Starting phenix.real_space_refine on Wed Mar 20 09:58:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/03_2024/7ole_12979_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/03_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_12979/03_2024/7ole_12979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/03_2024/7ole_12979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/03_2024/7ole_12979_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/03_2024/7ole_12979_neut_updated.pdb" } 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-5265/modules/chem_data/mon_lib" Total number of atoms: 26995 Number of models: 1 Model: "" Number of chains: 14 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: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 1949 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 339} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 376} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1123 Unresolved non-hydrogen angles: 1443 Unresolved non-hydrogen dihedrals: 884 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 7, 'ASN:plan1': 5, 'TYR:plan': 3, 'UNK:plan-1': 36, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 11, 'GLU:plan': 24, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 573 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: 14.97, 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: 13.12 Conformation dependent library (CDL) restraints added in 4.2 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... running ksdssp... Secondary structure from input PDB file: 176 helices and 23 sheets defined 71.9% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.74 Creating SS restraints... Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 183 through 186 No H-bonds generated for 'chain 'A' and resid 183 through 186' Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 275 through 281 Processing helix chain 'A' and resid 338 through 346 removed outlier: 3.911A pdb=" N ALA A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 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 407 through 416 removed outlier: 4.688A pdb=" N HIS A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ARG A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA A 416 " --> pdb=" O TYR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 486 through 498 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 501 through 518 removed outlier: 4.798A pdb=" N GLN A 506 " --> pdb=" O ARG A 502 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N THR A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Proline residue: A 510 - end of helix Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.714A pdb=" N GLU A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 551 removed outlier: 5.660A pdb=" N LYS A 551 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 26 No H-bonds generated for 'chain 'B' and resid 24 through 26' Processing helix chain 'B' and resid 50 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 83 through 94 Processing helix chain 'B' and resid 105 through 108 removed outlier: 3.868A pdb=" N ILE B 108 " --> pdb=" O GLY B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 108' Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.739A pdb=" N GLU B 180 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 270 through 283 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 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 348 through 351 No H-bonds generated for 'chain 'B' and resid 348 through 351' Processing helix chain 'B' and resid 364 through 375 removed outlier: 4.287A pdb=" N ILE B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 396 removed outlier: 3.572A pdb=" N ILE B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 436 through 451 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 43 through 55 Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 98 through 101 removed outlier: 3.743A pdb=" N VAL C 101 " --> pdb=" O GLY C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 101' Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 177 through 182 removed outlier: 5.356A pdb=" N LYS C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 273 through 289 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 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 317 through 320 No H-bonds generated for 'chain 'C' and resid 317 through 320' Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 368 through 382 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 388 through 400 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 403 through 420 removed outlier: 4.026A pdb=" N GLN C 408 " --> pdb=" O ARG C 404 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 409 " --> pdb=" O TYR C 405 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THR C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Proline residue: C 412 - end of helix removed outlier: 3.601A pdb=" N ASN C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 435 removed outlier: 3.951A pdb=" N GLU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 450 Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 105 through 108 removed outlier: 3.670A pdb=" N ILE D 108 " --> pdb=" O GLY D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 105 through 108' Processing helix chain 'D' and resid 115 through 125 Processing helix chain 'D' and resid 178 through 184 removed outlier: 3.950A pdb=" N LEU D 182 " --> pdb=" O MET D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 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 270 through 283 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 