 distance: 63 - 68: 31.541 distance: 65 - 66: 40.614 distance: 66 - 67: 33.801 distance: 68 - 69: 18.192 distance: 69 - 70: 28.114 distance: 69 - 72: 28.950 distance: 70 - 71: 24.373 distance: 70 - 79: 47.136 distance: 72 - 73: 50.013 distance: 73 - 74: 54.478 distance: 74 - 75: 32.926 distance: 75 - 76: 8.746 distance: 76 - 77: 19.176 distance: 76 - 78: 27.438 distance: 79 - 80: 14.267 distance: 80 - 81: 29.123 distance: 80 - 83: 16.478 distance: 81 - 82: 28.144 distance: 81 - 88: 18.018 distance: 83 - 84: 34.027 distance: 84 - 85: 29.844 distance: 85 - 86: 26.402 distance: 85 - 87: 26.091