Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 00:08:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/04_2023/6oa9_0665_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/04_2023/6oa9_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_0665/04_2023/6oa9_0665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/04_2023/6oa9_0665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/04_2023/6oa9_0665_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oa9_0665/04_2023/6oa9_0665_neut_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 14.81, 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: 11.78 Conformation dependent library (CDL) restraints added in 4.3 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: 3.07 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: 8.76 Time building geometry restraints manager: 12.44 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: 17397 30.26 - 60.51: 570 60.51 - 90.77: 35 90.77 - 121.03: 0 121.03 - 151.29: 3 Dihedral angle restraints: 18005 sinusoidal: 7347 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 18002 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.520 Check model and map are aligned: 0.400 Set scattering table: 0.220 Process input model: 75.520 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.110 ------------------------------------------------------------------------------- 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 : 14.185 151.287 11135 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 % 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 *********************** 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 : 3.424 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 outliers start: 14 outliers final: 5 residues processed: 815 average time/residue: 0.4561 time to fit residues: 563.9948 Evaluate side-chains 445 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 440 time to evaluate : 3.737 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3625 time to fit residues: 8.0825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 4.9990 chunk 277 optimal weight: 2.9990 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: 5.9990 chunk 174 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 332 optimal weight: 2.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 305 ASN G 491 ASN G 577 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.097 29499 Z= 0.269 Angle : 0.711 17.996 39933 Z= 0.355 Chirality : 0.045 0.196 4485 Planarity : 0.006 0.170 5212 Dihedral : 7.167 140.899 4042 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.35 % Favored : 93.59 % Rotamer Outliers : 2.82 % 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: -3.75 (0.12), residues: 3684 helix: -3.11 (0.10), residues: 1262 sheet: -1.56 (0.24), residues: 411 loop : -2.27 (0.12), residues: 2011 *********************** 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 523 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 436 time to evaluate : 3.274 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 outliers start: 87 outliers final: 57 residues processed: 496 average time/residue: 0.3984 time to fit residues: 313.7794 Evaluate side-chains 419 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 362 time to evaluate : 3.246 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 1 residues processed: 57 average time/residue: 0.2813 time to fit residues: 33.2834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 276 optimal weight: 10.0000 chunk 226 optimal weight: 0.3980 chunk 91 optimal weight: 7.9990 chunk 332 optimal weight: 2.9990 chunk 359 optimal weight: 0.0970 chunk 296 optimal weight: 30.0000 chunk 330 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 267 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 270 ASN ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 431 GLN ** 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 468 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 509 HIS F 512 GLN ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN K 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 29499 Z= 0.201 Angle : 0.640 15.322 39933 Z= 0.310 Chirality : 0.044 0.215 4485 Planarity : 0.005 0.152 5212 Dihedral : 6.964 141.898 4042 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.49 % Favored : 93.46 % Rotamer Outliers : 1.85 % 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: -2.85 (0.13), residues: 3684 helix: -1.99 (0.13), residues: 1273 sheet: -1.13 (0.24), residues: 426 loop : -1.99 (0.13), residues: 1985 *********************** 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 451 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 394 time to evaluate : 3.455 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 outliers start: 57 outliers final: 28 residues processed: 434 average time/residue: 0.4121 time to fit residues: 286.8929 Evaluate side-chains 368 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 340 time to evaluate : 3.717 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 1 residues processed: 28 average time/residue: 0.2849 time to fit residues: 19.7149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 0.7980 chunk 250 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 334 optimal weight: 5.9990 chunk 353 optimal weight: 0.5980 chunk 174 optimal weight: 5.9990 chunk 316 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN B 337 GLN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 GLN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 ASN E 394 HIS ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 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** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN H 102 GLN H 162 GLN J 249 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 29499 Z= 0.286 Angle : 0.684 14.409 39933 Z= 0.338 Chirality : 0.045 0.218 4485 Planarity : 0.005 0.144 5212 Dihedral : 6.943 142.540 4042 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.84 % Favored : 92.10 % Rotamer Outliers : 2.69 % 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: -2.39 (0.13), residues: 3684 helix: -1.41 (0.14), residues: 1295 sheet: -1.19 (0.24), residues: 444 loop : -1.78 (0.14), residues: 1945 *********************** 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 452 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 369 time to evaluate : 3.612 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 outliers start: 83 outliers final: 46 residues processed: 430 average time/residue: 0.4054 time to fit residues: 281.9734 Evaluate side-chains 362 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 316 time to evaluate : 3.468 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 1 residues processed: 46 average time/residue: 0.2625 time to fit residues: 27.7200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 7.9990 chunk 200 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 301 optimal weight: 2.9990 chunk 244 optimal weight: 0.0980 chunk 0 optimal weight: 7.9990 chunk 180 optimal weight: 0.6980 chunk 317 optimal weight: 9.9990 chunk 89 optimal weight: 0.0870 overall best weight: 1.1762 ------------------------------------------------------------------------------- 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 626 ASN B 668 ASN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 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** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN G 272 ASN ** G 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 29499 Z= 0.168 Angle : 0.629 13.678 39933 Z= 0.300 Chirality : 0.043 0.179 4485 Planarity : 0.004 0.132 5212 Dihedral : 6.704 140.692 4042 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.41 % Favored : 93.51 % Rotamer Outliers : 1.30 % 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: -2.06 (0.14), residues: 3684 helix: -1.04 (0.14), residues: 1290 sheet: -1.01 (0.24), residues: 429 loop : -1.66 (0.14), residues: 1965 *********************** 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 395 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 355 time to evaluate : 3.350 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 outliers start: 40 outliers final: 18 residues processed: 387 average time/residue: 0.3869 time to fit residues: 245.0689 Evaluate side-chains 339 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 321 time to evaluate : 3.467 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.2687 time to fit residues: 13.7429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 6.9990 chunk 318 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 354 optimal weight: 0.8980 chunk 293 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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** B 414 HIS B 470 ASN ** C 350 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 270 ASN ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 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** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 293 GLN ** G 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 29499 Z= 0.285 Angle : 0.686 14.558 39933 Z= 0.337 Chirality : 0.045 0.239 4485 Planarity : 0.005 0.133 5212 Dihedral : 6.783 135.855 4042 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.79 % Favored : 91.12 % Rotamer Outliers : 1.94 % 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: -0.91 (0.14), residues: 1295 sheet: -0.99 (0.24), residues: 444 loop : -1.62 (0.14), residues: 1945 *********************** 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 397 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 337 time to evaluate : 3.324 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 outliers start: 60 outliers final: 32 residues processed: 377 average time/residue: 0.4345 time to fit residues: 266.7498 Evaluate side-chains 339 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 307 time to evaluate : 3.533 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 1 residues processed: 32 average time/residue: 0.2790 time to fit residues: 21.2728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 201 optimal weight: 7.9990 chunk 258 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 298 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 352 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** B 361 ASN C 270 ASN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 ASN D 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 468 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** F 782 GLN ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 ASN G 526 ASN ** G 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 29499 Z= 0.182 Angle : 0.651 13.457 39933 Z= 0.310 Chirality : 0.044 0.203 4485 Planarity : 0.004 0.134 5212 Dihedral : 6.613 135.000 4042 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.89 % Favored : 93.05 % Rotamer Outliers : 1.20 % 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: -1.77 (0.14), residues: 3684 helix: -0.74 (0.15), residues: 1298 sheet: -0.80 (0.24), residues: 437 loop : -1.55 (0.14), residues: 1949 *********************** 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 373 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 336 time to evaluate : 3.487 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 outliers start: 37 outliers final: 16 residues processed: 363 average time/residue: 0.4122 time to fit residues: 248.1581 Evaluate side-chains 327 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 311 time to evaluate : 3.447 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.3189 time to fit residues: 13.7057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 240 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 277 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 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 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 