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 306 through 315 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 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 348 through 352 Processing helix chain 'D' and resid 364 through 378 Processing helix chain 'D' and resid 386 through 389 No H-bonds generated for 'chain 'D' and resid 386 through 389' Processing helix chain 'D' and resid 391 through 394 No H-bonds generated for 'chain 'D' and resid 391 through 394' Processing helix chain 'D' and resid 399 through 416 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 423 through 429 removed outlier: 3.628A pdb=" N ARG D 428 " --> pdb=" O ASP D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 439 No H-bonds generated for 'chain 'D' and resid 436 through 439' Processing helix chain 'D' and resid 441 through 450 Processing helix chain 'E' and resid 12 through 14 No H-bonds generated for 'chain 'E' and resid 12 through 14' Processing helix chain 'E' and resid 17 through 20 removed outlier: 4.123A pdb=" N HIS E 20 " --> pdb=" O SER E 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 17 through 20' Processing helix chain 'E' and resid 43 through 58 Processing helix chain 'E' and resid 76 through 87 Processing helix chain 'E' and resid 98 through 101 Processing helix chain 'E' and resid 108 through 120 Processing helix chain 'E' and resid 181 through 183 No H-bonds generated for 'chain 'E' and resid 181 through 183' Processing helix chain 'E' and resid 240 through 246 Processing helix chain 'E' and resid 273 through 289 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 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 309 through 319 Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'E' and resid 352 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 368 through 382 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 388 through 400 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 403 through 406 No H-bonds generated for 'chain 'E' and resid 403 through 406' Processing helix chain 'E' and resid 408 through 419 Proline residue: E 412 - end of helix removed outlier: 3.956A pdb=" N LEU E 416 " --> pdb=" O PRO E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 436 removed outlier: 3.667A pdb=" N ILE E 433 " --> pdb=" O HIS E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 450 Processing helix chain 'F' and resid 50 through 64 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 105 through 108 removed outlier: 3.583A pdb=" N ILE F 108 " --> pdb=" O GLY F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 105 through 108' Processing helix chain 'F' and resid 115 through 126 Processing helix chain 'F' and resid 179 through 184 Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 270 through 286 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 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 343 through 345 No H-bonds generated for 'chain 'F' and resid 343 through 345' Processing helix chain 'F' and resid 348 through 351 No H-bonds generated for 'chain 'F' and resid 348 through 351' Processing helix chain 'F' and resid 364 through 378 removed outlier: 3.572A pdb=" N GLU F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 396 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 400 through 415 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 423 through 432 Processing helix chain 'F' and resid 436 through 451 Processing helix chain 'H' and resid 40 through 54 Processing helix chain 'H' and resid 64 through 81 Processing helix chain 'H' and resid 88 through 110 Processing helix chain 'H' and resid 114 through 134 removed outlier: 3.768A pdb=" N UNK H 133 " --> pdb=" O UNK H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 155 Processing helix chain 'H' and resid 157 through 160 No H-bonds generated for 'chain 'H' and resid 157 through 160' Processing helix chain 'H' and resid 162 through 175 removed outlier: 4.160A pdb=" N UNK H 166 " --> pdb=" O UNK H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 190 Processing helix chain 'H' and resid 192 through 218 removed outlier: 6.771A pdb=" N UNK H 200 " --> pdb=" O UNK H 197 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N UNK H 218 " --> pdb=" O UNK H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 238 Processing helix chain 'H' and resid 241 through 244 No H-bonds generated for 'chain 'H' and resid 241 through 244' Processing helix chain 'H' and resid 246 through 255 Processing helix chain 'H' and resid 264 through 276 Processing helix chain 'H' and resid 282 through 292 Processing helix chain 'H' and resid 297 through 309 Processing helix chain 'H' and resid 314 through 334 Processing helix chain 'H' and resid 340 through 359 Processing helix chain 'H' and resid 363 through 375 Processing helix chain 'H' and resid 379 through 389 Processing helix chain 'H' and resid 392 through 399 Processing helix chain 'H' and resid 402 through 413 Processing helix chain 'H' and resid 417 through 428 Processing helix chain 'H' and resid 435 through 449 Processing helix chain 'H' and resid 453 through 474 removed outlier: 3.509A pdb=" N UNK H 457 " --> pdb=" O UNK H 454 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK H 472 " --> pdb=" O UNK H 469 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N UNK H 474 " --> pdb=" O UNK H 471 " (cutoff:3.500A) Processing helix chain 'H' and resid 477 through 494 Processing helix chain 'H' and resid 498 through 515 removed outlier: 3.827A pdb=" N UNK H 502 " --> pdb=" O UNK H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 521 through 539 Processing helix chain 'H' and resid 542 through 553 Processing helix chain 'H' and resid 