Starting phenix.real_space_refine on Tue Feb 20 22:25:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/02_2024/6oa9_0665_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/02_2024/6oa9_0665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/02_2024/6oa9_0665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/02_2024/6oa9_0665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/02_2024/6oa9_0665_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/02_2024/6oa9_0665_neut_updated.pdb" } resolution = 3.9 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= 0.017 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 29 5.49 5 S 129 5.16 5 C 18142 2.51 5 N 5035 2.21 5 O 5669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ASP 324": "OD1" <-> "OD2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A ARG 609": "NH1" <-> "NH2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 776": "NH1" <-> "NH2" Residue "A ARG 788": "NH1" <-> "NH2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 348": "NH1" <-> "NH2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B ASP 487": "OD1" <-> "OD2" Residue "B TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "C ARG 235": "NH1" <-> "NH2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 348": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "C ASP 378": "OD1" <-> "OD2" Residue "C TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C ARG 596": "NH1" <-> "NH2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C ASP 650": "OD1" <-> "OD2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 348": "NH1" <-> "NH2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D ARG 392": "NH1" <-> "NH2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D ASP 487": "OD1" <-> "OD2" Residue "D TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D PHE 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 648": "NH1" <-> "NH2" Residue "D TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 717": "NH1" <-> "NH2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E ASP 324": "OD1" <-> "OD2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 392": "NH1" <-> "NH2" Residue "E GLU 504": "OE1" <-> "OE2" Residue "E TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 596": "NH1" <-> "NH2" Residue "E TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 210": "OE1" <-> "OE2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F ARG 297": "NH1" <-> "NH2" Residue "F PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 323": "NH1" <-> "NH2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F ARG 348": "NH1" <-> "NH2" Residue "F ARG 392": "NH1" <-> "NH2" Residue "F ASP 405": "OD1" <-> "OD2" Residue "F GLU 476": "OE1" <-> "OE2" Residue "F GLU 480": "OE1" <-> "OE2" Residue "F GLU 504": "OE1" <-> "OE2" Residue "F TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 574": "OD1" <-> "OD2" Residue "F ARG 609": "NH1" <-> "NH2" Residue "F ARG 645": "NH1" <-> "NH2" Residue "F PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 776": "NH1" <-> "NH2" Residue "F TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K ASP 39": "OD1" <-> "OD2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 242": "NH1" <-> "NH2" Residue "J TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "G ARG 142": "NH1" <-> "NH2" Residue "G PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G GLU 209": "OE1" <-> "OE2" Residue "G GLU 230": "OE1" <-> "OE2" Residue "G PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 312": "NH1" <-> "NH2" Residue "G ARG 321": "NH1" <-> "NH2" Residue "G PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 364": "NH1" <-> "NH2" Residue "G PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 404": "OE1" <-> "OE2" Residue "G GLU 406": "OE1" <-> "OE2" Residue "G ASP 430": "OD1" <-> "OD2" Residue "G ARG 432": "NH1" <-> "NH2" Residue "G PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 474": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29006 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4206 Classifications: {'peptide': 547} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 518} Chain breaks: 1 Chain: "B" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3767 Classifications: {'peptide': 493} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 3759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3759 Classifications: {'peptide': 492} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 464} Chain breaks: 1 Chain: "D" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3747 Classifications: {'peptide': 489} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 461} Chain breaks: 1 Chain: "E" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3786 Classifications: {'peptide': 496} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 468} Chain breaks: 1 Chain: "F" Number of atoms: 4093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4093 Classifications: {'peptide': 533} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 505} Chain breaks: 2 Chain: "K" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "H" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "J" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "G" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3762 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 447} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'ATP': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25196 SG CYS G 145 47.953 81.487 84.359 1.00137.84 S ATOM 25812 SG CYS G 219 71.508 37.375 89.822 1.00142.70 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N LEU H 173 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU H 173 " occ=0.45 residue: pdb=" N ARG H 174 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG H 174 " occ=0.45 residue: pdb=" N GLY H 175 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY H 175 " occ=0.25 residue: pdb=" N GLY H 176 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY H 176 " occ=0.25 residue: pdb=" N LEU J 273 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU J 273 " occ=0.45 residue: pdb=" N ARG J 274 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG J 274 " occ=0.45 residue: pdb=" N GLY J 275 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY J 275 " occ=0.25 residue: pdb=" N GLY J 276 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY J 276 " occ=0.25 Time building chain proxies: 14.80, per 1000 atoms: 0.51 Number of scatterers: 29006 At special positions: 0 Unit cell: (144.45, 140.4, 178.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 129 16.00 P 29 15.00 O 5669 8.00 N 5035 7.00 C 18142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.51 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 139 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 145 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 219 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 208 " 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6870 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 157 helices and 19 sheets defined 32.8% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.78 Creating SS restraints... Processing helix chain 'A' and resid 220 through 235 removed outlier: 3.663A pdb=" N GLN A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.867A pdb=" N ILE A 243 " --> pdb=" O PHE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 removed outlier: 3.562A pdb=" N GLU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 285 No H-bonds generated for 'chain 'A' and resid 282 through 285' Processing helix chain 'A' and resid 289 through 305 removed outlier: 3.877A pdb=" N GLU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 No H-bonds generated for 'chain 'A' and resid 316 through 319' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.547A pdb=" N LEU A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 418 through 435 removed outlier: 3.665A pdb=" N SER A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 496 through 501 removed outlier: 3.746A pdb=" N GLU A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 536 through 538 No H-bonds generated for 'chain 'A' and resid 536 through 538' Processing helix chain 'A' and resid 567 through 577 removed outlier: 3.650A pdb=" N ILE A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 596 No H-bonds generated for 'chain 'A' and resid 593 through 596' Processing helix chain 'A' and resid 611 through 620 removed outlier: 3.845A pdb=" N THR A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU A 617 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 620 " --> pdb=" O THR A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 664 through 669 removed outlier: 3.824A pdb=" N ALA A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 706 through 708 No H-bonds generated for 'chain 'A' and resid 706 through 708' Processing helix chain 'A' and resid 755 through 764 removed outlier: 3.542A pdb=" N PHE A 758 " --> pdb=" O LYS A 755 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 759 " --> pdb=" O GLU A 756 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU A 760 " --> pdb=" O HIS A 757 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 761 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET A 762 " --> pdb=" O ALA A 759 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 763 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR A 764 " --> pdb=" O ALA A 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 764' Processing helix chain 'A' and resid 771 through 778 removed outlier: 4.107A pdb=" N ARG A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 261 through 270 removed outlier: 3.674A pdb=" N ALA B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG B 266 " --> pdb=" O THR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 removed outlier: 3.529A pdb=" N ALA B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 304 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 330 through 345 removed outlier: 3.526A pdb=" N VAL B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 384 through 392 Processing helix chain 'B' and resid 406 through 412 Processing helix chain 'B' and resid 420 through 435 removed outlier: 3.767A pdb=" N CYS B 425 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 468 Processing helix chain 'B' and resid 496 through 499 No H-bonds generated for 'chain 'B' and resid 496 through 499' Processing helix chain 'B' and resid 505 through 508 No H-bonds generated for 'chain 'B' and resid 505 through 508' Processing helix chain 'B' and resid 510 through 516 removed outlier: 3.507A pdb=" N TYR B 513 " --> pdb=" O PRO B 510 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS B 515 " --> pdb=" O GLN B 512 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 516 " --> pdb=" O TYR B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 578 removed outlier: 3.851A pdb=" N ASP B 571 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 572 " --> pdb=" O ASN B 568 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS B 575 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 591 No H-bonds generated for 'chain 'B' and resid 589 through 591' Processing helix chain 'B' and resid 613 through 619 removed outlier: 3.544A pdb=" N GLU B 617 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N MET B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 613 through 619' Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 660 through 667 removed outlier: 3.959A pdb=" N LEU B 664 " --> pdb=" O GLU B 660 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 688 removed outlier: 3.938A pdb=" N ALA B 688 " --> pdb=" O ALA B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 712 removed outlier: 3.790A pdb=" N ARG B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR B 707 " --> pdb=" O ARG B 703 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 709 " --> pdb=" O ALA B 705 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 220 through 226 Processing helix chain 'C' and resid 228 through 231 No H-bonds generated for 'chain 'C' and resid 228 through 231' Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 291 through 304 removed outlier: 4.014A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 343 removed outlier: 3.992A pdb=" N VAL C 335 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER C 336 " --> pdb=" O ARG C 333 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 340 " --> pdb=" O GLN C 337 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 341 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET C 342 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP C 343 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 396 removed outlier: 3.866A pdb=" N LYS C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 4.228A pdb=" N ALA C 410 " --> pdb=" O GLU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 432 removed outlier: 3.537A pdb=" N SER C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 467 removed outlier: 3.779A pdb=" N GLY C 467 " --> pdb=" O ARG C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 488 No H-bonds generated for 'chain 'C' and resid 486 through 488' Processing helix chain 'C' and resid 493 through 501 removed outlier: 3.703A pdb=" N LYS C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU C 501 " --> pdb=" O GLU C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 516 Processing helix chain 'C' and resid 536 through 544 removed outlier: 3.749A pdb=" N VAL C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 543 " --> pdb=" O LYS C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 557 No H-bonds generated for 'chain 'C' and resid 554 through 557' Processing helix chain 'C' and resid 563 through 565 No H-bonds generated for 'chain 'C' and resid 563 through 565' Processing helix chain 'C' and resid 568 through 578 removed outlier: 3.720A pdb=" N ILE C 572 " --> pdb=" O ASN C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 591 No H-bonds generated for 'chain 'C' and resid 589 through 591' Processing helix chain 'C' and resid 611 through 617 removed outlier: 4.362A pdb=" N THR C 616 " --> pdb=" O ASN C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 625 No H-bonds generated for 'chain 'C' and resid 623 through 625' Processing helix chain 'C' and resid 664 through 671 removed outlier: 3.526A pdb=" N ASN C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 688 removed outlier: 3.999A pdb=" N ALA C 686 " --> pdb=" O LEU C 682 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA C 688 " --> pdb=" O ALA C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 703 removed outlier: 3.600A pdb=" N VAL C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 220 through 227 removed outlier: 3.816A pdb=" N GLN D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 235 No H-bonds generated for 'chain 'D' and resid 232 through 235' Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 261 through 270 removed outlier: 3.922A pdb=" N ALA D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 266 " --> pdb=" O THR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 284 No H-bonds generated for 'chain 'D' and resid 281 through 284' Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 316 through 319 No H-bonds generated for 'chain 'D' and resid 316 through 319' Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 384 through 393 Processing helix chain 'D' and resid 407 through 411 Processing helix chain 'D' and resid 418 through 436 removed outlier: 4.232A pdb=" N ALA D 422 " --> pdb=" O GLY D 418 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS D 436 " --> pdb=" O GLN D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.695A pdb=" N GLU D 497 " --> pdb=" O ASP D 493 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.534A pdb=" N ALA D 542 " --> pdb=" O ALA D 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 554 through 556 No H-bonds generated for 'chain 'D' and resid 554 through 556' Processing helix chain 'D' and resid 571 through 578 Processing helix chain 'D' and resid 610 through 617 removed outlier: 3.846A pdb=" N THR D 616 " --> pdb=" O ASN D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 670 removed outlier: 4.078A pdb=" N ALA D 669 " --> pdb=" O SER D 665 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 688 Processing helix chain 'D' and resid 694 through 716 removed outlier: 3.601A pdb=" N ILE D 700 " --> pdb=" O ASP D 696 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA D 715 " --> pdb=" O ASP D 711 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS D 716 " --> pdb=" O SER D 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 227 Processing helix chain 'E' and resid 231 through 235 Processing helix chain 'E' and resid 261 through 272 removed outlier: 3.767A pdb=" N ARG E 266 " --> pdb=" O THR E 262 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 284 No H-bonds generated for 'chain 'E' and resid 281 through 284' Processing helix chain 'E' and resid 289 through 304 Processing helix chain 'E' and resid 316 through 318 No H-bonds generated for 'chain 'E' and resid 316 through 318' Processing helix chain 'E' and resid 332 through 341 removed outlier: 3.575A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN E 337 " --> pdb=" O ARG E 333 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 339 " --> pdb=" O VAL E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 367 No H-bonds generated for 'chain 'E' and resid 365 through 367' Processing helix chain 'E' and resid 387 through 396 removed outlier: 3.537A pdb=" N LYS E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 421 through 436 removed outlier: 3.779A pdb=" N CYS E 425 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN E 431 " --> pdb=" O GLU E 427 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS E 436 " --> pdb=" O GLN E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 455 No H-bonds generated for 'chain 'E' and resid 453 through 455' Processing helix chain 'E' and resid 459 through 467 removed outlier: 3.554A pdb=" N ARG E 463 " --> pdb=" O MET E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 498 removed outlier: 3.542A pdb=" N GLU E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 508 No H-bonds generated for 'chain 'E' and resid 505 through 508' Processing helix chain 'E' and resid 512 through 516 removed outlier: 3.970A pdb=" N PHE E 516 " --> pdb=" O GLN E 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 512 through 516' Processing helix chain 'E' and resid 539 through 542 No H-bonds generated for 'chain 'E' and resid 539 through 542' Processing helix chain 'E' and resid 573 through 578 removed outlier: 3.761A pdb=" N ARG E 577 " --> pdb=" O PHE E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 591 No H-bonds generated for 'chain 'E' and resid 589 through 591' Processing helix chain 'E' and resid 602 through 607 Processing helix chain 'E' and resid 611 through 620 removed outlier: 4.347A pdb=" N ASP E 619 " --> pdb=" O LEU E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 665 through 668 removed outlier: 3.932A pdb=" N ASN E 668 " --> pdb=" O SER E 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 665 through 668' Processing helix chain 'E' and resid 682 through 686 Processing helix chain 'E' and resid 710 through 712 No H-bonds generated for 'chain 'E' and resid 710 through 712' Processing helix chain 'F' and resid 221 through 229 removed outlier: 3.593A pdb=" N GLN F 225 " --> pdb=" O LYS F 221 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 235 Processing helix chain 'F' and resid 261 through 272 removed outlier: 4.089A pdb=" N VAL F 268 " --> pdb=" O MET F 264 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA F 269 " --> pdb=" O ALA F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 285 Processing helix chain 'F' and resid 289 through 303 removed outlier: 3.514A pdb=" N GLU F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 297 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU F 302 " --> pdb=" O LYS F 298 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ALA F 303 " --> pdb=" O ALA F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 319 No H-bonds generated for 'chain 'F' and resid 316 through 319' Processing helix chain 'F' and resid 333 through 342 removed outlier: 4.341A pdb=" N LEU F 338 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 339 " --> pdb=" O VAL F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 384 through 394 removed outlier: 3.644A pdb=" N LEU F 388 " --> pdb=" O ALA F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 418 through 434 removed outlier: 3.630A pdb=" N SER F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 466 Processing helix chain 'F' and resid 493 through 500 removed outlier: 3.657A pdb=" N GLU F 497 " --> pdb=" O ASP F 493 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU F 498 " --> pdb=" O GLU F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 514 Processing helix chain 'F' and resid 534 through 544 removed outlier: 3.645A pdb=" N VAL F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ALA F 542 " --> pdb=" O ALA F 538 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR F 543 " --> pdb=" O LYS F 539 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU F 544 " --> pdb=" O ALA F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 559 removed outlier: 3.855A pdb=" N SER F 559 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 571 Processing helix chain 'F' and resid 573 through 578 Processing helix chain 'F' and resid 611 through 617 removed outlier: 4.379A pdb=" N LEU F 615 " --> pdb=" O VAL F 611 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N THR F 616 " --> pdb=" O ASN F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 660 through 670 removed outlier: 3.502A pdb=" N LEU F 664 " --> pdb=" O GLU F 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 686 No H-bonds generated for 'chain 'F' and resid 683 through 686' Processing helix chain 'F' and resid 700 through 706 removed outlier: 4.337A pdb=" N ALA F 705 " --> pdb=" O VAL F 701 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS F 706 " --> pdb=" O GLN F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 710 through 713 No H-bonds generated for 'chain 'F' and resid 710 through 713' Processing helix chain 'K' and resid 23 through 30 removed outlier: 3.578A pdb=" N SER K 28 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 134 removed outlier: 3.727A pdb=" N LYS H 133 " --> pdb=" O LYS H 129 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 233 Processing helix chain 'J' and resid 256 through 259 No H-bonds generated for 'chain 'J' and resid 256 through 259' Processing helix chain 'G' and resid 117 through 124 removed outlier: 3.729A pdb=" N GLU G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 161 Processing helix chain 'G' and resid 169 through 180 removed outlier: 3.982A pdb=" N ASN G 179 " --> pdb=" O LYS G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 255 removed outlier: 3.921A pdb=" N PHE G 248 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 317 removed outlier: 4.393A pdb=" N GLN G 309 " --> pdb=" O ASN G 305 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE G 310 " --> pdb=" O GLU G 306 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG G 312 " --> pdb=" O LEU G 308 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN G 315 " --> pdb=" O ASP G 311 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU G 316 " --> pdb=" O ARG G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 364 removed outlier: 3.762A pdb=" N ILE G 356 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET G 357 " --> pdb=" O LEU G 353 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS G 361 " --> pdb=" O MET G 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 409 No H-bonds generated for 'chain 'G' and resid 406 through 409' Processing helix chain 'G' and resid 502 through 507 removed outlier: 3.606A pdb=" N LYS G 506 " --> pdb=" O GLN G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 517 through 520 No H-bonds generated for 'chain 'G' and resid 517 through 520' Processing helix chain 'G' and resid 527 through 536 removed outlier: 3.608A pdb=" N ASN G 534 " --> pdb=" O LEU G 530 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER G 535 " --> pdb=" O LEU G 531 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU G 536 " --> pdb=" O TYR G 532 " (cutoff:3.500A) Processing helix chain 'G' and resid 541 through 552 Processing helix chain 'G' and resid 557 through 565 removed outlier: 3.736A pdb=" N LEU G 561 " --> pdb=" O