Starting phenix.real_space_refine on Sun Sep 29 13:50:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njk_12377/09_2024/7njk_12377_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njk_12377/09_2024/7njk_12377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njk_12377/09_2024/7njk_12377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njk_12377/09_2024/7njk_12377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njk_12377/09_2024/7njk_12377_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njk_12377/09_2024/7njk_12377_trim.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 107 5.16 5 C 23577 2.51 5 N 6406 2.21 5 O 7180 1.98 5 H 37359 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74650 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 507, 7670 Classifications: {'peptide': 507} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 507, 7670 Classifications: {'peptide': 507} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} Chain breaks: 2 bond proxies already assigned to first conformer: 7705 Chain: "B" Number of atoms: 7628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 7628 Classifications: {'peptide': 504} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 482} Chain breaks: 2 Chain: "C" Number of atoms: 8041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 8041 Classifications: {'peptide': 531} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Chain breaks: 2 Chain: "D" Number of atoms: 7162 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Conformer: "B" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} bond proxies already assigned to first conformer: 7190 Chain: "E" Number of atoms: 7087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 7087 Classifications: {'peptide': 464} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Chain: "F" Number of atoms: 7166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7166 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "G" Number of atoms: 4551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 4551 Classifications: {'peptide': 296} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 286} Chain breaks: 1 Chain: "H" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1802 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2172 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "d" Number of atoms: 6656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6656 Classifications: {'peptide': 438} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 33.41, per 1000 atoms: 0.45 Number of scatterers: 74650 At special positions: 0 Unit cell: (136.95, 129.48, 249.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 107 16.00 P 16 15.00 Mg 5 11.99 O 7180 8.00 N 6406 7.00 C 23577 6.00 H 37359 1.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.50 Conformation dependent library (CDL) restraints added in 5.3 seconds 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8884 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 27 sheets defined 61.5% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 3.726A pdb=" N GLY A 13 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 138 through 142 removed outlier: 4.032A pdb=" N ARG A 142 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.674A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.178A pdb=" N GLY A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 242 through 262 Proline residue: A 250 - end of helix removed outlier: 3.656A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.577A pdb=" N GLN A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.644A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 392 through 404 Processing helix chain 'A' and resid 414 through 432 removed outlier: 3.643A pdb=" N LYS A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 478 Processing helix chain 'A' and resid 479 through 490 removed outlier: 4.435A pdb=" N PHE A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 509 removed outlier: 3.669A pdb=" N LYS A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 21 removed outlier: 3.913A pdb=" N ASP B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.920A pdb=" N ARG B 142 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 189 through 195 Processing helix chain 'B' and resid 212 through 226 Processing helix chain 'B' and resid 227 through 230 removed outlier: 3.692A pdb=" N GLU B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 242 through 262 Proline residue: B 250 - end of helix removed outlier: 3.677A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.508A pdb=" N GLN B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 300 through 311 removed outlier: 3.653A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 392 through 406 removed outlier: 3.661A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 493 through 511 Processing helix chain 'C' and resid 7 through 22 removed outlier: 3.550A pdb=" N ILE C 11 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 81 through 85 removed outlier: 4.037A pdb=" N LYS C 84 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.823A pdb=" N ARG C 142 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.615A pdb=" N MET C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 removed outlier: 3.725A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.929A pdb=" N GLY C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 227 through 230 removed outlier: 3.553A pdb=" N GLU C 230 " --> pdb=" O GLY C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 242 through 262 Proline residue: C 250 - end of helix removed outlier: 3.640A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.519A pdb=" N GLN C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 298 through 299 No H-bonds generated for 'chain 'C' and resid 298 through 299' Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.590A pdb=" N HIS