561 through 572 Processing helix chain 'H' and resid 583 through 597 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) Processing helix chain 'H' and resid 602 through 617 Processing helix chain 'H' and resid 622 through 635 removed outlier: 3.557A pdb=" N UNK H 635 " --> pdb=" O UNK H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 646 Processing helix chain 'H' and resid 651 through 659 Processing helix chain 'H' and resid 670 through 681 Processing helix chain 'J' and resid 45 through 59 Processing helix chain 'J' and resid 71 through 82 Processing helix chain 'J' and resid 88 through 100 Processing helix chain 'J' and resid 102 through 121 Processing helix chain 'J' and resid 127 through 146 Processing helix chain 'J' and resid 153 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 175 through 189 Processing helix chain 'J' and resid 195 through 210 removed outlier: 3.672A pdb=" N UNK J 200 " --> pdb=" O UNK J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 230 Processing helix chain 'J' and resid 234 through 238 Processing helix chain 'J' and resid 244 through 262 Processing helix chain 'J' and resid 266 through 279 Processing helix chain 'J' and resid 288 through 303 removed outlier: 3.820A pdb=" N UNK J 295 " --> pdb=" O UNK J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 328 Processing helix chain 'J' and resid 332 through 348 Processing helix chain 'J' and resid 352 through 375 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 378 through 419 removed outlier: 7.472A pdb=" N UNK J 398 " --> pdb=" O UNK J 394 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N UNK J 399 " --> pdb=" O UNK J 395 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 444 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 447 through 450 No H-bonds generated for 'chain 'J' and resid 447 through 450' Processing helix chain 'J' and resid 457 through 474 Processing helix chain 'J' and resid 480 through 493 Processing helix chain 'J' and resid 497 through 507 Processing helix chain 'K' and resid 12 through 21 Processing helix chain 'K' and resid 25 through 37 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 41 through 66 removed outlier: 3.970A pdb=" N UNK K 45 " --> pdb=" O UNK K 41 " (cutoff:3.500A) Proline residue: K 50 - end of helix Proline residue: K 61 - end of helix removed outlier: 3.823A pdb=" N LEU K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 87 removed outlier: 3.813A pdb=" N ALA K 79 " --> pdb=" O PRO K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 102 Processing helix chain 'K' and resid 106 through 136 Proline residue: K 127 - end of helix Processing helix chain 'K' and resid 143 through 162 removed outlier: 4.388A pdb=" N UNK K 156 " --> pdb=" O UNK K 152 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY K 157 " --> pdb=" O UNK K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 189 Processing helix chain 'K' and resid 197 through 213 Processing helix chain 'K' and resid 216 through 232 Proline residue: K 225 - end of helix Processing helix chain 'K' and resid 236 through 244 Processing helix chain 'K' and resid 249 through 263 Processing helix chain 'K' and resid 265 through 276 Processing helix chain 'K' and resid 283 through 294 Processing helix chain 'K' and resid 300 through 316 Processing helix chain 'K' and resid 318 through 332 removed outlier: 3.913A pdb=" N LEU K 321 " --> pdb=" O ARG K 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 339 No H-bonds generated for 'chain 'K' and resid 336 through 339' Processing helix chain 'K' and resid 344 through 358 Processing helix chain 'K' and resid 364 through 385 Processing helix chain 'K' and resid 389 through 402 Processing sheet with id= A, first strand: chain 'A' and resid 222 through 229 Processing sheet with id= B, first strand: chain 'A' and resid 257 through 259 Processing sheet with id= C, first strand: chain 'B' and resid 72 through 76 Processing sheet with id= D, first strand: chain 'B' and resid 100 through 102 removed outlier: 7.131A pdb=" N VAL B 295 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 323 " --> pdb=" O LEU B 296 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 132 through 138 Processing sheet with id= F, first strand: chain 'B' and resid 161 through 163 Processing sheet with id= G, first strand: chain 'B' and resid 332 through 334 Processing sheet with id= H, first strand: chain 'C' and resid 94 through 97 removed outlier: 3.704A pdb=" N CYS C 94 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE C 300 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE C 326 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL C 301 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE C 328 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 236 through 239 Processing sheet with id= J, first strand: chain 'C' and resid 127 through 130 Processing sheet with id= K, first strand: chain 'C' and resid 131 through 133 Processing sheet with id= L, first strand: chain 'C' and resid 157 through 162 Processing sheet with id= M, first strand: chain 'C' and resid 335 through 337 Processing sheet with id= N, first strand: chain 'D' and resid 354 through 357 removed outlier: 6.860A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP D 299 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 332 through 334 Processing sheet with id= P, first strand: chain 'E' and resid 358 through 363 removed outlier: 6.536A pdb=" N ALA E 65 " --> pdb=" O MET E 359 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE E 361 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU E 67 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR E 363 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA E 69 " --> pdb=" O THR E 363 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 292 through 294 Processing sheet with id= R, first strand: chain 'E' and resid 157 through 159 Processing sheet with id= S, first strand: chain 'E' and resid 335 through 337 Processing sheet with id= T, first strand: chain 'F' and resid 354 through 358 removed outlier: 6.715A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 290 through 293 Processing sheet with id= V, first strand: chain 'F' and resid 160 through 163 Processing sheet with id= W, first strand: chain 'F' and resid 332 through 334 1397 hydrogen bonds defined for protein. 