GLU G 557 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS G 562 " --> pdb=" O GLU G 558 " (cutoff:3.500A) Processing helix chain 'G' and resid 567 through 578 removed outlier: 3.663A pdb=" N GLU G 578 " --> pdb=" O MET G 574 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 375 through 379 removed outlier: 4.152A pdb=" N ARG A 375 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 353 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N MET A 253 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA A 355 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N GLY A 255 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 356 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE A 275 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 312 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE A 277 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 524 through 528 removed outlier: 7.773A pdb=" N GLN A 651 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N TYR A 527 " --> pdb=" O GLN A 651 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE A 653 " --> pdb=" O TYR A 527 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 549 through 552 removed outlier: 6.717A pdb=" N VAL A 583 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL A 552 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE A 585 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 375 through 379 removed outlier: 6.779A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 523 through 527 removed outlier: 9.191A pdb=" N VAL B 524 " --> pdb=" O VAL B 627 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL B 629 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N PHE B 526 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY B 631 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR B 582 " --> pdb=" O PHE B 628 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE B 630 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL B 584 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ALA B 632 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU B 586 " --> pdb=" O ALA B 632 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 376 through 378 removed outlier: 8.180A pdb=" N VAL C 377 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU C 252 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N VAL C 251 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL C 353 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N MET C 253 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA C 355 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA C 309 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE C 354 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE C 311 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ALA C 356 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE C 313 " --> pdb=" O ALA C 356 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 524 through 528 removed outlier: 6.033A pdb=" N GLN C 651 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N TYR C 527 " --> pdb=" O GLN C 651 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 653 " --> pdb=" O TYR C 527 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 375 through 378 removed outlier: 3.739A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N VAL D 251 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL D 353 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N MET D 253 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA D 355 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 651 through 655 removed outlier: 3.948A pdb=" N GLN D 651 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR D 527 " --> pdb=" O ILE D 653 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 629 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N PHE D 526 " --> pdb=" O VAL D 629 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY D 631 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLY D 528 " --> pdb=" O GLY D 631 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE D 628 " --> pdb=" O THR D 582 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 584 " --> pdb=" O PHE D 628 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 586 " --> pdb=" O ILE D 630 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA D 632 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 375 through 378 removed outlier: 3.547A pdb=" N TYR E 254 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL E 251 " --> pdb=" O VAL E 351 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL E 353 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N MET E 253 " --> pdb=" O VAL E 353 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA E 355 " --> pdb=" O MET E 253 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA E 309 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE E 354 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE E 311 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA E 356 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE E 313 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 630 through 632 removed outlier: 6.413A pdb=" N VAL E 524 " --> pdb=" O GLY E 631 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLN E 651 " --> pdb=" O LEU E 525 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR E 527 " --> pdb=" O GLN E 651 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE E 653 " --> pdb=" O TYR E 527 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 548 through 553 Processing sheet with id= M, first strand: chain 'F' and resid 376 through 379 removed outlier: 6.440A pdb=" N LEU F 252 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE F 379 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR F 254 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY F 255 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL F 352 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 311 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N PHE F 275 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE F 312 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE F 277 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ASP F 314 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE F 279 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 582 through 585 removed outlier: 3.877A pdb=" N PHE F 628 " --> pdb=" O THR F 582 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 523 through 528 removed outlier: 3.631A pdb=" N ASP F 650 " --> pdb=" O GLY F 523 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU F 525 " --> pdb=" O ASP F 650 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU F 652 " --> pdb=" O LEU F 525 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TYR F 527 " --> pdb=" O LEU F 652 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR F 654 " --> pdb=" O TYR F 527 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 112 through 116 removed outlier: 3.605A pdb=" N LEU H 115 " --> pdb=" O ILE H 103 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 212 through 216 removed outlier: 3.672A pdb=" N LEU J 215 " --> pdb=" O ILE J 203 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE J 203 " --> pdb=" O LEU J 215 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER J 265 " --> pdb=" O PHE J 204 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LYS J 206 " --> pdb=" O SER J 265 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU J 267 " --> pdb=" O LYS J 206 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS J 268 " --> pdb=" O ILE J 244 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 236 through 238 removed outlier: 3.932A pdb=" N HIS G 236 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL G 281 " --> pdb=" O GLU G 238 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY G 276 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER G 268 " --> pdb=" O LYS G 278 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TYR G 264 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE G 284 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N TYR G 262 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY G 265 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ARG G 321 " --> pdb=" O GLY G 265 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL G 382 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N PHE G 326 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N CYS G 384 " --> pdb=" O PHE G 326 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 399 through 401 515 hydrogen bonds defined for protein. 1476 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: 8.71 Time building geometry restraints manager: 12.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5059 1.31 - 1.44: 6993 1.44 - 1.57: 17161 1.57 - 1.69: 48 1.69 - 1.82: 238 Bond restraints: 29499 Sorted by residual: bond pdb=" C4 ATP D 902 " pdb=" C5 ATP D 902 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.02e+01 bond pdb=" C4 ATP C1003 " pdb=" C5 ATP C1003 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.99e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.97e+01 bond pdb=" C4 ATP C1002 " pdb=" C5 ATP C1002 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP B 901 " pdb=" C5 ATP B 901 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.89e+01 ... (remaining 29494 not shown) Histogram of bond angle deviations from ideal: 70.76 - 83.84: 1 83.84 - 96.92: 1 96.92 - 109.99: 4251 109.99 - 123.07: 34102 123.07 - 136.15: 1578 Bond angle restraints: 39933 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP C1002 " pdb=" O3B ATP C1002 " pdb=" PG ATP C1002 " ideal model delta sigma weight residual 139.87 120.47 19.40 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP C1003 " pdb=" O3B ATP C1003 " pdb=" PG ATP C1003 " ideal model delta sigma weight residual 139.87 120.47 19.40 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 120.49 19.38 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB ATP C1001 " pdb=" O3B ATP C1001 " pdb=" PG ATP C1001 " ideal model delta sigma weight residual 139.87 120.50 19.37 1.00e+00 1.00e+00 3.75e+02 ... (remaining 39928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.26: 17561 30.26 - 60.51: 634 60.51 - 90.77: 86 90.77 - 121.03: 0 121.03 - 151.29: 3 Dihedral angle restraints: 18284 sinusoidal: 7626 harmonic: 10658 Sorted by residual: dihedral pdb=" C LEU K 43 " pdb=" N LEU K 43 " pdb=" CA LEU K 43 " pdb=" CB LEU K 43 " ideal model delta harmonic sigma weight residual -122.60 -141.64 19.04 0 2.50e+00 1.60e-01 5.80e+01 dihedral pdb=" CA ASN G 510 " pdb=" C ASN G 510 " pdb=" N VAL G 511 " pdb=" CA VAL G 511 " ideal model delta harmonic sigma weight residual -180.00 -145.37 -34.63 0 5.00e+00 4.00e-02 4.80e+01 dihedral pdb=" N LEU K 43 " pdb=" C LEU K 43 " pdb=" CA LEU K 43 " pdb=" CB LEU K 43 " ideal model delta harmonic sigma weight residual 122.80 139.88 -17.08 0 2.50e+00 1.60e-01 4.67e+01 ... (remaining 18281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 4475 0.196 - 0.391: 8 0.391 - 0.587: 1 0.587 - 0.782: 0 0.782 - 0.978: 1 Chirality restraints: 4485 Sorted by residual: chirality pdb=" CA LEU K 43 " pdb=" N LEU K 43 " pdb=" C LEU K 43 " pdb=" CB LEU K 43 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CG LEU K 43 " pdb=" CB LEU K 43 " pdb=" CD1 LEU K 43 " pdb=" CD2 LEU K 43 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CA ARG K 42 " pdb=" N ARG K 42 " pdb=" C ARG K 42 " pdb=" CB ARG K 42 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 4482 not shown) Planarity restraints: 5212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE K 36 " 0.168 5.00e-02 4.00e+02 2.67e-01 1.14e+02 pdb=" N PRO K 37 " -0.458 5.00e-02 4.00e+02 pdb=" CA PRO K 37 " 0.194 5.00e-02 4.00e+02 pdb=" CD PRO K 37 " 0.096 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 37 " -0.135 5.00e-02 4.00e+02 2.15e-01 7.39e+01 pdb=" N PRO K 38 " 0.371 5.00e-02 4.00e+02 pdb=" CA PRO K 38 " -0.143 5.00e-02 4.00e+02 pdb=" CD PRO K 38 " -0.092 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN K 41 " -0.014 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLN K 41 " 0.055 2.00e-02 2.50e+03 pdb=" O GLN K 41 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG K 42 " -0.019 2.00e-02 2.50e+03 ... (remaining 5209 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 27 2.25 - 2.91: 11429 2.91 - 3.57: 39558 3.57 - 4.24: 66482 4.24 - 4.90: 105721 Nonbonded interactions: 223217 Sorted by model distance: nonbonded pdb=" O GLY B 531 " pdb=" O5' ATP C1001 " model vdw 1.585 3.040 nonbonded pdb=" NH1 ARG C 645 " pdb=" O1B ATP C1001 " model vdw 1.654 2.496 nonbonded pdb=" OG SER D 559 " pdb=" CE1 TYR E 562 " model vdw 1.865 3.340 nonbonded pdb=" O THR B 532 " pdb=" O2B ATP C1001 " model vdw 1.913 3.040 nonbonded pdb=" CE1 TYR D 562 " pdb=" NH2 ARG D 609 " model vdw 1.917 3.420 ... (remaining 223212 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 209 through 437 or resid 459 through 713 or resid 901)) selection = (chain 'B' and (resid 209 through 437 or resid 459 through 713 or resid 901)) selection = (chain 'C' and (resid 209 through 437 or resid 459 through 713 or resid 1003)) selection = (chain 'D' and (resid 209 through 713 or resid 902)) selection = (chain 'E' and (resid 209 through 437 or resid 459 through 713 or resid 902)) selection = (chain 'F' and (resid 209 through 437 or resid 459 through 713 or resid 901)) } ncs_group { reference = chain 'H' selection = chain 'J' } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.330 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 78.440 Find NCS groups from input model: 2.230 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 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 : 0.004 0.084 29499 Z= 0.270 Angle : 0.991 54.241 39933 Z= 0.642 Chirality : 0.051 0.978 4485 Planarity : 0.007 0.267 5212 Dihedral : 15.455 151.287 11414 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.54 % Favored : 93.24 % Rotamer: Outliers : 0.45 % Allowed : 7.74 % Favored : 91.