C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.609A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 407 Processing helix chain 'C' and resid 414 through 432 Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 478 Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 493 through 508 Processing helix chain 'C' and resid 509 through 511 No H-bonds generated for 'chain 'C' and resid 509 through 511' Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 126 through 130 Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 165 through 177 Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 223 through 244 removed outlier: 4.821A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 266 removed outlier: 3.930A pdb=" N THR D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 271 Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 282 through 292 Processing helix chain 'D' and resid 311 through 314 Processing helix chain 'D' and resid 317 through 325 removed outlier: 4.367A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 341 Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 362 through 390 removed outlier: 4.707A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 394 Processing helix chain 'D' and resid 395 through 413 removed outlier: 3.623A pdb=" N SER D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 451 through 456 Processing helix chain 'D' and resid 460 through 471 Processing helix chain 'E' and resid 25 through 29 removed outlier: 4.228A pdb=" N VAL E 29 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.511A pdb=" N VAL E 94 " --> pdb=" O GLY E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 130 Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 165 through 181 removed outlier: 3.505A pdb=" N PHE E 181 " --> pdb=" O ILE E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 207 Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.741A pdb=" N ARG E 227 " --> pdb=" O PRO E 223 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 270 Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 282 through 292 Processing helix chain 'E' and resid 310 through 314 Processing helix chain 'E' and resid 317 through 325 Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 357 through 390 removed outlier: 7.479A pdb=" N ASP E 363 " --> pdb=" O ALA E 359 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLU E 364 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS E 365 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 394 Processing helix chain 'E' and resid 395 through 413 removed outlier: 3.671A pdb=" N SER E 413 " --> pdb=" O GLU E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 420 removed outlier: 3.582A pdb=" N GLU E 420 " --> pdb=" O MET E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 445 Processing helix chain 'E' and resid 451 through 456 Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'F' and resid 126 through 130 Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'F' and resid 165 through 178 Processing helix chain 'F' and resid 193 through 207 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 223 through 245 removed outlier: 5.126A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN F 245 " --> pdb=" O PHE F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 270 removed outlier: 3.674A pdb=" N PHE F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 282 through 294 removed outlier: 3.987A pdb=" N ARG F 293 " --> pdb=" O GLU F 289 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 314 Processing helix chain 'F' and resid 317 through 324 Processing helix chain 'F' and resid 325 through 327 No H-bonds generated for 'chain 'F' and resid 325 through 327' Processing helix chain 'F' and resid 334 through 341 Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 362 through 390 removed outlier: 4.531A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 413 removed outlier: 3.819A pdb=" N SER F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 418 No H-bonds generated for 'chain 'F' and resid 416 through 418' Processing helix chain 'F' and resid 419 through 424 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 451 through 456 Processing helix chain 'F' and resid 460 through 472 Processing helix chain 'G' and resid 4 through 60 removed outlier: 3.594A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 91 through 110 Processing helix chain 'G' and resid 120 through 130 removed outlier: 3.661A pdb=" N LEU G 124 " --> pdb=" O GLY G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 164 Processing helix chain 'G' and resid 172 through 176 removed outlier: 4.168A pdb=" N ASP G 175 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 303 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 91 through 99 removed outlier: 3.528A pdb=" N ALA H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 118 Processing helix chain 'L' and resid 4 through 46 removed outlier: 3.525A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 81 removed outlier: 4.128A pdb=" N THR L 55 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 4.076A pdb=" N ALA L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET L 75 " --> pdb=" O ASN L 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 Processing helix chain 'M' and resid 49 through 81 removed outlier: 4.669A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.588A pdb=" N TYR M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 removed outlier: 3.669A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 80 removed outlier: 3.872A pdb=" N PHE N 54 " --> pdb=" O GLN N 50 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.796A pdb=" N ALA N 66 " --> pdb=" O GLY N 62 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR N 68 " --> pdb=" O VAL N 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 removed outlier: 3.750A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 80 removed outlier: 4.055A pdb=" N PHE