3849 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: 8.30 Time building geometry restraints manager: 13.88 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: 5698 1.40 - 1.54: 16338 1.54 - 1.68: 214 1.68 - 1.83: 151 Bond restraints: 27233 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 27228 not shown) Histogram of bond angle deviations from ideal: 81.57 - 96.12: 16 96.12 - 110.67: 9943 110.67 - 125.22: 26610 125.22 - 139.77: 526 139.77 - 154.32: 3 Bond angle restraints: 37098 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 37093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 16318 35.01 - 70.03: 272 70.03 - 105.04: 30 105.04 - 140.05: 6 140.05 - 175.07: 2 Dihedral angle restraints: 16628 sinusoidal: 4978 harmonic: 11650 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 16625 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: 4906 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 4903 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 58 2.14 - 2.83: 10872 2.83 - 3.52: 46258 3.52 - 4.21: 64747 4.21 - 4.90: 104143 Nonbonded interactions: 226078 Sorted by model distance: nonbonded pdb=" O UNK H 376 " pdb=" CB UNK H 381 " model vdw 1.448 3.440 nonbonded pdb=" CB UNK J 393 " pdb=" O GLY J 400 " model vdw 1.456 3.440 nonbonded pdb=" O GLN K 171 " pdb=" CB PHE K 174 " model vdw 1.614 3.440 nonbonded pdb=" O ALA K 91 " pdb=" CB SER K 94 " model vdw 1.699 3.440 nonbonded pdb=" O LEU A 124 " pdb=" OG SER B 410 " model vdw 1.781 2.440 ... (remaining 226073 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: 1.000 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: 0.030 Extract box with map and model: 6.450 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 73.260 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.240 ------------------------------------------------------------------------------- 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 27233 Z= 0.783 Angle : 1.742 43.583 37098 Z= 0.969 Chirality : 0.099 1.687 4610 Planarity : 0.009 0.139 4906 Dihedral : 15.117 175.065 9044 Min Nonbonded Distance : 1.448 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 : 2.625 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: 0.3913 time to fit residues: 215.5444 Evaluate side-chains 212 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 2.706 ------------------------------------------------------------------------------- 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: 288 random chunks: chunk 243 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 302 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 HIS F 447 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2907 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27233 Z= 0.243 Angle : 0.872 15.620 37098 Z= 0.427 Chirality : 0.044 0.271 4610 Planarity : 0.005 0.085 4906 Dihedral : 8.658 147.479 4260 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.52 % Favored : 89.03 % Rotamer: Outliers : 3.90 % Allowed : 19.01 % Favored : 77.09 % 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: -3.60 (0.14), residues: 2853 helix: -1.29 (0.14), residues: 1214 sheet: -1.98 (0.30), residues: 263 loop : -3.60 (0.14), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 283 HIS 0.011 0.002 HIS B 27 PHE 0.023 0.002 PHE F 297 TYR 0.029 0.002 TYR E 192 ARG 0.009 0.001 ARG F 438 *********************** 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 311 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 229 time to evaluate : 2.957 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 154 ILE cc_start: 0.5248 (pt) cc_final: 0.4900 (pt) REVERT: A 159 MET cc_start: 0.6667 (ptm) cc_final: 0.6195 (ppp) REVERT: A 212 GLU cc_start: 0.6859 (tp30) cc_final: 0.6312 (tp30) REVERT: A 216 ARG cc_start: 0.4473 (tpm170) cc_final: 0.3511 (ptm160) REVERT: A 304 CYS cc_start: 0.7883 (m) cc_final: 0.7576 (p) REVERT: A 476 ARG cc_start: 0.2611 (mmt180) cc_final: 0.1431 (mtt180) REVERT: B 125 ARG cc_start: 0.6610 (tpp80) cc_final: 0.5959 (tpt90) REVERT: B 168 MET cc_start: 0.2229 (ptp) cc_final: 0.2001 (ttp) REVERT: B 170 THR cc_start: 0.3697 (OUTLIER) cc_final: 0.3381 (p) REVERT: B 371 LEU cc_start: 0.3762 (OUTLIER) cc_final: 0.3547 (mp) REVERT: B 382 MET cc_start: 0.3526 (tpt) cc_final: 0.2980 (ttt) REVERT: D 113 MET cc_start: 0.6441 (mmt) cc_final: 0.5774 (mtm) outliers start: 82 outliers final: 29 residues processed: 293 average time/residue: 0.3635 time to fit residues: 173.0058 Evaluate side-chains 221 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 2.758 ------------------------------------------------------------------------------- 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 443 THR 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 170 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 371 LEU 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 326 ILE Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 190 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 