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.28 (0.10), residues: 3684 helix: -4.93 (0.04), residues: 1291 sheet: -1.97 (0.23), residues: 411 loop : -2.84 (0.11), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 211 HIS 0.004 0.001 HIS G 208 PHE 0.014 0.001 PHE G 340 TYR 0.009 0.001 TYR E 562 ARG 0.005 0.000 ARG K 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 805 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ILE cc_start: 0.8309 (tp) cc_final: 0.8085 (tp) REVERT: A 310 ILE cc_start: 0.8598 (mt) cc_final: 0.8346 (tt) REVERT: A 332 ARG cc_start: 0.7717 (ptt180) cc_final: 0.7348 (ptt-90) REVERT: A 350 ASN cc_start: 0.7778 (p0) cc_final: 0.7508 (p0) REVERT: A 459 MET cc_start: 0.8290 (ptm) cc_final: 0.8044 (ttp) REVERT: A 526 PHE cc_start: 0.9379 (m-80) cc_final: 0.9044 (m-80) REVERT: A 624 LYS cc_start: 0.5577 (tttm) cc_final: 0.4282 (mmtm) REVERT: A 628 PHE cc_start: 0.7926 (m-80) cc_final: 0.7557 (m-80) REVERT: A 784 MET cc_start: 0.1607 (tpp) cc_final: 0.0475 (tpt) REVERT: B 264 MET cc_start: 0.8429 (ttp) cc_final: 0.8096 (ttp) REVERT: B 283 GLU cc_start: 0.7900 (tt0) cc_final: 0.7690 (mt-10) REVERT: B 285 MET cc_start: 0.7218 (tmm) cc_final: 0.6921 (tmm) REVERT: B 301 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 302 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8105 (tp30) REVERT: B 326 THR cc_start: 0.5099 (t) cc_final: 0.4523 (m) REVERT: B 331 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8649 (tp30) REVERT: B 420 ASP cc_start: 0.8267 (m-30) cc_final: 0.7982 (m-30) REVERT: B 427 GLU cc_start: 0.8380 (tt0) cc_final: 0.8162 (tp30) REVERT: B 477 THR cc_start: 0.6773 (t) cc_final: 0.6319 (m) REVERT: B 496 LYS cc_start: 0.8573 (mtmt) cc_final: 0.8279 (mtpt) REVERT: B 560 MET cc_start: 0.4964 (ttt) cc_final: 0.4743 (tpt) REVERT: B 614 LEU cc_start: 0.8863 (mt) cc_final: 0.8245 (pp) REVERT: C 229 MET cc_start: 0.7513 (mtm) cc_final: 0.7111 (tmm) REVERT: C 236 HIS cc_start: 0.5433 (t-170) cc_final: 0.5077 (t-170) REVERT: C 264 MET cc_start: 0.8751 (tpt) cc_final: 0.8447 (tpp) REVERT: C 304 GLU cc_start: 0.8161 (tt0) cc_final: 0.7895 (tt0) REVERT: C 324 ASP cc_start: 0.8450 (p0) cc_final: 0.7964 (t0) REVERT: C 430 MET cc_start: 0.8482 (mmt) cc_final: 0.8243 (mmm) REVERT: C 474 LEU cc_start: 0.6597 (mt) cc_final: 0.6170 (tt) REVERT: C 513 TYR cc_start: 0.8239 (m-80) cc_final: 0.7481 (m-80) REVERT: C 518 LEU cc_start: 0.7976 (tp) cc_final: 0.7684 (mt) REVERT: C 574 ASP cc_start: 0.8602 (t0) cc_final: 0.8083 (t0) REVERT: C 621 MET cc_start: 0.6050 (mmm) cc_final: 0.5818 (mmm) REVERT: D 251 VAL cc_start: 0.9011 (p) cc_final: 0.8801 (p) REVERT: D 302 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7836 (mm-30) REVERT: D 513 TYR cc_start: 0.6819 (m-80) cc_final: 0.6364 (m-10) REVERT: D 621 MET cc_start: 0.8453 (ppp) cc_final: 0.8049 (ppp) REVERT: D 698 LEU cc_start: 0.7778 (mt) cc_final: 0.7416 (mt) REVERT: E 278 LEU cc_start: 0.8516 (mt) cc_final: 0.8309 (mt) REVERT: E 342 MET cc_start: 0.8382 (mmm) cc_final: 0.8108 (ttm) REVERT: E 345 MET cc_start: 0.7484 (ptp) cc_final: 0.6898 (ptt) REVERT: E 513 TYR cc_start: 0.7861 (p90) cc_final: 0.7491 (p90) REVERT: E 636 PRO cc_start: 0.6351 (Cg_endo) cc_final: 0.6109 (Cg_exo) REVERT: F 264 MET cc_start: 0.9032 (ptp) cc_final: 0.8678 (ptm) REVERT: F 285 MET cc_start: 0.8809 (tpp) cc_final: 0.7523 (tpp) REVERT: F 291 GLU cc_start: 0.8676 (tp30) cc_final: 0.8289 (tp30) REVERT: F 324 ASP cc_start: 0.9069 (m-30) cc_final: 0.8472 (p0) REVERT: F 367 LEU cc_start: 0.8869 (mp) cc_final: 0.8653 (mp) REVERT: F 398 MET cc_start: 0.8701 (mmm) cc_final: 0.8474 (mmm) REVERT: F 504 GLU cc_start: 0.7610 (pp20) cc_final: 0.6980 (mp0) REVERT: F 618 MET cc_start: 0.6638 (ttm) cc_final: 0.6217 (ttm) REVERT: K 6 LYS cc_start: 0.5018 (mmmm) cc_final: 0.4712 (mmmt) REVERT: K 15 LEU cc_start: 0.7748 (mm) cc_final: 0.7497 (mm) REVERT: H 118 GLU cc_start: 0.9230 (mp0) cc_final: 0.8972 (mp0) REVERT: H 123 ILE cc_start: 0.8333 (mm) cc_final: 0.8118 (mm) REVERT: H 141 GLN cc_start: 0.7119 (mt0) cc_final: 0.6037 (mt0) REVERT: J 201 MET cc_start: 0.8342 (ptt) cc_final: 0.7846 (ppp) REVERT: J 221 ASP cc_start: 0.6974 (t0) cc_final: 0.6260 (t0) REVERT: J 250 LEU cc_start: 0.6903 (mt) cc_final: 0.6291 (tt) REVERT: G 121 GLU cc_start: 0.8342 (tt0) cc_final: 0.8026 (tp30) REVERT: G 161 LYS cc_start: 0.8447 (tmtt) cc_final: 0.8149 (ttmt) REVERT: G 191 SER cc_start: 0.7502 (t) cc_final: 0.6928 (p) REVERT: G 257 MET cc_start: 0.8585 (mmt) cc_final: 0.8284 (mmm) REVERT: G 370 LYS cc_start: 0.7917 (ttmt) cc_final: 0.7006 (tptt) REVERT: G 406 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7978 (tm-30) REVERT: G 424 TYR cc_start: 0.6078 (t80) cc_final: 0.5612 (t80) REVERT: G 429 THR cc_start: 0.7752 (p) cc_final: 0.7536 (t) REVERT: G 430 ASP cc_start: 0.7764 (t0) cc_final: 0.6900 (t0) REVERT: G 485 THR cc_start: 0.5559 (p) cc_final: 0.5214 (m) REVERT: G 539 LEU cc_start: 0.7750 (mt) cc_final: 0.7530 (tp) outliers start: 14 outliers final: 5 residues processed: 815 average time/residue: 0.4533 time to fit residues: 558.8784 Evaluate side-chains 461 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 456 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 562 TYR Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 562 TYR Chi-restraints excluded: chain K residue 44 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 148 optimal weight: 0.0870 chunk 286 optimal weight: 50.0000 chunk 111 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 213 optimal weight: 0.2980 chunk 332 optimal weight: 2.9990 overall best weight: 2.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 GLN B 238 GLN B 432 GLN B 626 ASN B 690 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN C 337 GLN C 394 HIS ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 702 GLN D 295 ASN D 337 GLN ** D 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN E 236 HIS E 432 GLN ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 ASN ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 ASN E 612 ASN F 337 GLN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 468 ASN ** F 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN K 2 GLN K 25 ASN K 31 GLN H 125 ASN H 149 GLN H 162 GLN ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN G 170 HIS G 272 ASN G 293 GLN G 305 ASN G 491 ASN G 577 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29499 Z= 0.228 Angle : 0.674 18.600 39933 Z= 0.335 Chirality : 0.044 0.207 4485 Planarity : 0.006 0.172 5212 Dihedral : 11.984 141.267 4332 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.19 % Favored : 93.76 % Rotamer: Outliers : 2.66 % Allowed : 15.93 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.11), residues: 3684 helix: -3.22 (0.10), residues: 1262 sheet: -1.43 (0.24), residues: 400 loop : -2.31 (0.12), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 561 HIS 0.014 0.001 HIS D 414 PHE 0.018 0.002 PHE G 487 TYR 0.019 0.002 TYR E 654 ARG 0.016 0.001 ARG E 369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 467 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 ASN cc_start: 0.8237 (p0) cc_final: 0.7994 (p0) REVERT: A 443 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8425 (t0) REVERT: A 459 MET cc_start: 0.8601 (ptm) cc_final: 0.8171 (ttp) REVERT: A 526 PHE cc_start: 0.9382 (m-80) cc_final: 0.9129 (m-80) REVERT: A 618 MET cc_start: 0.8322 (ptm) cc_final: 0.7960 (ppp) REVERT: A 624 LYS cc_start: 0.5346 (tttm) cc_final: 0.4168 (mmtm) REVERT: A 628 PHE cc_start: 0.8027 (m-80) cc_final: 0.7648 (m-80) REVERT: A 784 MET cc_start: 0.1230 (tpp) cc_final: -0.0086 (tpt) REVERT: B 245 ILE cc_start: 0.8942 (mm) cc_final: 0.8735 (mm) REVERT: B 264 MET cc_start: 0.8029 (ttp) cc_final: 0.7714 (ttp) REVERT: B 285 MET cc_start: 0.8535 (tmm) cc_final: 0.8315 (tmm) REVERT: B 301 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7612 (tm-30) REVERT: B 302 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7954 (tp30) REVERT: B 331 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8114 (tp30) REVERT: B 427 GLU cc_start: 0.8193 (tt0) cc_final: 0.7681 (tt0) REVERT: B 479 VAL cc_start: 0.6114 (OUTLIER) cc_final: 0.5865 (t) REVERT: B 526 PHE cc_start: 0.9280 (m-10) cc_final: 0.9077 (m-10) REVERT: B 706 LYS cc_start: 0.9277 (mmtm) cc_final: 0.9010 (pptt) REVERT: C 229 MET cc_start: 0.7637 (mtm) cc_final: 0.7399 (mpp) REVERT: C 264 MET cc_start: 0.8693 (tpt) cc_final: 0.8398 (tpp) REVERT: C 288 MET cc_start: 0.7164 (tpp) cc_final: 0.6408 (tpp) REVERT: C 304 GLU cc_start: 0.8136 (tt0) cc_final: 0.7911 (tt0) REVERT: C 324 ASP cc_start: 0.8533 (p0) cc_final: 0.7991 (t0) REVERT: C 332 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7498 (ttt-90) REVERT: C 430 MET cc_start: 0.8657 (mmt) cc_final: 0.8453 (mmm) REVERT: C 474 LEU cc_start: 0.6559 (mt) cc_final: 0.6272 (tt) REVERT: C 513 TYR cc_start: 0.8558 (m-80) cc_final: 0.7693 (m-80) REVERT: D 339 LEU cc_start: 0.8175 (mt) cc_final: 0.7622 (mt) REVERT: D 505 TYR cc_start: 0.8517 (m-10) cc_final: 0.8312 (m-10) REVERT: D 513 TYR cc_start: 0.6687 (m-80) cc_final: 0.6286 (m-80) REVERT: D 621 MET cc_start: 0.8477 (ppp) cc_final: 0.8110 (ppp) REVERT: E 223 MET cc_start: 0.8405 (ppp) cc_final: 0.8094 (ppp) REVERT: E 229 MET cc_start: 0.7973 (mpp) cc_final: 0.7650 (mtm) REVERT: E 261 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6865 (mttm) REVERT: E 302 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7652 (mt-10) REVERT: E 342 MET cc_start: 0.8611 (mmm) cc_final: 0.8121 (ttm) REVERT: E 345 MET cc_start: 0.7381 (ptp) cc_final: 0.7073 (ptt) REVERT: E 398 MET cc_start: 0.3452 (ttp) cc_final: 0.2298 (tpp) REVERT: E 501 GLU cc_start: 0.8551 (mp0) cc_final: 0.7928 (pm20) REVERT: E 513 TYR cc_start: 0.7665 (p90) cc_final: 0.7310 (p90) REVERT: E 527 TYR cc_start: 0.6688 (p90) cc_final: 0.6465 (p90) REVERT: F 264 MET cc_start: 0.9031 (ptp) cc_final: 0.8261 (ptm) REVERT: F 285 MET cc_start: 0.8945 (tpp) cc_final: 0.8352 (tpp) REVERT: F 291 GLU cc_start: 0.8874 (tp30) cc_final: 0.8412 (tt0) REVERT: F 314 ASP cc_start: 0.8392 (t70) cc_final: 0.7300 (t0) REVERT: F 324 ASP cc_start: 0.9046 (m-30) cc_final: 0.8341 (p0) REVERT: F 342 MET cc_start: 0.8390 (mmm) cc_final: 0.8120 (mmm) REVERT: F 430 MET cc_start: 0.8571 (mmm) cc_final: 0.8331 (mmm) REVERT: F 504 GLU cc_start: 0.7877 (pp20) cc_final: 0.7135 (mp0) REVERT: F 564 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7103 (mp0) REVERT: K 16 GLU cc_start: 0.5865 (mp0) cc_final: 0.5132 (mp0) REVERT: H 163 LYS cc_start: 0.8812 (tppp) cc_final: 0.8218 (mmmm) REVERT: J 201 MET cc_start: 0.8399 (ptt) cc_final: 0.7896 (ppp) REVERT: J 221 ASP cc_start: 0.6455 (t0) cc_final: 0.6245 (t0) REVERT: G 121 GLU cc_start: 0.8096 (tt0) cc_final: 0.7694 (tp30) REVERT: G 161 LYS cc_start: 0.8379 (tmtt) cc_final: 0.8167 (ttmt) REVERT: G 191 SER cc_start: 0.7034 (t) cc_final: 0.6781 (p) REVERT: G 233 MET cc_start: 0.9003 (mmm) cc_final: 0.8785 (mmm) REVERT: G 257 MET cc_start: 0.8458 (mmt) cc_final: 0.8155 (mmm) REVERT: G 370 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7054 (tptt) REVERT: G 406 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7995 (tm-30) REVERT: G 427 ASP cc_start: 0.7844 (t0) cc_final: 0.7394 (t0) REVERT: G 430 ASP cc_start: 0.8263 (t0) cc_final: 0.7697 (t0) REVERT: G 539 LEU cc_start: 0.8041 (mt) cc_final: 0.7766 (tp) REVERT: G 574 MET cc_start: 0.8674 (tpt) cc_final: 0.8329 (tpp) outliers start: 82 outliers final: 54 residues processed: 525 average time/residue: 0.4022 time to fit residues: 335.3917 Evaluate side-chains 445 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 388 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 693 SER Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain E residue 560 MET Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 661 ASN Chi-restraints excluded: chain K residue 2 GLN Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain J residue 233 LYS Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 181 ASN Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 542 ASP Chi-restraints excluded: chain G residue 544 TRP Chi-restraints excluded: chain G residue 546 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 chunk 226 optimal weight: 0.0670 chunk 91 optimal weight: 0.4980 chunk 332 optimal weight: 2.9990 chunk 359 optimal weight: 5.9990 chunk 296 optimal weight: 30.0000 chunk 330 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 267 optimal weight: 0.0870 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 HIS ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN C 270 ASN ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN G 577 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29499 Z= 0.157 Angle : 0.608 17.026 39933 Z= 0.294 Chirality : 0.043 0.198 4485 Planarity : 0.005 0.162 5212 Dihedral : 11.642 142.683 4326 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.70 % Favored : 94.25 % Rotamer: Outliers : 2.75 % Allowed : 18.33 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.13), residues: 3684 helix: -2.07 (0.13), residues: 1258 sheet: -1.13 (0.25), residues: 415 loop : -1.99 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 486 HIS 0.008 0.001 HIS D 414 PHE 0.019 0.001 PHE G 509 TYR 0.017 0.001 TYR E 527 ARG 0.007 0.000 ARG E 369 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 418 time to evaluate : 3.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 MET cc_start: 0.8611 (tpp) cc_final: 0.8273 (tpt) REVERT: A 350 ASN cc_start: 0.8234 (p0) cc_final: 0.7912 (p0) REVERT: A 443 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8471 (t0) REVERT: A 459 MET cc_start: 0.8501 (ptm) cc_final: 0.8147 (ttp) REVERT: A 526 PHE cc_start: 0.9418 (m-80) cc_final: 0.9145 (m-80) REVERT: A 621 MET cc_start: 0.8823 (mmt) cc_final: 0.7868 (mmm) REVERT: A 624 LYS cc_start: 0.5192 (tttm) cc_final: 0.4150 (mmtm) REVERT: A 784 MET cc_start: 0.1274 (tpp) cc_final: -0.0028 (tpt) REVERT: B 245 ILE cc_start: 0.8937 (mm) cc_final: 0.8727 (mm) REVERT: B 264 MET cc_start: 0.7997 (ttp) cc_final: 0.7680 (ttp) REVERT: B 301 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7610 (tm-30) REVERT: B 302 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7950 (tp30) REVERT: B 329 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8562 (mm-30) REVERT: B 331 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7929 (mm-30) REVERT: B 345 MET cc_start: 0.7829 (mtm) cc_final: 0.7559 (mtm) REVERT: B 427 GLU cc_start: 0.8084 (tt0) cc_final: 0.7611 (tt0) REVERT: B 430 MET cc_start: 0.8179 (tpp) cc_final: 0.7851 (tpp) REVERT: B 479 VAL cc_start: 0.5990 (OUTLIER) cc_final: 0.5755 (t) REVERT: B 526 PHE cc_start: 0.9278 (m-10) cc_final: 0.9066 (m-10) REVERT: B 614 LEU cc_start: 0.8619 (mt) cc_final: 0.7988 (pp) REVERT: B 621 MET cc_start: 0.6207 (tpt) cc_final: 0.5976 (tpt) REVERT: B 706 LYS cc_start: 0.9161 (mmtm) cc_final: 0.8854 (pptt) REVERT: C 288 MET cc_start: 0.7037 (tpp) cc_final: 0.6361 (tpp) REVERT: C 324 ASP cc_start: 0.8549 (p0) cc_final: 0.8069 (t0) REVERT: C 332 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7499 (ttt-90) REVERT: C 430 MET cc_start: 0.8742 (mmt) cc_final: 0.8495 (mmm) REVERT: C 474 LEU cc_start: 0.6609 (mt) cc_final: 0.6309 (tt) REVERT: C 513 TYR cc_start: 0.8533 (m-80) cc_final: 0.7736 (m-80) REVERT: C 518 LEU cc_start: 0.8224 (mt) cc_final: 0.7863 (mt) REVERT: C 573 PHE cc_start: 0.8925 (m-80) cc_final: 0.8712 (m-10) REVERT: D 288 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7540 (ppp) REVERT: D 339 LEU cc_start: 0.8349 (mt) cc_final: 0.8109 (mt) REVERT: D 391 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8454 (mm) REVERT: D 513 TYR cc_start: 0.6899 (m-80) cc_final: 0.6489 (m-80) REVERT: D 621 MET cc_start: 0.8480 (ppp) cc_final: 0.8078 (ppp) REVERT: E 223 MET cc_start: 0.8425 (ppp) cc_final: 0.8126 (ppp) REVERT: E 229 MET cc_start: 0.8115 (mpp) cc_final: 0.7740 (ptp) REVERT: E 234 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8619 (pp) REVERT: E 302 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7689 (mt-10) REVERT: E 342 MET cc_start: 0.8672 (mmm) cc_final: 0.7985 (ttm) REVERT: E 345 MET cc_start: 0.7235 (ptp) cc_final: 0.6952 (ptt) REVERT: E 398 MET cc_start: 0.3695 (ttp) cc_final: 0.2422 (tpp) REVERT: E 501 GLU cc_start: 0.8609 (mp0) cc_final: 0.7992 (pm20) REVERT: E 513 TYR cc_start: 0.7555 (p90) cc_final: 0.7181 (p90) REVERT: E 609 ARG cc_start: 0.5452 (ttt180) cc_final: 0.4899 (tpm170) REVERT: F 264 MET cc_start: 0.9144 (ptp) cc_final: 0.8773 (ptm) REVERT: F 291 GLU cc_start: 0.8793 (tp30) cc_final: 0.8404 (tp30) REVERT: F 324 ASP cc_start: 0.9060 (m-30) cc_final: 0.8408 (p0) REVERT: F 342 MET cc_start: 0.8344 (mmm) cc_final: 0.8129 (mmm) REVERT: F 430 MET cc_start: 0.8589 (mmm) cc_final: 0.8379 (mmm) REVERT: F 504 GLU cc_start: 0.7794 (pp20) cc_final: 0.7173 (mp0) REVERT: F 564 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7538 (mp0) REVERT: K 16 GLU cc_start: 0.5840 (mp0) cc_final: 0.5216 (mp0) REVERT: H 104 PHE cc_start: 0.6696 (m-10) cc_final: 0.6390 (m-10) REVERT: J 201 MET cc_start: 0.8573 (ptt) cc_final: 0.7937 (ppp) REVERT: J 221 ASP cc_start: 0.6501 (t0) cc_final: 0.6268 (t0) REVERT: J 250 LEU cc_start: 0.6217 (mt) cc_final: 0.5925 (mp) REVERT: G 157 GLU cc_start: 0.7676 (tm-30) cc_final: 0.6913 (tm-30) REVERT: G 160 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8071 (pm20) REVERT: G 161 LYS cc_start: 0.8345 (tmtt) cc_final: 0.8012 (ttmt) REVERT: G 191 SER cc_start: 0.7051 (t) cc_final: 0.6800 (p) REVERT: G 233 MET cc_start: 0.9062 (mmm) cc_final: 0.8770 (mmm) REVERT: G 257 MET cc_start: 0.8412 (mmt) cc_final: 0.8159 (mmm) REVERT: G 370 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7217 (tptt) REVERT: G 406 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7892 (tm-30) REVERT: G 422 MET cc_start: 0.8308 (mtp) cc_final: 0.7919 (mtp) REVERT: G 427 ASP cc_start: 0.8112 (t0) cc_final: 0.7542 (t0) REVERT: G 430 ASP cc_start: 0.8093 (t0) cc_final: 0.7512 (t0) REVERT: G 537 GLN cc_start: 0.8518 (pm20) cc_final: 0.8277 (pm20) REVERT: G 539 LEU cc_start: 0.8294 (mt) cc_final: 0.7886 (tp) REVERT: G 574 MET cc_start: 0.8749 (tpt) cc_final: 0.8350 (tpp) REVERT: G 577 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8579 (pp30) outliers start: 85 outliers final: 51 residues processed: 475 average time/residue: 0.3873 time to fit residues: 295.5089 Evaluate side-chains 425 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 367 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 332 ARG Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 693 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain E residue 560 MET Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain J residue 205 VAL Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 181 ASN Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 516 ASP Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 577 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 4.9990 chunk 250 optimal weight: 10.0000 chunk 172 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 158 optimal weight: 0.1980 chunk 223 optimal weight: 20.0000 chunk 334 optimal weight: 2.9990 chunk 353 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 316 optimal weight: 30.0000 chunk 95 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 HIS ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN K 25 ASN H 162 GLN G 272 ASN G 497 GLN G 502 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29499 Z= 0.225 Angle : 0.617 14.974 39933 Z= 0.303 Chirality : 0.043 0.180 4485 Planarity : 0.005 0.151 5212 Dihedral : 11.366 146.125 4322 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.84 % Favored : 93.11 % Rotamer: Outliers : 3.43 % Allowed : 19.27 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.13), residues: 3684 helix: -1.45 (0.14), residues: 1294 sheet: -0.93 (0.24), residues: 440 loop : -1.79 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 486 HIS 0.005 0.001 HIS D 716 PHE 0.015 0.001 PHE A 240 TYR 0.015 0.001 TYR D 505 ARG 0.008 0.001 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 383 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 MET cc_start: 0.8696 (tpp) cc_final: 0.8388 (tpt) REVERT: A 458 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8855 (p) REVERT: A 459 MET cc_start: 0.8261 (ptm) cc_final: 0.7996 (ttp) REVERT: A 526 PHE cc_start: 0.9438 (m-80) cc_final: 0.9163 (m-80) REVERT: A 621 MET cc_start: 0.8902 (mmt) cc_final: 0.8013 (mmm) REVERT: A 624 LYS cc_start: 0.5359 (tttm) cc_final: 0.4345 (mmtm) REVERT: B 264 MET cc_start: 0.8079 (ttp) cc_final: 0.7712 (ttp) REVERT: B 301 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7698 (tm-30) REVERT: B 302 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8281 (tp30) REVERT: B 329 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8714 (mm-30) REVERT: B 424 LEU cc_start: 0.8141 (tp) cc_final: 0.7779 (tt) REVERT: B 430 MET cc_start: 0.8259 (tpp) cc_final: 0.7929 (tpp) REVERT: B 553 LYS cc_start: 0.7369 (mmtt) cc_final: 0.7096 (ptpp) REVERT: B 621 MET cc_start: 0.6335 (tpt) cc_final: 0.6083 (tpt) REVERT: B 706 LYS cc_start: 0.9149 (mmtm) cc_final: 0.8863 (pptt) REVERT: C 253 MET cc_start: 0.8927 (mtm) cc_final: 0.8661 (ptp) REVERT: C 288 MET cc_start: 0.7124 (tpp) cc_final: 0.6745 (tpp) REVERT: C 324 ASP cc_start: 0.8522 (p0) cc_final: 0.8038 (t0) REVERT: C 332 ARG cc_start: 0.7755 (ttm-80) cc_final: 0.7459 (ttt-90) REVERT: C 369 ARG cc_start: 0.7659 (ttt180) cc_final: 0.7437 (tpp80) REVERT: C 430 MET cc_start: 0.8869 (mmt) cc_final: 0.8371 (mmm) REVERT: C 513 TYR cc_start: 0.8566 (m-80) cc_final: 0.7770 (m-80) REVERT: C 518 LEU cc_start: 0.8064 (mt) cc_final: 0.7753 (mt) REVERT: D 288 MET cc_start: 0.8417 (pmm) cc_final: 0.7777 (ppp) REVERT: D 437 MET cc_start: 0.7871 (mmm) cc_final: 0.7469 (mmm) REVERT: D 505 TYR cc_start: 0.8313 (m-10) cc_final: 0.8103 (m-10) REVERT: D 513 TYR cc_start: 0.6759 (m-80) cc_final: 0.6292 (m-80) REVERT: D 621 MET cc_start: 0.8441 (ppp) cc_final: 0.8066 (ppp) REVERT: E 223 MET cc_start: 0.8442 (ppp) cc_final: 0.8156 (ppp) REVERT: E 234 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8647 (pp) REVERT: E 278 LEU cc_start: 0.8636 (mt) cc_final: 0.8412 (mm) REVERT: E 302 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7751 (mt-10) REVERT: E 342 MET cc_start: 0.8760 (mmm) cc_final: 0.8294 (ttm) REVERT: E 345 MET cc_start: 0.7144 (ptp) cc_final: 0.6757 (ptt) REVERT: E 398 MET cc_start: 0.4107 (ttp) cc_final: 0.2672 (tpp) REVERT: E 509 HIS cc_start: 0.3904 (m170) cc_final: 0.3648 (m-70) REVERT: E 513 TYR cc_start: 0.7505 (p90) cc_final: 0.7129 (p90) REVERT: F 264 MET cc_start: 0.9160 (ptp) cc_final: 0.8835 (ptm) REVERT: F 291 GLU cc_start: 0.8827 (tp30) cc_final: 0.8437 (tp30) REVERT: F 324 ASP cc_start: 0.9083 (m-30) cc_final: 0.8400 (p0) REVERT: F 430 MET cc_start: 0.8653 (mmm) cc_final: 0.8393 (mmm) REVERT: F 504 GLU cc_start: 0.8146 (pp20) cc_final: 0.7558 (mp0) REVERT: F 564 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7650 (mp0) REVERT: H 104 PHE cc_start: 0.6427 (m-10) cc_final: 0.6213 (m-10) REVERT: H 162 GLN cc_start: 0.9353 (tp-100) cc_final: 0.9060 (tp-100) REVERT: J 201 MET cc_start: 0.8665 (ptt) cc_final: 0.8052 (ppp) REVERT: J 221 ASP cc_start: 0.6527 (t0) cc_final: 0.6294 (t0) REVERT: G 126 ASP cc_start: 0.9000 (t0) cc_final: 0.8798 (t0) REVERT: G 156 LYS cc_start: 0.7433 (pptt) cc_final: 0.6863 (ptmt) REVERT: G 157 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7050 (tm-30) REVERT: G 160 GLU cc_start: 0.8522 (pm20) cc_final: 0.8210 (pm20) REVERT: G 161 LYS cc_start: 0.8390 (tmtt) cc_final: 0.7928 (ttmt) REVERT: G 257 MET cc_start: 0.8576 (mmt) cc_final: 0.8171 (mmm) REVERT: G 406 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7809 (tm-30) REVERT: G 422 MET cc_start: 0.8155 (mtp) cc_final: 0.7937 (mtp) REVERT: G 427 ASP cc_start: 0.8009 (t0) cc_final: 0.7502 (t0) REVERT: G 430 ASP cc_start: 0.8348 (t0) cc_final: 0.7825 (t0) REVERT: G 539 LEU cc_start: 0.8513 (mt) cc_final: 0.8010 (tp) REVERT: G 570 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7588 (pp30) REVERT: G 574 MET cc_start: 0.8640 (tpt) cc_final: 0.8145 (tpp) REVERT: G 577 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8316 (tm-30) outliers start: 106 outliers final: 71 residues processed: 462 average time/residue: 0.3963 time to fit residues: 293.8587 Evaluate side-chains 417 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 342 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 654 TYR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 693 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain E residue 560 MET Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 661 ASN Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 181 ASN Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain G residue 577 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 8.9990 chunk 200 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 263 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 301 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 180 optimal weight: 9.9990 chunk 317 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 668 ASN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 ASN D 225 GLN ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 GLN J 249 GLN G 497 GLN G 521 HIS G 577 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29499 Z= 0.278 Angle : 0.655 14.591 39933 Z= 0.327 Chirality : 0.044 0.210 4485 Planarity : 0.005 0.141 5212 Dihedral : 11.311 140.105 4322 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.55 % Favored : 92.37 % Rotamer: Outliers : 4.08 % Allowed : 20.34 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.14), residues: 3684 helix: -1.15 (0.14), residues: 1312 sheet: -0.97 (0.25), residues: 422 loop : -1.67 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 561 HIS 0.006 0.001 HIS D 716 PHE 0.020 0.002 PHE G 377 TYR 0.012 0.001 TYR G 147 ARG 0.007 0.001 ARG E 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 360 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.8238 (mmp) cc_final: 0.7950 (mmp) REVERT: A 342 MET cc_start: 0.8732 (tpp) cc_final: 0.8373 (tpt) REVERT: A 350 ASN cc_start: 0.8255 (p0) cc_final: 0.7789 (p0) REVERT: A 459 MET cc_start: 0.8272 (ptm) cc_final: 0.8008 (ttp) REVERT: A 526 PHE cc_start: 0.9500 (m-80) cc_final: 0.9123 (m-80) REVERT: A 621 MET cc_start: 0.8931 (mmt) cc_final: 0.8080 (mmm) REVERT: A 628 PHE cc_start: 0.8319 (m-80) cc_final: 0.7927 (m-80) REVERT: A 784 MET cc_start: 0.0308 (mmt) cc_final: -0.1354 (tpt) REVERT: B 264 MET cc_start: 0.8206 (ttp) cc_final: 0.7858 (ttp) REVERT: B 301 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7713 (tm-30) REVERT: B 302 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8282 (tp30) REVERT: B 329 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8683 (mm-30) REVERT: B 424 LEU cc_start: 0.8342 (tp) cc_final: 0.8003 (tt) REVERT: B 430 MET cc_start: 0.8621 (tpp) cc_final: 0.8235 (tpp) REVERT: B 706 LYS cc_start: 0.9065 (mmtm) cc_final: 0.8836 (pptt) REVERT: C 253 MET cc_start: 0.9097 (mtm) cc_final: 0.8867 (ptp) REVERT: C 288 MET cc_start: 0.6882 (tpp) cc_final: 0.6582 (tpp) REVERT: C 324 ASP cc_start: 0.8387 (p0) cc_final: 0.7998 (t0) REVERT: C 369 ARG cc_start: 0.8058 (ttt180) cc_final: 0.7593 (tpp-160) REVERT: C 372 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7392 (ptp90) REVERT: C 430 MET cc_start: 0.8922 (mmt) cc_final: 0.8555 (mmm) REVERT: C 513 TYR cc_start: 0.8806 (m-80) cc_final: 0.8001 (m-80) REVERT: C 518 LEU cc_start: 0.8033 (mt) cc_final: 0.7701 (mt) REVERT: C 569 ILE cc_start: 0.8719 (mp) cc_final: 0.8379 (mp) REVERT: D 223 MET cc_start: 0.7642 (tpp) cc_final: 0.7384 (tpp) REVERT: D 437 MET cc_start: 0.8132 (mmm) cc_final: 0.7835 (mmm) REVERT: D 513 TYR cc_start: 0.7031 (m-80) cc_final: 0.6639 (m-80) REVERT: D 621 MET cc_start: 0.8388 (ppp) cc_final: 0.8021 (ppp) REVERT: E 223 MET cc_start: 0.8361 (ppp) cc_final: 0.8056 (ppp) REVERT: E 234 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8803 (pp) REVERT: E 296 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8673 (mp) REVERT: E 302 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7622 (mt-10) REVERT: E 342 MET cc_start: 0.8793 (mmm) cc_final: 0.8042 (tpp) REVERT: E 345 MET cc_start: 0.7287 (ptp) cc_final: 0.6819 (ptp) REVERT: E 398 MET cc_start: 0.4167 (ttp) cc_final: 0.2684 (tpp) REVERT: F 264 MET cc_start: 0.9141 (ptp) cc_final: 0.8401 (ptm) REVERT: F 291 GLU cc_start: 0.8824 (tp30) cc_final: 0.8443 (tp30) REVERT: F 387 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6570 (mtm180) REVERT: F 430 MET cc_start: 0.8705 (mmm) cc_final: 0.8434 (mmm) REVERT: F 504 GLU cc_start: 0.8375 (pp20) cc_final: 0.7906 (mp0) REVERT: K 18 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8060 (pp20) REVERT: K 36 ILE cc_start: 0.9139 (mm) cc_final: 0.8855 (mm) REVERT: K 37 PRO cc_start: 0.9073 (OUTLIER) cc_final: 0.8688 (Cg_endo) REVERT: H 162 GLN cc_start: 0.9326 (tp-100) cc_final: 0.9037 (tp-100) REVERT: J 250 LEU cc_start: 0.7023 (mp) cc_final: 0.6785 (mt) REVERT: G 126 ASP cc_start: 0.9057 (t0) cc_final: 0.8822 (t0) REVERT: G 156 LYS cc_start: 0.7701 (pptt) cc_final: 0.7326 (ptmt) REVERT: G 157 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7361 (tm-30) REVERT: G 160 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: G 161 LYS cc_start: 0.8325 (tmtt) cc_final: 0.7917 (ttmt) REVERT: G 257 MET cc_start: 0.8526 (mmt) cc_final: 0.7952 (mmm) REVERT: G 406 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7674 (tm-30) REVERT: G 426 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8353 (p0) REVERT: G 427 ASP cc_start: 0.7914 (t0) cc_final: 0.7455 (t0) REVERT: G 430 ASP cc_start: 0.8348 (t0) cc_final: 0.7918 (t0) REVERT: G 460 ASP cc_start: 0.8568 (p0) cc_final: 0.7851 (m-30) REVERT: G 539 LEU cc_start: 0.8898 (mt) cc_final: 0.8282 (tp) REVERT: G 546 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7322 (pp) REVERT: G 570 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7752 (pp30) REVERT: G 577 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8446 (pp30) outliers start: 126 outliers final: 79 residues processed: 456 average time/residue: 0.3720 time to fit residues: 275.9012 Evaluate side-chains 418 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 328 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 654 TYR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 693 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 560 MET Chi-restraints excluded: chain E residue 621 MET Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 661 ASN Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain J residue 204 PHE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 233 LYS Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 426 ASN Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 546 LEU Chi-restraints excluded: chain G residue 570 GLN Chi-restraints excluded: chain G residue 577 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 0.8980 chunk 318 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 354 optimal weight: 1.9990 chunk 293 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN B 414 HIS ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29499 Z= 0.264 Angle : 0.664 14.043 39933 Z= 0.324 Chirality : 0.044 0.171 4485 Planarity : 0.005 0.143 5212 Dihedral : 11.192 136.487 4322 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.74 % Favored : 92.18 % Rotamer: Outliers : 4.21 % Allowed : 20.98 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.14), residues: 3684 helix: -0.92 (0.14), residues: 1304 sheet: -0.94 (0.24), residues: 423 loop : -1.62 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 556 HIS 0.028 0.001 HIS G 521 PHE 0.032 0.002 PHE J 204 TYR 0.021 0.001 TYR D 505 ARG 0.006 0.000 ARG E 663 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 346 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.8387 (tpp) cc_final: 0.8063 (tpp) REVERT: A 342 MET cc_start: 0.8731 (tpp) cc_final: 0.8399 (tpt) REVERT: A 353 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7982 (p) REVERT: A 459 MET cc_start: 0.8174 (ptm) cc_final: 0.7864 (ttp) REVERT: A 526 PHE cc_start: 0.9522 (m-80) cc_final: 0.9156 (m-80) REVERT: A 621 MET cc_start: 0.8901 (mmt) cc_final: 0.8108 (mmm) REVERT: B 301 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7710 (tm-30) REVERT: B 302 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8290 (tp30) REVERT: B 329 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8663 (mm-30) REVERT: B 424 LEU cc_start: 0.8223 (tp) cc_final: 0.7937 (tt) REVERT: B 427 GLU cc_start: 0.8366 (tt0) cc_final: 0.7927 (tm-30) REVERT: B 430 MET cc_start: 0.8688 (tpp) cc_final: 0.8310 (tpp) REVERT: B 706 LYS cc_start: 0.9003 (mmtm) cc_final: 0.8780 (pptt) REVERT: C 213 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7475 (m-10) REVERT: C 288 MET cc_start: 0.7170 (tpp) cc_final: 0.6802 (tpp) REVERT: C 324 ASP cc_start: 0.8257 (p0) cc_final: 0.7867 (t0) REVERT: C 369 ARG cc_start: 0.7891 (ttt180) cc_final: 0.7261 (tpp-160) REVERT: C 430 MET cc_start: 0.8915 (mmt) cc_final: 0.8629 (mmm) REVERT: C 513 TYR cc_start: 0.8812 (m-80) cc_final: 0.8006 (m-80) REVERT: C 518 LEU cc_start: 0.7975 (mt) cc_final: 0.7620 (mt) REVERT: D 437 MET cc_start: 0.8329 (mmm) cc_final: 0.7986 (mmm) REVERT: D 513 TYR cc_start: 0.6978 (m-80) cc_final: 0.6594 (m-80) REVERT: D 621 MET cc_start: 0.8425 (ppp) cc_final: 0.8085 (ppp) REVERT: E 223 MET cc_start: 0.8239 (ppp) cc_final: 0.7861 (ppp) REVERT: E 234 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8842 (pp) REVERT: E 296 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8643 (mp) REVERT: E 302 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7625 (mt-10) REVERT: E 342 MET cc_start: 0.8853 (mmm) cc_final: 0.7942 (tpp) REVERT: E 345 MET cc_start: 0.7221 (ptp) cc_final: 0.6733 (ptp) REVERT: E 398 MET cc_start: 0.4334 (ttp) cc_final: 0.4035 (ttp) REVERT: F 264 MET cc_start: 0.9121 (ptp) cc_final: 0.8423 (ptm) REVERT: F 291 GLU cc_start: 0.8819 (tp30) cc_final: 0.8429 (tp30) REVERT: F 430 MET cc_start: 0.8681 (mmm) cc_final: 0.8415 (mmm) REVERT: F 504 GLU cc_start: 0.8530 (pp20) cc_final: 0.7919 (mp0) REVERT: K 18 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7962 (pp20) REVERT: K 36 ILE cc_start: 0.9187 (mm) cc_final: 0.8095 (tp) REVERT: K 37 PRO cc_start: 0.9005 (OUTLIER) cc_final: 0.8371 (Cg_endo) REVERT: H 163 LYS cc_start: 0.8536 (mmmm) cc_final: 0.7643 (mmmm) REVERT: J 201 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.6104 (pmm) REVERT: G 126 ASP cc_start: 0.9040 (t0) cc_final: 0.8764 (t0) REVERT: G 156 LYS cc_start: 0.7852 (pptt) cc_final: 0.7500 (ptmt) REVERT: G 157 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7420 (tm-30) REVERT: G 160 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: G 161 LYS cc_start: 0.8325 (tmtt) cc_final: 0.7921 (ttmt) REVERT: G 211 TRP cc_start: 0.6990 (OUTLIER) cc_final: 0.6682 (t-100) REVERT: G 257 MET cc_start: 0.8530 (mmt) cc_final: 0.7942 (mmm) REVERT: G 427 ASP cc_start: 0.7785 (t0) cc_final: 0.7560 (t0) REVERT: G 460 ASP cc_start: 0.8730 (p0) cc_final: 0.7844 (m-30) REVERT: G 539 LEU cc_start: 0.8994 (mt) cc_final: 0.8295 (tp) REVERT: G 555 