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** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 29499 Z= 0.176 Angle : 0.646 14.091 39933 Z= 0.307 Chirality : 0.044 0.289 4485 Planarity : 0.004 0.141 5212 Dihedral : 6.471 133.861 4042 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.44 % Favored : 92.51 % Rotamer Outliers : 0.68 % 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: -1.64 (0.14), residues: 3684 helix: -0.60 (0.15), residues: 1293 sheet: -0.65 (0.25), residues: 433 loop : -1.51 (0.14), residues: 1958 *********************** 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 345 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 324 time to evaluate : 3.847 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 outliers start: 21 outliers final: 11 residues processed: 335 average time/residue: 0.4105 time to fit residues: 225.1783 Evaluate side-chains 316 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 305 time to evaluate : 3.334 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.2629 time to fit residues: 10.0676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 0.8980 chunk 337 optimal weight: 2.9990 chunk 308 optimal weight: 6.9990 chunk 328 optimal weight: 0.0670 chunk 197 optimal weight: 30.0000 chunk 143 optimal weight: 0.0970 chunk 258 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 297 optimal weight: 8.9990 chunk 310 optimal weight: 6.9990 chunk 327 optimal weight: 4.9990 overall best weight: 1.8120 ------------------------------------------------------------------------------- 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** ** C 350 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 468 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** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 29499 Z= 0.192 Angle : 0.655 13.272 39933 Z= 0.312 Chirality : 0.043 0.186 4485 Planarity : 0.004 0.145 5212 Dihedral : 6.451 130.876 4042 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.27 % Favored : 92.67 % Rotamer Outliers : 0.55 % 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: -1.56 (0.14), residues: 3684 helix: -0.55 (0.15), residues: 1292 sheet: -0.62 (0.25), residues: 435 loop : -1.45 (0.15), residues: 1957 *********************** 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 334 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 317 time to evaluate : 3.645 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 outliers start: 17 outliers final: 10 residues processed: 328 average time/residue: 0.3960 time to fit residues: 213.0578 Evaluate side-chains 316 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 306 time to evaluate : 3.629 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2823 time to fit residues: 9.7872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 0.1980 chunk 347 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 364 optimal weight: 3.9990 chunk 335 optimal weight: 0.9990 chunk 290 optimal weight: 6.9990 chunk 30 optimal weight: 40.0000 chunk 224 optimal weight: 0.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN ** 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 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 612 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN G 521 HIS ** G 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 29499 Z= 0.195 Angle : 0.663 14.695 39933 Z= 0.315 Chirality : 0.044 0.178 4485 Planarity : 0.004 0.147 5212 Dihedral : 6.406 127.518 4042 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.74 % Favored : 92.21 % Rotamer Outliers : 0.52 % 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: -0.52 (0.15), residues: 1287 sheet: -0.61 (0.25), residues: 439 loop : -1.43 (0.15), residues: 1958 ********************** 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 338 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 322 time to evaluate : 3.274 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 outliers start: 16 outliers final: 10 residues processed: 331 average time/residue: 0.3856 time to fit residues: 208.8842 Evaluate side-chains 314 residues out of total 3088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 304 time to evaluate : 3.292 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2722 time to fit residues: 9.5899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 1.9990 chunk 309 optimal weight: 0.0970 chunk 88 optimal weight: 3.9990 chunk 267 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 290 optimal weight: 0.0050 chunk 121 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 chunk 36 optimal weight: 0.0070 chunk 53 optimal weight: 8.9990 overall best weight: 1.2214 ------------------------------------------------------------------------------- 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** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 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** ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 521 HIS ** G 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.129610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.099966 restraints weight = 87632.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.097804 restraints weight = 54574.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098811 restraints weight = 48039.522| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 29499 Z= 0.174 Angle : 0.664 14.671 39933 Z= 0.313 Chirality : 0.043 0.183 4485 Planarity : 0.004 0.148 5212 Dihedral : 6.322 124.872 4042 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.76 % Favored : 93.21 % Rotamer Outliers : 0.29 % 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: -1.46 (0.14), residues: 3684 helix: -0.46 (0.15), residues: 1278 sheet: -0.55 (0.25), residues: 440 loop : -1.41 (0.14), residues: 1966 =============================================================================== Job complete usr+sys time: 5753.12 seconds wall clock time: 106 minutes 13.47 seconds (6373.47 seconds total)