50 LEU Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 431 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 50.0000 chunk 81 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 262 optimal weight: 40.0000 chunk 283 optimal weight: 9.9990 chunk 233 optimal weight: 8.9990 chunk 259 optimal weight: 50.0000 chunk 89 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 483 ASN B 41 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** 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 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS F 226 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3338 moved from start: 0.7388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 27233 Z= 0.341 Angle : 0.916 15.850 37098 Z= 0.452 Chirality : 0.046 0.317 4610 Planarity : 0.006 0.109 4906 Dihedral : 7.893 159.914 4258 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 27.31 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.88 % Favored : 87.73 % Rotamer: Outliers : 5.66 % Allowed : 21.58 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.29 % 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: -3.15 (0.14), residues: 2853 helix: -0.83 (0.14), residues: 1167 sheet: -1.98 (0.29), residues: 285 loop : -3.32 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 283 HIS 0.013 0.002 HIS A 118 PHE 0.025 0.003 PHE F 109 TYR 0.025 0.002 TYR D 387 ARG 0.025 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 309 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 190 time to evaluate : 3.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6988 (tp30) cc_final: 0.6664 (tp30) REVERT: A 304 CYS cc_start: 0.7860 (m) cc_final: 0.7469 (p) REVERT: A 384 TYR cc_start: 0.5397 (OUTLIER) cc_final: 0.5158 (m-10) REVERT: A 458 ILE cc_start: 0.3134 (OUTLIER) cc_final: 0.2872 (tt) REVERT: A 469 MET cc_start: 0.8579 (mtp) cc_final: 0.8368 (mtm) REVERT: B 88 MET cc_start: 0.7059 (tpt) cc_final: 0.6831 (tpp) REVERT: B 168 MET cc_start: 0.2302 (ptp) cc_final: 0.2041 (ttp) REVERT: B 232 LEU cc_start: 0.1047 (OUTLIER) cc_final: 0.0556 (mt) REVERT: B 317 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8000 (mm-30) REVERT: B 404 GLN cc_start: 0.2477 (OUTLIER) cc_final: 0.2160 (mm-40) REVERT: B 434 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5496 (pp) REVERT: C 52 ILE cc_start: 0.1468 (OUTLIER) cc_final: 0.0687 (tt) REVERT: C 358 VAL cc_start: 0.8846 (t) cc_final: 0.8639 (m) REVERT: D 46 MET cc_start: 0.6971 (tpp) cc_final: 0.6230 (ttm) REVERT: D 113 MET cc_start: 0.6617 (mmt) cc_final: 0.6316 (mtm) REVERT: E 359 MET cc_start: 0.8250 (mpp) cc_final: 0.8028 (mtt) REVERT: F 178 MET cc_start: -0.2481 (ttt) cc_final: -0.3897 (pmm) outliers start: 119 outliers final: 48 residues processed: 295 average time/residue: 0.3396 time to fit residues: 167.0851 Evaluate side-chains 198 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 143 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 THR 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 324 LEU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 404 GLN Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 77 THR 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 309 ILE 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 D residue 110 SER Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 248 ASP 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 228 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain F residue 50 LEU 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 316 LEU Chi-restraints excluded: chain F residue 317 GLU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 329 ASN Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 20.0000 chunk 196 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 262 optimal weight: 40.0000 chunk 278 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 249 optimal weight: 30.0000 chunk 75 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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** B 41 GLN B 92 GLN B 233 GLN ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3490 moved from start: 0.9480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 27233 Z= 0.326 Angle : 0.834 12.810 37098 Z= 0.412 Chirality : 0.044 0.305 4610 Planarity : 0.005 0.095 4906 Dihedral : 7.411 157.711 4258 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 24.48 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.97 % Favored : 88.71 % Rotamer: Outliers : 4.85 % Allowed : 24.48 % 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: -2.80 (0.15), residues: 2853 helix: -0.52 (0.14), residues: 1209 sheet: -1.73 (0.30), residues: 282 loop : -3.25 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 283 HIS 0.013 0.002 HIS D 245 PHE 0.023 0.002 PHE A 427 TYR 0.016 0.002 TYR A 503 ARG 0.010 0.001 ARG B 438 *********************** 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 248 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 146 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6319 (tpm170) cc_final: 0.6024 (ttp-170) REVERT: A 304 CYS cc_start: 0.7771 (m) cc_final: 0.7469 (p) REVERT: A 429 SER cc_start: 0.5925 (m) cc_final: 0.5677 (t) REVERT: B 168 MET cc_start: 0.1809 (ptp) cc_final: 0.1374 (ttp) REVERT: B 232 LEU cc_start: 0.1143 (OUTLIER) cc_final: 0.0504 (tp) REVERT: B 317 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8553 (mm-30) REVERT: D 46 MET cc_start: 0.6131 (tpp) cc_final: 0.5332 (ttm) REVERT: D 113 MET cc_start: 0.6590 (mmt) cc_final: 0.6359 (mtm) outliers start: 102 outliers final: 44 residues processed: 239 average time/residue: 0.3392 time to fit residues: 133.0145 Evaluate side-chains 172 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 127 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 79 LEU 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 313 THR Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 397 THR 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 228 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 73 VAL 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 316 LEU Chi-restraints excluded: chain F residue 382 MET 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: 288 random chunks: chunk 231 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 237 optimal weight: 0.6980 chunk 192 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 249 optimal weight: 50.0000 chunk 70 optimal weight: 1.