O 54 " --> pdb=" O GLN O 50 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix Processing helix chain 'P' and resid 4 through 46 Processing helix chain 'P' and resid 49 through 81 removed outlier: 3.717A pdb=" N PHE P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.519A pdb=" N ILE P 59 " --> pdb=" O THR P 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 46 Processing helix chain 'Q' and resid 49 through 80 removed outlier: 3.692A pdb=" N PHE Q 54 " --> pdb=" O GLN Q 50 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Proline residue: Q 56 - end of helix Processing helix chain 'R' and resid 4 through 46 removed outlier: 3.760A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 81 removed outlier: 4.112A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix Processing helix chain 'S' and resid 4 through 46 removed outlier: 3.546A pdb=" N ILE S 8 " --> pdb=" O ASP S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 80 removed outlier: 3.747A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 4.205A pdb=" N ALA S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.710A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 81 removed outlier: 3.965A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.997A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 51 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 107 removed outlier: 4.046A pdb=" N ALA a 107 " --> pdb=" O SER a 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 153 removed outlier: 3.621A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.568A pdb=" N ILE a 160 " --> pdb=" O VAL a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 169 No H-bonds generated for 'chain 'a' and resid 167 through 169' Processing helix chain 'a' and resid 170 through 204 removed outlier: 3.849A pdb=" N VAL a 176 " --> pdb=" O PRO a 172 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU a 177 " --> pdb=" O ILE a 173 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 3.525A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL a 200 " --> pdb=" O GLY a 196 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 3.806A pdb=" N TRP a 212 " --> pdb=" O TRP a 208 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.713A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 49 removed outlier: 3.646A pdb=" N ALA b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL b 41 " --> pdb=" O ILE b 37 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 145 Processing helix chain 'b' and resid 147 through 161 Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 137 Processing helix chain 'd' and resid 139 through 156 Processing helix chain 'd' and resid 173 through 191 Processing helix chain 'd' and resid 195 through 216 Processing helix chain 'd' and resid 216 through 225 removed outlier: 3.514A pdb=" N ASN d 220 " --> pdb=" O GLU d 216 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU d 225 " --> pdb=" O LYS d 221 " (cutoff:3.500A) Processing helix chain 'd' and resid 230 through 242 Processing helix chain 'd' and resid 246 through 259 Processing helix chain 'd' and resid 263 through 287 removed outlier: 3.942A pdb=" N LEU d 267 " --> pdb=" O THR d 263 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 288 through 306 Processing helix chain 'd' and resid 306 through 314 Processing helix chain 'd' and resid 319 through 331 Processing helix chain 'd' and resid 338 through 351 Processing helix chain 'd' and resid 356 through 372 removed outlier: 4.083A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 386 through 402 Processing helix chain 'd' and resid 412 through 416 Processing helix chain 'd' and resid 431 through 442 Processing sheet with id=A, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.415A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 36 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=C, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.533A pdb=" N LEU A 169 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU A 355 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 171 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'A' and resid 232 through 237 removed outlier: 6.576A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER A 323 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE A 269 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR A 325 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE A 271 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 327 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 31 through 33 removed outlier: 4.187A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL B 34 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 99 through 102 Processing sheet with id=G, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.526A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE B 171 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'B' and resid 232 through 237 removed outlier: 6.608A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER B 323 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE B 269 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR B 325 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N PHE B 271 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 327 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.706A pdb=" N HIS C 43 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C 77 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ALA C 66 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=K, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.377A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 171 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'C' and resid 232 through 237 removed outlier: 8.588A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS C 266 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL C 205 " --> pdb=" O HIS C 266 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU C 268 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL C 270 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE C 209 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP C 272 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 327 " --> pdb=" O PHE C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=L Processing sheet with id=M, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.529A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 87 through 89 Processing sheet with id=O, first strand: chain 'D' and resid 329 through 332 removed outlier: 7.327A pdb=" N ILE D 156 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER D 304 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU D 158 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN D 306 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLY D 160 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL D 308 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA D 307 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE D 253 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N TYR D 309 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ASP D 254 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA D 188 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'E' and resid 11 through 16 removed outlier: 6.535A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL E 53 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'E' and resid 87 through 89 Processing sheet with id=R, first strand: chain 'E' and resid 329 through 332 removed outlier: 8.504A pdb=" N ILE E 156 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER E 304 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU E 158 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ASP E 254 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA E 188 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'F' and resid 11 through 16 removed outlier: 6.559A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL F 53 " --> pdb=" O ILE F 65 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'F' and resid 87 through 89 Processing sheet with id=U, first strand: chain 'F' and resid 329 through 332 removed outlier: 7.463A pdb=" N ILE F 156 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER F 304 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU F 158 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN F 306 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N GLY F 160 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL F 308 " --> pdb=" O GLY F 160 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASP F 254 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA F 188 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'G' and resid 113 through 119 removed outlier: 3.695A pdb=" N ALA G 77 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THR G 188 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE G 185 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ARG G 202 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE G 187 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA G 200 " --> pdb=" O PHE G 187 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU G 189 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ALA G 198 " --> pdb=" O GLU G 189 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.115A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA H 10 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'H' and resid 31 through 34 removed outlier: 4.125A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN H 83 " --> pdb=" O ASP H 66 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=Z, first strand: chain 'a' and resid 112 through 114 Processing sheet with id=AA, first strand: chain 'd' and resid 405 through 409 removed outlier: 6.187A pdb=" N VAL d 375 " --> pdb=" O SER d 406 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLN d 408 " --> pdb=" O VAL d 375 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA d 377 " --> pdb=" O GLN d 408 " (cutoff:3.500A) 2350 hydrogen bonds defined for protein. 6738 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: 29.46 Time building geometry restraints manager: 18.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 37339 1.03 - 1.23: 94 1.23 - 1.42: 15258 1.42 - 1.62: 22358 1.62 - 1.81: 194 Bond restraints: 75243 Sorted by residual: bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 2.03e+00 bond pdb=" CG PRO F 344 " pdb=" CD PRO F 344 " ideal model delta sigma weight residual 1.512 1.476 0.036 2.70e-02 1.37e+03 1.73e+00 bond pdb=" CA VAL B 374 " pdb=" CB VAL B 374 " ideal model delta sigma weight residual 1.550 1.538 0.012 1.03e-02 9.43e+03 1.47e+00 bond pdb=" CG MET M 75 " pdb=" SD MET M 75 " ideal model delta sigma weight residual 1.803 1.774 0.029 2.50e-02 1.60e+03 1.38e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.33e+00 ... (remaining 75238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 134234 1.49 - 2.99: 1840 2.99 - 4.48: 213 4.48 - 5.97: 36 5.97 - 7.46: 11 Bond angle restraints: 136334 Sorted by residual: angle pdb=" C ASP E 254 " pdb=" N ASN E 255 " pdb=" CA ASN E 255 " ideal model delta sigma weight residual 121.70 127.38 -5.68 1.80e+00 3.09e-01 9.95e+00 angle pdb=" C ASP A 272 " pdb=" N ASP A 273 " pdb=" CA ASP A 273 " ideal model delta sigma weight residual 121.70 127.36 -5.66 1.80e+00 3.09e-01 9.89e+00 angle pdb=" C ASP D 254 " pdb=" N ASN D 255 " pdb=" CA ASN D 255 " ideal model delta sigma weight residual 121.70 127.22 -5.52 1.80e+00 3.09e-01 9.42e+00 angle pdb=" C ASP F 254 " pdb=" N ASN F 255 " pdb=" CA ASN F 255 " ideal model delta sigma weight residual 121.70 127.21 -5.51 1.80e+00 3.09e-01 9.35e+00 angle pdb=" N ILE A 35 " pdb=" CA ILE A 35 " pdb=" C ILE A 35 " ideal model delta sigma weight residual 112.96 110.03 2.93 1.00e+00 1.00e+00 8.59e+00 ... (remaining 136329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.72: 