GLU cc_start: 0.8319 (pm20) cc_final: 0.8048 (pm20) REVERT: G 574 MET cc_start: 0.8662 (tpt) cc_final: 0.8156 (tpp) REVERT: G 577 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8438 (pp30) outliers start: 130 outliers final: 87 residues processed: 443 average time/residue: 0.3855 time to fit residues: 279.1533 Evaluate side-chains 415 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 318 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 654 TYR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain D residue 693 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 560 MET Chi-restraints excluded: chain E residue 618 MET Chi-restraints excluded: chain E residue 621 MET Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 585 PHE Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 661 ASN Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain J residue 201 MET Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 233 LYS Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 344 HIS Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 394 ILE Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 542 ASP Chi-restraints excluded: chain G residue 577 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 201 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 200 optimal weight: 20.0000 chunk 298 optimal weight: 30.0000 chunk 197 optimal weight: 30.0000 chunk 352 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 ASN ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 GLN G 502 GLN G 521 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29499 Z= 0.152 Angle : 0.616 13.977 39933 Z= 0.294 Chirality : 0.043 0.163 4485 Planarity : 0.004 0.143 5212 Dihedral : 10.908 136.061 4321 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.57 % Favored : 93.38 % Rotamer: Outliers : 2.82 % Allowed : 22.90 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 3684 helix: -0.62 (0.15), residues: 1285 sheet: -0.77 (0.24), residues: 432 loop : -1.50 (0.15), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 556 HIS 0.004 0.001 HIS G 521 PHE 0.019 0.001 PHE J 204 TYR 0.011 0.001 TYR G 267 ARG 0.005 0.000 ARG E 663 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 344 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 MET cc_start: 0.8704 (tpp) cc_final: 0.8116 (tpt) REVERT: A 353 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7929 (p) REVERT: A 459 MET cc_start: 0.8265 (ptm) cc_final: 0.7956 (ttp) REVERT: A 526 PHE cc_start: 0.9522 (m-80) cc_final: 0.9142 (m-80) REVERT: A 570 ARG cc_start: 0.9311 (mtt-85) cc_final: 0.9090 (mtt180) REVERT: A 621 MET cc_start: 0.8911 (mmt) cc_final: 0.8162 (mmm) REVERT: A 784 MET cc_start: 0.0471 (mmt) cc_final: -0.1064 (tpt) REVERT: B 264 MET cc_start: 0.8177 (ttp) cc_final: 0.7933 (ttp) REVERT: B 301 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7658 (tm-30) REVERT: B 302 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8296 (tp30) REVERT: B 329 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8723 (mm-30) REVERT: B 424 LEU cc_start: 0.8152 (tp) cc_final: 0.7891 (tt) REVERT: B 430 MET cc_start: 0.8396 (tpp) cc_final: 0.8070 (tpp) REVERT: B 706 LYS cc_start: 0.9030 (mmtm) cc_final: 0.8794 (pptt) REVERT: C 288 MET cc_start: 0.6977 (tpp) cc_final: 0.6609 (tpp) REVERT: C 324 ASP cc_start: 0.8146 (p0) cc_final: 0.7751 (t0) REVERT: C 332 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7598 (ttt-90) REVERT: C 369 ARG cc_start: 0.7812 (ttt180) cc_final: 0.7505 (tpp-160) REVERT: C 430 MET cc_start: 0.8967 (mmt) cc_final: 0.8760 (mmm) REVERT: C 513 TYR cc_start: 0.8797 (m-80) cc_final: 0.7977 (m-80) REVERT: C 518 LEU cc_start: 0.7998 (mt) cc_final: 0.7595 (mt) REVERT: D 288 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7717 (ppp) REVERT: D 437 MET cc_start: 0.8386 (mmm) cc_final: 0.8077 (mmm) REVERT: D 513 TYR cc_start: 0.7109 (m-80) cc_final: 0.6738 (m-10) REVERT: D 621 MET cc_start: 0.8374 (ppp) cc_final: 0.8035 (ppp) REVERT: E 223 MET cc_start: 0.8134 (ppp) cc_final: 0.7813 (ppp) REVERT: E 234 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8786 (pp) REVERT: E 296 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8595 (mp) REVERT: E 302 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7726 (mt-10) REVERT: E 342 MET cc_start: 0.8711 (mmm) cc_final: 0.7735 (tpp) REVERT: E 345 MET cc_start: 0.7361 (ptp) cc_final: 0.6811 (ptp) REVERT: E 374 ASP cc_start: 0.8423 (p0) cc_final: 0.8027 (m-30) REVERT: E 398 MET cc_start: 0.4234 (ttp) cc_final: 0.3953 (ttp) REVERT: F 264 MET cc_start: 0.9101 (ptp) cc_final: 0.8450 (ptm) REVERT: F 291 GLU cc_start: 0.8783 (tp30) cc_final: 0.8377 (tp30) REVERT: F 430 MET cc_start: 0.8613 (mmm) cc_final: 0.8402 (mmm) REVERT: F 504 GLU cc_start: 0.8468 (pp20) cc_final: 0.7867 (mp0) REVERT: K 18 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8077 (pp20) REVERT: K 36 ILE cc_start: 0.9088 (mm) cc_final: 0.8015 (tp) REVERT: K 37 PRO cc_start: 0.8881 (OUTLIER) cc_final: 0.8261 (Cg_endo) REVERT: J 201 MET cc_start: 0.7858 (ptp) cc_final: 0.6231 (pmm) REVERT: G 156 LYS cc_start: 0.7539 (pptt) cc_final: 0.7092 (ptmt) REVERT: G 157 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7445 (tm-30) REVERT: G 160 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: G 161 LYS cc_start: 0.8333 (tmtt) cc_final: 0.7901 (ttmt) REVERT: G 235 ASP cc_start: 0.9230 (t0) cc_final: 0.8988 (m-30) REVERT: G 257 MET cc_start: 0.8451 (mmt) cc_final: 0.7928 (mmm) REVERT: G 406 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7670 (tm-30) REVERT: G 426 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8075 (p0) REVERT: G 427 ASP cc_start: 0.7954 (t0) cc_final: 0.7748 (t0) REVERT: G 519 LEU cc_start: 0.9012 (mm) cc_final: 0.8725 (tp) REVERT: G 539 LEU cc_start: 0.8913 (mt) cc_final: 0.8231 (tp) REVERT: G 574 MET cc_start: 0.8741 (tpt) cc_final: 0.8303 (tpp) outliers start: 87 outliers final: 60 residues processed: 409 average time/residue: 0.3773 time to fit residues: 252.3160 Evaluate side-chains 387 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 319 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 654 TYR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain D residue 693 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 560 MET Chi-restraints excluded: chain E residue 618 MET Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 585 PHE Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 661 ASN Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain J residue 204 PHE Chi-restraints excluded: chain J residue 233 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 394 ILE Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 426 ASN Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 542 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 3.9990 chunk 140 optimal weight: 0.3980 chunk 210 optimal weight: 8.9990 chunk 106 optimal weight: 0.0870 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 240 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 32 optimal weight: 40.0000 chunk 277 optimal weight: 0.0050 overall best weight: 1.0976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 612 ASN ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 29499 Z= 0.159 Angle : 0.612 14.352 39933 Z= 0.292 Chirality : 0.043 0.191 4485 Planarity : 0.004 0.146 5212 Dihedral : 10.676 134.702 4321 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.79 % Favored : 93.19 % Rotamer: Outliers : 2.95 % Allowed : 22.93 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3684 helix: -0.50 (0.15), residues: 1287 sheet: -0.59 (0.25), residues: 421 loop : -1.45 (0.15), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP G 556 HIS 0.017 0.001 HIS G 521 PHE 0.020 0.001 PHE D 585 TYR 0.012 0.001 TYR E 699 ARG 0.006 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 337 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 MET cc_start: 0.8657 (tpp) cc_final: 0.8317 (tpt) REVERT: A 353 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7966 (p) REVERT: A 459 MET cc_start: 0.8247 (ptm) cc_final: 0.7988 (ttp) REVERT: A 525 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8439 (pt) REVERT: A 526 PHE cc_start: 0.9527 (m-80) cc_final: 0.9118 (m-80) REVERT: A 570 ARG cc_start: 0.9313 (mtt-85) cc_final: 0.9094 (mtt180) REVERT: A 621 MET cc_start: 0.8913 (mmt) cc_final: 0.8173 (mmm) REVERT: A 784 MET cc_start: 0.0401 (mmt) cc_final: -0.1103 (tpt) REVERT: B 264 MET cc_start: 0.8226 (ttp) cc_final: 0.7908 (ttp) REVERT: B 301 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7664 (tm-30) REVERT: B 302 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8315 (tp30) REVERT: B 329 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8727 (mm-30) REVERT: B 424 LEU cc_start: 0.8154 (tp) cc_final: 0.7882 (tt) REVERT: B 430 MET cc_start: 0.8389 (tpp) cc_final: 0.8036 (tpp) REVERT: B 706 LYS cc_start: 0.9034 (mmtm) cc_final: 0.8795 (pptt) REVERT: C 213 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7354 (m-10) REVERT: C 227 ARG cc_start: 0.8559 (mtp180) cc_final: 0.8133 (mtm-85) REVERT: C 288 MET cc_start: 0.6886 (tpp) cc_final: 0.6494 (tpp) REVERT: C 324 ASP cc_start: 0.8120 (p0) cc_final: 0.7732 (t0) REVERT: C 513 TYR cc_start: 0.8788 (m-80) cc_final: 0.7971 (m-80) REVERT: C 518 LEU cc_start: 0.7963 (mt) cc_final: 0.7535 (mt) REVERT: C 577 ARG cc_start: 0.5588 (ttt180) cc_final: 0.4863 (mtp-110) REVERT: D 223 MET cc_start: 0.7755 (tpp) cc_final: 0.7254 (tpp) REVERT: D 288 MET cc_start: 0.8222 (pmm) cc_final: 0.7704 (ppp) REVERT: D 391 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8506 (mm) REVERT: D 437 MET cc_start: 0.8419 (mmm) cc_final: 0.8131 (mmm) REVERT: D 513 TYR cc_start: 0.7337 (m-80) cc_final: 0.6977 (m-10) REVERT: D 621 MET cc_start: 0.8371 (ppp) cc_final: 0.8037 (ppp) REVERT: E 296 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8580 (mp) REVERT: E 302 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7702 (mt-10) REVERT: E 345 MET cc_start: 0.7291 (ptp) cc_final: 0.6814 (ptt) REVERT: E 359 ARG cc_start: 0.8768 (mpp80) cc_final: 0.8466 (mpp80) REVERT: E 374 ASP cc_start: 0.8431 (p0) cc_final: 0.8005 (m-30) REVERT: E 398 MET cc_start: 0.4398 (ttp) cc_final: 0.4084 (ttp) REVERT: F 253 MET cc_start: 0.7071 (ptp) cc_final: 0.6655 (ptm) REVERT: F 264 MET cc_start: 0.9088 (ptp) cc_final: 0.8463 (ptm) REVERT: F 291 GLU cc_start: 0.8779 (tp30) cc_final: 0.8366 (tp30) REVERT: F 504 GLU cc_start: 0.8484 (pp20) cc_final: 0.7875 (mp0) REVERT: F 564 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7825 (mp0) REVERT: K 18 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8071 (pp20) REVERT: K 36 ILE cc_start: 0.9048 (mm) cc_final: 0.8082 (tp) REVERT: K 37 PRO cc_start: 0.8701 (OUTLIER) cc_final: 0.8005 (Cg_endo) REVERT: K 39 ASP cc_start: 0.7859 (p0) cc_final: 0.7407 (m-30) REVERT: J 201 MET cc_start: 0.7903 (ptp) cc_final: 0.6338 (pmm) REVERT: J 250 LEU cc_start: 0.6740 (mp) cc_final: 0.6524 (mt) REVERT: G 156 LYS cc_start: 0.7572 (pptt) cc_final: 0.7137 (ptmt) REVERT: G 157 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7426 (tm-30) REVERT: G 160 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8016 (pm20) REVERT: G 161 LYS cc_start: 0.8315 (tmtt) cc_final: 0.7905 (ttmt) REVERT: G 227 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7569 (mm-40) REVERT: G 257 MET cc_start: 0.8483 (mmt) cc_final: 0.8047 (mmm) REVERT: G 406 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7664 (tm-30) REVERT: G 426 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.8109 (p0) REVERT: G 539 LEU cc_start: 0.8902 (mt) cc_final: 0.8225 (tp) REVERT: G 542 ASP cc_start: 0.9132 (OUTLIER) cc_final: 0.8924 (p0) outliers start: 91 outliers final: 65 residues processed: 408 average time/residue: 0.3798 time to fit residues: 252.7857 Evaluate side-chains 400 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 324 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 654 TYR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain D residue 693 SER Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 560 MET Chi-restraints excluded: chain E residue 618 MET Chi-restraints excluded: chain E residue 621 MET Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 585 PHE Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain F residue 661 