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** 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 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 HIS ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3569 moved from start: 1.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 27233 Z= 0.315 Angle : 0.812 12.872 37098 Z= 0.401 Chirality : 0.044 0.255 4610 Planarity : 0.005 0.077 4906 Dihedral : 7.287 153.453 4258 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.15 % Favored : 88.50 % Rotamer: Outliers : 4.42 % Allowed : 25.62 % Favored : 69.96 % 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: -2.57 (0.15), residues: 2853 helix: -0.34 (0.15), residues: 1220 sheet: -1.64 (0.30), residues: 279 loop : -3.12 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 283 HIS 0.010 0.002 HIS A 403 PHE 0.026 0.002 PHE A 427 TYR 0.016 0.002 TYR E 209 ARG 0.011 0.001 ARG E 362 *********************** 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 220 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 127 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 SER cc_start: 0.5482 (m) cc_final: 0.5274 (t) REVERT: B 28 ILE cc_start: 0.2607 (tp) cc_final: 0.1146 (pt) REVERT: B 136 GLU cc_start: -0.3350 (OUTLIER) cc_final: -0.4025 (mt-10) REVERT: B 168 MET cc_start: 0.1852 (ptp) cc_final: 0.1423 (ttp) REVERT: B 232 LEU cc_start: 0.1688 (OUTLIER) cc_final: 0.0840 (tp) REVERT: B 236 LYS cc_start: 0.8673 (tptt) cc_final: 0.8276 (mtmm) REVERT: B 243 SER cc_start: 0.4705 (OUTLIER) cc_final: 0.4487 (t) REVERT: B 317 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8475 (mm-30) REVERT: B 320 MET cc_start: 0.7028 (mmm) cc_final: 0.6635 (mmp) REVERT: D 46 MET cc_start: 0.6328 (tpp) cc_final: 0.5508 (ttm) REVERT: D 113 MET cc_start: 0.6334 (mmt) cc_final: 0.6070 (mtm) REVERT: D 204 LYS cc_start: 0.6049 (tptt) cc_final: 0.5696 (tptt) outliers start: 93 outliers final: 45 residues processed: 210 average time/residue: 0.3591 time to fit residues: 127.1704 Evaluate side-chains 166 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 117 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 79 LEU 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 353 ASP Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 248 ASP 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 E residue 6 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 316 LEU 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: 288 random chunks: chunk 93 optimal weight: 0.0980 chunk 250 optimal weight: 40.0000 chunk 55 optimal weight: 40.0000 chunk 163 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 278 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 HIS B 41 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3578 moved from start: 1.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27233 Z= 0.262 Angle : 0.753 15.838 37098 Z= 0.369 Chirality : 0.042 0.263 4610 Planarity : 0.004 0.069 4906 Dihedral : 6.974 147.516 4258 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.08 % Favored : 88.71 % Rotamer: Outliers : 3.75 % Allowed : 25.86 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.29 % 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: -2.43 (0.15), residues: 2853 helix: -0.20 (0.15), residues: 1230 sheet: -1.47 (0.30), residues: 281 loop : -3.12 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 283 HIS 0.008 0.001 HIS A 339 PHE 0.025 0.002 PHE F 100 TYR 0.022 0.002 TYR B 446 ARG 0.009 0.001 ARG B 53 *********************** 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 202 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 123 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 317 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8555 (mm-30) REVERT: B 320 MET cc_start: 0.6953 (mmm) cc_final: 0.6603 (mmp) REVERT: C 357 ARG cc_start: 0.6321 (mtm-85) cc_final: 0.5629 (mtm-85) REVERT: D 113 MET cc_start: 0.6415 (mmt) cc_final: 0.6179 (mtm) outliers start: 79 outliers final: 51 residues processed: 195 average time/residue: 0.3348 time to fit residues: 108.7871 Evaluate side-chains 168 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 117 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 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 342 GLU Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 119 LEU 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 366 ASP Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 114 SER 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 316 LEU Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 363 SER 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: 288 random chunks: chunk 268 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 203 optimal weight: 0.0770 chunk 157 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 277 optimal weight: 20.0000 chunk 173 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.7742 ------------------------------------------------------------------------------- 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 ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3552 moved from start: 1.