33436 28.72 - 57.44: 1578 57.44 - 86.15: 148 86.15 - 114.87: 12 114.87 - 143.59: 2 Dihedral angle restraints: 35176 sinusoidal: 19501 harmonic: 15675 Sorted by residual: dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 83.59 -143.59 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" O1B ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PB ADP E 600 " pdb=" PA ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 66.25 -126.25 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 -171.79 111.80 1 2.00e+01 2.50e-03 3.29e+01 ... (remaining 35173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 5230 0.060 - 0.120: 683 0.120 - 0.181: 43 0.181 - 0.241: 2 0.241 - 0.301: 10 Chirality restraints: 5968 Sorted by residual: chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C2' ATP C 600 " pdb=" C1' ATP C 600 " pdb=" C3' ATP C 600 " pdb=" O2' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 5965 not shown) Planarity restraints: 11425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN S 46 " -0.041 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO S 47 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO S 47 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO S 47 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 469 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C SER C 469 " 0.028 2.00e-02 2.50e+03 pdb=" O SER C 469 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU C 470 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 245 " 0.016 2.00e-02 2.50e+03 8.52e-03 2.18e+00 pdb=" CG PHE B 245 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE B 245 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 245 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 245 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 245 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 245 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE B 245 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE B 245 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE B 245 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 245 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 245 " -0.000 2.00e-02 2.50e+03 ... (remaining 11422 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 2717 2.15 - 2.76: 146581 2.76 - 3.37: 227009 3.37 - 3.99: 295757 3.99 - 4.60: 462689 Nonbonded interactions: 1134753 Sorted by model distance: nonbonded pdb="HH12 ARG R 52 " pdb=" O ILE S 43 " model vdw 1.535 2.450 nonbonded pdb=" OE1 GLU a 177 " pdb=" H GLU a 177 " model vdw 1.558 2.450 nonbonded pdb=" OD2 ASP G 167 " pdb=" H GLY G 179 " model vdw 1.561 2.450 nonbonded pdb="HH12 ARG G 39 " pdb=" O PRO G 145 " model vdw 1.564 2.450 nonbonded pdb="HH12 ARG F 26 " pdb=" OD2 ASP d 358 " model vdw 1.588 2.450 ... (remaining 1134748 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ )) or resid 7 through 173 or resid 175 through 406 or (resid 414 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name OD2 or nam \ e HA or name HB2 or name HB3)) or resid 415 through 521 or resid 600 through 601 \ )) selection = (chain 'B' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ )) or resid 7 through 173 or resid 175 through 521 or resid 600 through 601)) selection = (chain 'C' and (resid 6 through 22 or (resid 29 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3)) or resid 30 through 173 or resi \ d 175 through 406 or (resid 414 and (name N or name CA or name C or name O or na \ me CB or name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or \ resid 415 through 521 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 452 or resid 455 through 471)) selection = (chain 'E' and (resid 8 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 452 or resid 455 t \ hrough 471)) selection = (chain 'F' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 9 through 452 or resid 455 through 471)) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.490 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: 1.050 Extract box with map and model: 2.250 Check model and map are aligned: 0.440 Set scattering table: 0.530 Process input model: 132.800 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.390 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: 0.020 Load rotamer database and sin/cos tables:10.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 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 0.044 37884 Z= 0.253 Angle : 0.515 7.463 51382 Z= 0.273 Chirality : 0.042 0.301 5968 Planarity : 0.003 0.061 6721 Dihedral : 14.885 143.591 13873 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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 (0.12), residues: 4882 helix: 1.71 (0.10), residues: 2637 sheet: -0.16 (0.21), residues: 530 loop : 0.70 (0.16), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.004 0.001 HIS F 97 PHE 0.024 0.001 PHE B 245 TYR 0.012 0.001 TYR C 18 ARG 0.005 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 369 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 4.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 418 LYS cc_start: 0.7252 (mptt) cc_final: 0.7049 (mptt) REVERT: P 86 GLN cc_start: 0.7132 (pp30) cc_final: 0.6522 (pp30) REVERT: a 25 MET cc_start: 0.8000 (mtm) cc_final: 0.7729 (mtm) outliers start: 0 outliers final: 2 residues processed: 369 average time/residue: 3.1253 time to fit residues: 1387.7151 Evaluate side-chains 268 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 266 time to evaluate : 4.