ASN Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain J residue 204 PHE Chi-restraints excluded: chain J residue 233 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 394 ILE Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 426 ASN Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain G residue 542 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 0.6980 chunk 337 optimal weight: 0.0040 chunk 308 optimal weight: 0.8980 chunk 328 optimal weight: 0.0870 chunk 197 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 258 optimal weight: 0.9980 chunk 100 optimal weight: 0.0670 chunk 297 optimal weight: 6.9990 chunk 310 optimal weight: 1.9990 chunk 327 optimal weight: 4.9990 overall best weight: 0.3508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN C 350 ASN E 222 GLN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 29499 Z= 0.145 Angle : 0.616 14.694 39933 Z= 0.291 Chirality : 0.043 0.168 4485 Planarity : 0.004 0.148 5212 Dihedral : 10.425 132.937 4321 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.22 % Favored : 93.76 % Rotamer: Outliers : 2.46 % Allowed : 23.41 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3684 helix: -0.49 (0.15), residues: 1304 sheet: -0.44 (0.25), residues: 422 loop : -1.43 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 544 HIS 0.004 0.001 HIS G 166 PHE 0.014 0.001 PHE J 204 TYR 0.012 0.001 TYR E 699 ARG 0.004 0.000 ARG E 609 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 343 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 MET cc_start: 0.8678 (tpp) cc_final: 0.8459 (tpt) REVERT: A 345 MET cc_start: 0.8354 (ppp) cc_final: 0.8025 (ppp) REVERT: A 353 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7904 (p) REVERT: A 525 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8429 (pt) REVERT: A 526 PHE cc_start: 0.9530 (m-80) cc_final: 0.9103 (m-80) REVERT: A 621 MET cc_start: 0.8899 (mmt) cc_final: 0.8194 (mmm) REVERT: A 784 MET cc_start: 0.1030 (mmt) cc_final: -0.0699 (tpt) REVERT: B 264 MET cc_start: 0.8190 (ttp) cc_final: 0.7862 (ttp) REVERT: B 301 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7730 (tm-30) REVERT: B 302 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8332 (tp30) REVERT: B 329 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8726 (mm-30) REVERT: B 424 LEU cc_start: 0.8060 (tp) cc_final: 0.7804 (tt) REVERT: B 430 MET cc_start: 0.8333 (tpp) cc_final: 0.7951 (tpp) REVERT: B 706 LYS cc_start: 0.9036 (mmtm) cc_final: 0.8825 (pptt) REVERT: C 213 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7474 (m-10) REVERT: C 227 ARG cc_start: 0.8521 (mtp180) cc_final: 0.8147 (mtm-85) REVERT: C 288 MET cc_start: 0.6799 (tpp) cc_final: 0.6389 (tpp) REVERT: C 324 ASP cc_start: 0.8237 (p0) cc_final: 0.7752 (t0) REVERT: C 332 ARG cc_start: 0.7654 (ttm-80) cc_final: 0.7389 (ttt-90) REVERT: C 513 TYR cc_start: 0.8772 (m-80) cc_final: 0.8025 (m-80) REVERT: C 518 LEU cc_start: 0.8127 (mt) cc_final: 0.7708 (mt) REVERT: C 573 PHE cc_start: 0.9190 (m-80) cc_final: 0.8845 (m-10) REVERT: C 577 ARG cc_start: 0.5499 (ttt180) cc_final: 0.4811 (mtp-110) REVERT: D 223 MET cc_start: 0.7761 (tpp) cc_final: 0.7278 (tpp) REVERT: D 288 MET cc_start: 0.8187 (pmm) cc_final: 0.7615 (ppp) REVERT: D 391 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8469 (mm) REVERT: D 424 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7093 (tt) REVERT: D 437 MET cc_start: 0.8338 (mmm) cc_final: 0.8052 (mmm) REVERT: D 513 TYR cc_start: 0.7368 (m-80) cc_final: 0.6995 (m-10) REVERT: D 621 MET cc_start: 0.8293 (ppp) cc_final: 0.8008 (ppp) REVERT: E 302 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7693 (mt-10) REVERT: E 345 MET cc_start: 0.7024 (ptp) cc_final: 0.6748 (ptt) REVERT: E 359 ARG cc_start: 0.8729 (mpp80) cc_final: 0.8412 (mpp80) REVERT: F 253 MET cc_start: 0.6821 (ptp) cc_final: 0.6383 (ptm) REVERT: F 264 MET cc_start: 0.9101 (ptp) cc_final: 0.8486 (ptm) REVERT: F 291 GLU cc_start: 0.8760 (tp30) cc_final: 0.8332 (tp30) REVERT: F 504 GLU cc_start: 0.8465 (pp20) cc_final: 0.7888 (mp0) REVERT: F 564 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7797 (mp0) REVERT: K 18 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7639 (pp20) REVERT: K 36 ILE cc_start: 0.9017 (mm) cc_final: 0.8545 (pt) REVERT: K 37 PRO cc_start: 0.8622 (OUTLIER) cc_final: 0.8132 (Cg_endo) REVERT: K 39 ASP cc_start: 0.7957 (p0) cc_final: 0.7463 (m-30) REVERT: J 201 MET cc_start: 0.7673 (ptp) cc_final: 0.6250 (pmm) REVERT: J 250 LEU cc_start: 0.6838 (mp) cc_final: 0.6611 (mt) REVERT: G 157 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7567 (tm-30) REVERT: G 160 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: G 161 LYS cc_start: 0.8304 (tmtt) cc_final: 0.7904 (ttmt) REVERT: G 241 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8030 (mtmm) REVERT: G 242 SER cc_start: 0.9222 (m) cc_final: 0.9001 (p) REVERT: G 257 MET cc_start: 0.8437 (mmt) cc_final: 0.8017 (mmm) REVERT: G 357 MET cc_start: 0.7472 (ttp) cc_final: 0.7084 (ptp) REVERT: G 406 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7429 (tm-30) REVERT: G 426 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.8000 (p0) REVERT: G 519 LEU cc_start: 0.9107 (mp) cc_final: 0.8715 (tt) REVERT: G 539 LEU cc_start: 0.8832 (mt) cc_final: 0.8197 (tp) REVERT: G 574 MET cc_start: 0.8733 (tpt) cc_final: 0.8369 (tpp) outliers start: 76 outliers final: 53 residues processed: 402 average time/residue: 0.3831 time to fit residues: 249.5429 Evaluate side-chains 396 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 333 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 560 MET Chi-restraints excluded: chain E residue 618 MET Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain J residue 204 PHE Chi-restraints excluded: chain J residue 233 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 241 LYS Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 426 ASN Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 544 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 4.9990 chunk 347 optimal weight: 8.9990 chunk 212 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 241 optimal weight: 0.0470 chunk 364 optimal weight: 6.9990 chunk 335 optimal weight: 2.9990 chunk 290 optimal weight: 30.0000 chunk 30 optimal weight: 40.0000 chunk 224 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29499 Z= 0.199 Angle : 0.636 15.013 39933 Z= 0.305 Chirality : 0.043 0.170 4485 Planarity : 0.004 0.151 5212 Dihedral : 10.324 127.901 4321 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.33 % Favored : 92.64 % Rotamer: Outliers : 2.36 % Allowed : 23.64 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3684 helix: -0.45 (0.15), residues: 1296 sheet: -0.45 (0.25), residues: 428 loop : -1.33 (0.15), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 544 HIS 0.005 0.001 HIS G 521 PHE 0.020 0.001 PHE D 585 TYR 0.014 0.001 TYR B 505 ARG 0.006 0.000 ARG E 375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 337 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 PHE cc_start: 0.6769 (OUTLIER) cc_final: 0.5450 (m-80) REVERT: A 342 MET cc_start: 0.8701 (tpp) cc_final: 0.8459 (tpt) REVERT: A 353 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7954 (p) REVERT: A 525 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8416 (pt) REVERT: A 526 PHE cc_start: 0.9539 (m-80) cc_final: 0.9129 (m-80) REVERT: A 570 ARG cc_start: 0.9296 (mtt-85) cc_final: 0.9078 (mtt180) REVERT: A 621 MET cc_start: 0.8823 (mmt) cc_final: 0.8106 (mmm) REVERT: A 784 MET cc_start: 0.1040 (mmt) cc_final: -0.0689 (tpt) REVERT: B 264 MET cc_start: 0.8209 (ttp) cc_final: 0.7869 (ttp) REVERT: B 301 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 302 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8357 (tp30) REVERT: B 329 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8747 (mm-30) REVERT: B 331 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8387 (mm-30) REVERT: B 424 LEU cc_start: 0.8319 (tp) cc_final: 0.8044 (tt) REVERT: B 430 MET cc_start: 0.8575 (tpp) cc_final: 0.8146 (tpp) REVERT: B 706 LYS cc_start: 0.8992 (mmtm) cc_final: 0.8758 (pptt) REVERT: C 213 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7448 (m-10) REVERT: C 227 ARG cc_start: 0.8597 (mtp180) cc_final: 0.8216 (mtm-85) REVERT: C 288 MET cc_start: 0.6954 (tpp) cc_final: 0.6530 (tpp) REVERT: C 324 ASP cc_start: 0.8116 (p0) cc_final: 0.7736 (t0) REVERT: C 513 TYR cc_start: 0.8782 (m-80) cc_final: 0.8039 (m-80) REVERT: C 518 LEU cc_start: 0.8096 (mt) cc_final: 0.7685 (mt) REVERT: D 288 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7851 (ppp) REVERT: D 391 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8508 (mm) REVERT: D 437 MET cc_start: 0.8432 (mmm) cc_final: 0.8171 (mmm) REVERT: D 513 TYR cc_start: 0.7358 (m-80) cc_final: 0.6977 (m-10) REVERT: D 621 MET cc_start: 0.8293 (ppp) cc_final: 0.8003 (ppp) REVERT: E 302 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7718 (mt-10) REVERT: E 345 MET cc_start: 0.7107 (ptp) cc_final: 0.6788 (ptp) REVERT: E 359 ARG cc_start: 0.8802 (mpp80) cc_final: 0.8489 (mpp80) REVERT: F 253 MET cc_start: 0.7107 (ptp) cc_final: 0.6694 (ptm) REVERT: F 264 MET cc_start: 0.9089 (ptp) cc_final: 0.8507 (ptm) REVERT: F 291 GLU cc_start: 0.8774 (tp30) cc_final: 0.8346 (tp30) REVERT: F 504 GLU cc_start: 0.8522 (pp20) cc_final: 0.7874 (mp0) REVERT: K 36 ILE cc_start: 0.9069 (mm) cc_final: 0.8656 (pt) REVERT: K 37 PRO cc_start: 0.8858 (OUTLIER) cc_final: 0.8452 (Cg_endo) REVERT: J 201 MET cc_start: 0.7991 (ptp) cc_final: 0.6789 (pmm) REVERT: G 156 LYS cc_start: 0.7766 (pptt) cc_final: 0.7357 (ptmt) REVERT: G 157 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7500 (tm-30) REVERT: G 160 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: G 161 LYS cc_start: 0.8444 (tmtt) cc_final: 0.7967 (ttmt) REVERT: G 257 MET cc_start: 0.8453 (mmt) cc_final: 0.7965 (mmm) REVERT: G 406 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7530 (tm-30) REVERT: G 426 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8011 (p0) REVERT: G 519 LEU cc_start: 0.9103 (mp) cc_final: 0.8690 (tt) REVERT: G 539 LEU cc_start: 0.8900 (mt) cc_final: 0.8243 (tp) outliers start: 73 outliers final: 60 residues processed: 391 average time/residue: 0.3787 time to fit residues: 241.2649 Evaluate side-chains 390 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 321 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 513 TYR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 628 PHE Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 560 MET Chi-restraints excluded: chain E residue 618 MET Chi-restraints excluded: chain E residue 621 MET Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 628 PHE Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 627 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 37 PRO Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain J residue 233 LYS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 426 ASN Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 536 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 0.9980 chunk 309 optimal weight: 0.0170 chunk 88 optimal weight: 1.9990 chunk 267 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 chunk 121 optimal weight: 0.0770 chunk 298 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.130821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.101192 restraints weight = 87353.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.099028 restraints weight = 51914.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.099994 restraints weight = 47249.277| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 29499 Z= 0.159 Angle : 0.631 15.298 39933 Z= 0.298 Chirality : 0.043 0.211 4485 Planarity : 0.004 0.151 5212 Dihedral : 10.201 125.103 4321 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.54 % Favored : 93.43 % Rotamer: Outliers : 2.53 % Allowed : 23.48 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3684 helix: -0.43 (0.15), residues: 1303 sheet: -0.38 (0.25), residues: 433 loop : -1.29 (0.15), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 544 HIS 0.004 0.001 HIS G 521 PHE 0.018 0.001 PHE J 204 TYR 0.013 0.001 TYR B 505 ARG 0.003 0.000 ARG E 609 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6163.98 seconds wall clock time: 112 minutes 56.45 seconds (6776.45 seconds total)