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27233 Z= 0.185 Angle : 0.699 14.973 37098 Z= 0.338 Chirality : 0.040 0.253 4610 Planarity : 0.004 0.092 4906 Dihedral : 6.607 136.934 4258 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.13 % Favored : 89.62 % Rotamer: Outliers : 2.99 % Allowed : 26.90 % Favored : 70.10 % 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: -2.17 (0.16), residues: 2853 helix: 0.04 (0.15), residues: 1238 sheet: -1.35 (0.31), residues: 275 loop : -3.01 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 283 HIS 0.007 0.001 HIS A 327 PHE 0.015 0.001 PHE E 300 TYR 0.017 0.001 TYR B 446 ARG 0.007 0.000 ARG D 428 *********************** 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 184 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 121 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 GLU cc_start: 0.5542 (mp0) cc_final: 0.4401 (mp0) REVERT: B 317 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8520 (mm-30) REVERT: B 320 MET cc_start: 0.7125 (mmm) cc_final: 0.6820 (mmp) REVERT: C 173 ASP cc_start: 0.2563 (OUTLIER) cc_final: 0.2113 (t70) REVERT: D 46 MET cc_start: 0.5982 (tpp) cc_final: 0.5280 (ttm) REVERT: D 113 MET cc_start: 0.6650 (mmt) cc_final: 0.6322 (mtm) REVERT: D 204 LYS cc_start: 0.5772 (tptt) cc_final: 0.5417 (tptt) REVERT: D 443 MET cc_start: 0.6558 (mtt) cc_final: 0.6340 (mtt) REVERT: F 326 MET cc_start: 0.8016 (mpp) cc_final: 0.7374 (mtm) outliers start: 63 outliers final: 41 residues processed: 178 average time/residue: 0.3393 time to fit residues: 101.7707 Evaluate side-chains 154 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 112 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE 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 B residue 58 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 77 THR 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 173 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 135 THR 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 366 ASP Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 316 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.9990 chunk 110 optimal weight: 20.0000 chunk 165 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3640 moved from start: 1.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 27233 Z= 0.337 Angle : 0.803 18.627 37098 Z= 0.394 Chirality : 0.043 0.283 4610 Planarity : 0.005 0.096 4906 Dihedral : 7.099 141.224 4258 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 26.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.92 % Favored : 87.84 % Rotamer: Outliers : 3.85 % Allowed : 26.24 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.29 % 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: -2.36 (0.15), residues: 2853 helix: -0.15 (0.15), residues: 1228 sheet: -1.40 (0.31), residues: 285 loop : -3.07 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 283 HIS 0.013 0.002 HIS A 339 PHE 0.031 0.002 PHE A 427 TYR 0.022 0.002 TYR B 387 ARG 0.009 0.001 ARG B 374 *********************** 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 200 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 119 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ILE cc_start: 0.5229 (mt) cc_final: 0.4959 (mt) REVERT: A 401 GLU cc_start: 0.5318 (mp0) cc_final: 0.4883 (mp0) REVERT: B 46 MET cc_start: 0.0934 (mmm) cc_final: 0.0134 (mmt) REVERT: B 236 LYS cc_start: 0.8644 (tptt) cc_final: 0.8228 (mtmm) REVERT: B 317 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8549 (mm-30) REVERT: B 320 MET cc_start: 0.6817 (mmm) cc_final: 0.6496 (mmp) REVERT: D 46 MET cc_start: 0.6197 (tpp) cc_final: 0.5370 (ttm) REVERT: D 113 MET cc_start: 0.6341 (mmt) cc_final: 0.6079 (mtm) REVERT: D 204 LYS cc_start: 0.5681 (tptt) cc_final: 0.5344 (tptt) REVERT: D 443 MET cc_start: 0.6959 (mtt) cc_final: 0.6625 (mtt) REVERT: E 61 MET cc_start: 0.7737 (mmm) cc_final: 0.7340 (mpp) REVERT: F 326 MET cc_start: 0.7979 (mpp) cc_final: 0.7315 (mtm) outliers start: 81 outliers final: 53 residues processed: 192 average time/residue: 0.3420 time to fit residues: 109.0500 Evaluate side-chains 166 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 113 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 277 SER 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 A residue 437 ARG Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 79 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 342 GLU Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 40.0000 chunk 265 optimal weight: 9.9990 chunk 242 optimal weight: 8.9990 chunk 258 optimal weight: 50.0000 chunk 155 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 233 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 257 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3600 moved from start: 1.