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain b residue 117 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 3.9990 chunk 366 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 378 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN C 53 GLN C 399 GLN ** C 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN F 421 GLN G 288 GLN N 71 ASN T 86 GLN d 127 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 37884 Z= 0.316 Angle : 0.546 7.901 51382 Z= 0.292 Chirality : 0.041 0.170 5968 Planarity : 0.004 0.057 6721 Dihedral : 7.521 125.063 5415 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.66 % Favored : 98.28 % Rotamer: Outliers : 0.44 % Allowed : 5.48 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.83 (0.12), residues: 4882 helix: 2.02 (0.10), residues: 2643 sheet: -0.37 (0.21), residues: 531 loop : 0.63 (0.16), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.005 0.001 HIS F 97 PHE 0.022 0.001 PHE P 74 TYR 0.028 0.001 TYR a 145 ARG 0.006 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 281 time to evaluate : 4.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 75 MET cc_start: 0.8496 (tmm) cc_final: 0.8264 (tmm) REVERT: P 86 GLN cc_start: 0.7160 (pp30) cc_final: 0.6690 (pp30) REVERT: a 177 GLU cc_start: 0.8030 (mp0) cc_final: 0.7725 (mp0) outliers start: 17 outliers final: 5 residues processed: 290 average time/residue: 3.2719 time to fit residues: 1143.1822 Evaluate side-chains 264 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 259 time to evaluate : 4.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 77 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 365 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 439 optimal weight: 3.9990 chunk 474 optimal weight: 4.9990 chunk 391 optimal weight: 0.9990 chunk 435 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 352 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN F 245 GLN G 288 GLN a 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 37884 Z= 0.353 Angle : 0.553 8.319 51382 Z= 0.294 Chirality : 0.042 0.198 5968 Planarity : 0.004 0.059 6721 Dihedral : 7.419 121.621 5409 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.99 % Favored : 97.95 % Rotamer: Outliers : 0.44 % Allowed : 7.17 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.80 (0.12), residues: 4882 helix: 2.06 (0.10), residues: 2648 sheet: -0.53 (0.21), residues: 533 loop : 0.54 (0.16), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.005 0.001 HIS F 97 PHE 0.019 0.002 PHE P 74 TYR 0.025 0.001 TYR a 145 ARG 0.009 0.000 ARG d 308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 278 time to evaluate : 4.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 476 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7983 (tmtt) REVERT: P 50 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7837 (tp-100) REVERT: P 86 GLN cc_start: 0.7174 (pp30) cc_final: 0.6728 (pp30) REVERT: a 122 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: b 72 ARG cc_start: 0.7670 (tmm-80) cc_final: 0.7334 (tmm-80) outliers start: 17 outliers final: 9 residues processed: 288 average time/residue: 2.8826 time to fit residues: 1005.5035 Evaluate side-chains 266 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 255 time to evaluate : 4.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain b residue 70 ASP Chi-restraints excluded: chain b residue 73 LYS Chi-restraints excluded: chain d residue 201 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 4.9990 chunk 330 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 295 optimal weight: 0.9990 chunk 440 optimal weight: 2.9990 chunk 466 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 417 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN F 245 GLN a 75 GLN d 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37884 Z= 0.297 Angle : 0.536 8.258 51382 Z= 0.284 Chirality : 0.041 0.195 5968 Planarity : 0.004 0.061 6721 Dihedral : 7.348 119.897 5409 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.89 % Favored : 98.05 % Rotamer: Outliers : 0.55 % Allowed : 8.11 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.83 (0.12), residues: 4882 helix: 2.13 (0.10), residues: 2640 sheet: -0.59 (0.21), residues: 533 loop : 0.51 (0.16), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.005 0.001 HIS F 97 PHE 0.015 0.001 PHE P 74 TYR 0.022 0.001 TYR a 145 ARG 0.007 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 274 time to evaluate : 4.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 476 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7989 (tmtt) REVERT: P 50 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7812 (tp-100) REVERT: P 86 GLN cc_start: 0.7172 (pp30) cc_final: 0.6629 (pp30) REVERT: a 122 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7238 (mt-10) outliers start: 21 outliers final: 10 residues processed: 286 average time/residue: 2.9149 time to fit residues: 1019.6894 Evaluate side-chains 265 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 253 time to evaluate : 4.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain P residue 21 MET Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 201 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 347 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 398 optimal weight: 1.9990 chunk 322 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 chunk 419 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN F 245 GLN G 288 GLN T 86 GLN a 75 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 37884 Z= 0.356 Angle : 0.556 8.466 51382 Z= 0.294 Chirality : 0.042 0.215 5968 Planarity : 0.004 0.083 6721 Dihedral : 7.386 120.841 5409 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 0.70 % Allowed : 8.53 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.83 (0.12), residues: 4882 helix: 2.13 (0.10), residues: 2644 sheet: -0.63 (0.21), residues: 545 loop : 0.50 (0.16), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.005 0.001 HIS F 97 PHE 0.015 0.001 PHE B 106 TYR 0.022 0.001 TYR a 145 ARG 0.012 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 294 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 267 time to evaluate : 4.