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27233 Z= 0.203 Angle : 0.709 12.135 37098 Z= 0.345 Chirality : 0.040 0.257 4610 Planarity : 0.004 0.103 4906 Dihedral : 6.654 134.475 4258 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.23 % Favored : 89.55 % Rotamer: Outliers : 2.57 % Allowed : 27.23 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % 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: -2.11 (0.16), residues: 2853 helix: 0.12 (0.15), residues: 1224 sheet: -1.28 (0.32), residues: 275 loop : -3.00 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 283 HIS 0.008 0.001 HIS A 327 PHE 0.067 0.002 PHE F 309 TYR 0.015 0.001 TYR A 318 ARG 0.008 0.000 ARG C 357 *********************** 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 170 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 116 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ARG cc_start: 0.4217 (tmm160) cc_final: 0.3753 (mtt-85) REVERT: B 46 MET cc_start: 0.0945 (mmm) cc_final: -0.0805 (mmt) REVERT: B 317 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8567 (mm-30) REVERT: B 320 MET cc_start: 0.6872 (mmm) cc_final: 0.6557 (mmp) REVERT: D 46 MET cc_start: 0.6326 (tpp) cc_final: 0.5474 (ttm) REVERT: D 113 MET cc_start: 0.6623 (mmt) cc_final: 0.6342 (mtm) REVERT: E 61 MET cc_start: 0.7694 (mmm) cc_final: 0.7278 (mpp) REVERT: F 326 MET cc_start: 0.7908 (mpp) cc_final: 0.7243 (mtm) outliers start: 54 outliers final: 42 residues processed: 165 average time/residue: 0.3376 time to fit residues: 94.3018 Evaluate side-chains 154 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 112 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 73 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 268 ILE 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 77 THR 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 342 GLU Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 225 VAL 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 430 TYR 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 242 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 316 LEU 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 ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 7.9990 chunk 273 optimal weight: 50.0000 chunk 166 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 286 optimal weight: 20.0000 chunk 264 optimal weight: 0.7980 chunk 228 optimal weight: 40.0000 chunk 23 optimal weight: 0.0170 chunk 176 optimal weight: 2.9990 chunk 140 optimal weight: 30.0000 overall best weight: 2.3624 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** 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 49 GLN F 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3604 moved from start: 1.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27233 Z= 0.206 Angle : 0.706 12.188 37098 Z= 0.343 Chirality : 0.040 0.269 4610 Planarity : 0.004 0.102 4906 Dihedral : 6.467 121.662 4258 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.73 % Favored : 89.06 % Rotamer: Outliers : 2.28 % Allowed : 27.47 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % 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: -1.97 (0.16), residues: 2853 helix: 0.25 (0.15), residues: 1224 sheet: -1.18 (0.32), residues: 277 loop : -2.93 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 283 HIS 0.007 0.001 HIS B 27 PHE 0.025 0.002 PHE F 309 TYR 0.015 0.001 TYR D 446 ARG 0.008 0.000 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 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 165 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 117 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.1907 (ppp) cc_final: 0.1697 (ppp) REVERT: B 46 MET cc_start: 0.0121 (mmm) cc_final: -0.0752 (mmt) REVERT: B 113 MET cc_start: 0.5674 (mpp) cc_final: 0.5316 (mtt) REVERT: B 236 LYS cc_start: 0.8759 (tptt) cc_final: 0.8384 (mtmm) REVERT: B 317 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8552 (mm-30) REVERT: B 320 MET cc_start: 0.6806 (mmm) cc_final: 0.6481 (mmp) REVERT: D 46 MET cc_start: 0.6275 (tpp) cc_final: 0.5475 (ttm) REVERT: D 113 MET cc_start: 0.6451 (mmt) cc_final: 0.6149 (ttp) REVERT: E 61 MET cc_start: 0.7704 (mmm) cc_final: 0.7302 (mpp) REVERT: F 326 MET cc_start: 0.7791 (mpp) cc_final: 0.7198 (mtm) outliers start: 48 outliers final: 43 residues processed: 161 average time/residue: 0.3753 time to fit residues: 102.1821 Evaluate side-chains 156 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 113 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG 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 472 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 77 THR 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 342 GLU Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 135 THR 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 366 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 242 ASP Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 450 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 20.0000 chunk 243 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 228 optimal weight: 0.0070 chunk 95 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 GLN ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.096997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.074696 restraints weight = 189211.820| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 8.52 r_work: 0.3466 rms_B_bonded: 8.22 restraints_weight: 2.0000 r_work: 0.3558 rms_B_bonded: 5.38 restraints_weight: 4.0000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 1.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.216 27233 Z= 0.274 Angle : 0.819 59.193 37098 Z= 0.426 Chirality : 0.040 0.293 4610 Planarity : 0.004 0.103 4906 Dihedral : 6.462 121.583 4258 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.80 % Favored : 88.99 % Rotamer: Outliers : 2.38 % Allowed : 27.52 % Favored : 70.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % 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: -1.97 (0.16), residues: 2853 helix: 0.25 (0.15), residues: 1224 sheet: -1.18 (0.32), residues: 277 loop : -2.93 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 283 HIS 0.006 0.001 HIS A 327 PHE 0.028 0.002 PHE D 452 TYR 0.029 0.002 TYR B 442 ARG 0.008 0.000 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6240.26 seconds wall clock time: 113 minutes 10.10 seconds (6790.10 seconds total)