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 476 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7988 (tmtt) REVERT: F 433 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7945 (tppp) REVERT: P 50 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7809 (tp-100) REVERT: P 86 GLN cc_start: 0.7176 (pp30) cc_final: 0.6770 (pp30) REVERT: T 65 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: a 122 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7227 (mt-10) REVERT: a 177 GLU cc_start: 0.7936 (mp0) cc_final: 0.7624 (mp0) outliers start: 27 outliers final: 10 residues processed: 280 average time/residue: 2.8582 time to fit residues: 970.7729 Evaluate side-chains 268 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 254 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain F residue 433 LYS Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 201 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 157 optimal weight: 1.9990 chunk 420 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 467 optimal weight: 3.9990 chunk 387 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 245 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN F 245 GLN G 288 GLN a 75 GLN ** d 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37884 Z= 0.229 Angle : 0.519 8.091 51382 Z= 0.273 Chirality : 0.040 0.214 5968 Planarity : 0.004 0.086 6721 Dihedral : 7.234 119.034 5409 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.80 % Favored : 98.15 % Rotamer: Outliers : 0.52 % Allowed : 9.20 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.96 (0.12), residues: 4882 helix: 2.29 (0.10), residues: 2633 sheet: -0.73 (0.21), residues: 550 loop : 0.55 (0.16), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.004 0.001 HIS F 97 PHE 0.013 0.001 PHE B 302 TYR 0.021 0.001 TYR a 145 ARG 0.011 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 272 time to evaluate : 4.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 476 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7986 (tmtt) REVERT: P 50 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7605 (tp-100) REVERT: P 86 GLN cc_start: 0.7156 (pp30) cc_final: 0.6842 (pp30) REVERT: T 65 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: a 78 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7930 (mt-10) REVERT: a 122 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: a 177 GLU cc_start: 0.7885 (mp0) cc_final: 0.7630 (mp0) REVERT: b 72 ARG cc_start: 0.7487 (tmm-80) cc_final: 0.7237 (tmm-80) REVERT: b 76 GLU cc_start: 0.8716 (pp20) cc_final: 0.8479 (pp20) outliers start: 20 outliers final: 9 residues processed: 284 average time/residue: 2.8451 time to fit residues: 985.3466 Evaluate side-chains 270 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 258 time to evaluate : 4.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 201 ASN Chi-restraints excluded: chain d residue 344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 341 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 393 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 465 optimal weight: 4.9990 chunk 291 optimal weight: 0.9990 chunk 283 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN F 245 GLN a 75 GLN d 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37884 Z= 0.269 Angle : 0.528 8.152 51382 Z= 0.278 Chirality : 0.040 0.220 5968 Planarity : 0.004 0.090 6721 Dihedral : 7.229 119.225 5409 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 0.55 % Allowed : 9.49 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.97 (0.12), residues: 4882 helix: 2.29 (0.10), residues: 2641 sheet: -0.72 (0.21), residues: 550 loop : 0.56 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.004 0.001 HIS F 97 PHE 0.012 0.001 PHE B 302 TYR 0.021 0.001 TYR a 145 ARG 0.012 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 269 time to evaluate : 4.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 476 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7980 (tmtt) REVERT: H 69 PHE cc_start: 0.8291 (m-80) cc_final: 0.7727 (m-10) REVERT: P 50 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7557 (tp-100) REVERT: P 86 GLN cc_start: 0.7144 (pp30) cc_final: 0.6836 (pp30) REVERT: T 65 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: a 122 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: a 177 GLU cc_start: 0.7853 (mp0) cc_final: 0.7559 (mp0) REVERT: b 76 GLU cc_start: 0.8721 (pp20) cc_final: 0.8483 (pp20) outliers start: 21 outliers final: 9 residues processed: 282 average time/residue: 2.9236 time to fit residues: 1001.9420 Evaluate side-chains 270 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 258 time to evaluate : 4.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 201 ASN Chi-restraints excluded: chain d residue 344 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 295 optimal weight: 0.5980 chunk 317 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 365 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN F 245 GLN a 75 GLN ** d 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 37884 Z= 0.312 Angle : 0.545 8.272 51382 Z= 0.287 Chirality : 0.041 0.243 5968 Planarity : 0.004 0.096 6721 Dihedral : 7.278 120.226 5409 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.89 % Favored : 98.07 % Rotamer: Outliers : 0.57 % Allowed : 9.77 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.94 (0.12), residues: 4882 helix: 2.28 (0.10), residues: 2635 sheet: -0.72 (0.21), residues: 550 loop : 0.53 (0.16), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.005 0.001 HIS F 97 PHE 0.017 0.001 PHE E 422 TYR 0.020 0.001 TYR a 145 ARG 0.013 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 266 time to evaluate : 4.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 476 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7974 (tmtt) REVERT: P 50 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7557 (tp-100) REVERT: P 86 GLN cc_start: 0.7151 (pp30) cc_final: 0.6758 (pp30) REVERT: T 65 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: a 122 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7209 (mt-10) outliers start: 22 outliers final: 11 residues processed: 277 average time/residue: 2.8885 time to fit residues: 976.3279 Evaluate side-chains 269 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 255 time to evaluate : 4.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain D residue 383 GLN Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 201 ASN Chi-restraints excluded: chain d residue 344 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 2.9990 chunk 445 optimal weight: 5.9990 chunk 406 optimal weight: 3.9990 chunk 433 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 340 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 392 optimal weight: 0.5980 chunk 410 optimal weight: 0.1980 chunk 432 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 245 GLN a 75 GLN d 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37884 Z= 0.177 Angle : 0.508 8.571 51382 Z= 0.264 Chirality : 0.040 0.260 5968 Planarity : 0.004 0.099 6721 Dihedral : 7.039 115.640 5409 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.68 % Favored : 98.28 % Rotamer: Outliers : 0.47 % Allowed : 9.85 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 2.16 (0.12), residues: 4882 helix: 2.46 (0.10), residues: 2636 sheet: -0.82 (0.21), residues: 530 loop : 0.67 (0.16), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.004 0.001 HIS D 121 PHE 0.016 0.001 PHE E 422 TYR 0.021 0.001 TYR a 145 ARG 0.014 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 296 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 278 time to evaluate : 4.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 476 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7996 (tmtt) REVERT: G 197 THR cc_start: 0.8740 (m) cc_final: 0.8287 (p) REVERT: O 32 ASP cc_start: 0.7681 (m-30) cc_final: 0.7384 (m-30) REVERT: O 65 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7667 (mp0) REVERT: P 86 GLN cc_start: 0.7123 (pp30) cc_final: 0.6717 (pp30) REVERT: T 32 ASP cc_start: 0.8025 (m-30) cc_final: 0.7753 (m-30) REVERT: T 65 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: a 122 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7202 (mt-10) outliers start: 18 outliers final: 3 residues processed: 287 average time/residue: 2.8519 time to fit residues: 1005.6639 Evaluate side-chains 264 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 258 time to evaluate : 4.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 1.9990 chunk 458 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 318 optimal weight: 0.7980 chunk 481 optimal weight: 3.9990 chunk 442 optimal weight: 0.9980 chunk 383 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 295 optimal weight: 0.3980 chunk 234 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN C 53 GLN C 335 ASN F 245 GLN O 6 ASN T 86 GLN a 75 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37884 Z= 0.214 Angle : 0.521 7.700 51382 Z= 0.271 Chirality : 0.040 0.232 5968 Planarity : 0.004 0.099 6721 Dihedral : 7.023 113.992 5409 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.76 % Favored : 98.20 % Rotamer: Outliers : 0.26 % Allowed : 10.55 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 2.18 (0.12), residues: 4882 helix: 2.48 (0.10), residues: 2646 sheet: -0.81 (0.21), residues: 538 loop : 0.66 (0.16), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.004 0.001 HIS F 97 PHE 0.019 0.001 PHE E 422 TYR 0.021 0.001 TYR a 145 ARG 0.016 0.000 ARG E 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 261 time to evaluate : 4.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 476 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8001 (tmtt) REVERT: G 197 THR cc_start: 0.8757 (m) cc_final: 0.8304 (p) REVERT: O 32 ASP cc_start: 0.7677 (m-30) cc_final: 0.7389 (m-30) REVERT: O 65 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7679 (mp0) REVERT: P 21 MET cc_start: 0.7897 (mmp) cc_final: 0.7620 (mmp) REVERT: P 86 GLN cc_start: 0.7132 (pp30) cc_final: 0.6634 (pp30) REVERT: T 32 ASP cc_start: 0.8059 (m-30) cc_final: 0.7803 (m-30) REVERT: T 65 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: a 122 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7207 (mt-10) outliers start: 10 outliers final: 3 residues processed: 267 average time/residue: 2.8700 time to fit residues: 930.2421 Evaluate side-chains 260 residues out of total 3843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 254 time to evaluate : 4.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain T residue 65 GLU Chi-restraints excluded: chain a residue 122 GLU Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 1.9990 chunk 408 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 353 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 383 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 394 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN F 245 GLN O 6 ASN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.072941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.055487 restraints weight = 257540.794| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.61 r_work: 0.2789 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 37884 Z= 0.279 Angle : 0.538 9.100 51382 Z= 0.281 Chirality : 0.040 0.229 5968 Planarity : 0.004 0.099 6721 Dihedral : 7.127 113.076 5409 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.80 % Favored : 98.15 % Rotamer: Outliers : 0.26 % Allowed : 10.63 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 2.11 (0.12), residues: 4882 helix: 2.42 (0.10), residues: 2649 sheet: -0.74 (0.21), residues: 552 loop : 0.63 (0.16), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 218 HIS 0.004 0.001 HIS F 97 PHE 0.017 0.001 PHE E 422 TYR 0.020 0.001 TYR a 145 ARG 0.014 0.000 ARG E 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18911.57 seconds wall clock time: 324 minutes 0.36 seconds (19440.36 seconds total)