Starting phenix.real_space_refine on Sun Sep 29 13:50:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njq_12407/09_2024/7njq_12407_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njq_12407/09_2024/7njq_12407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njq_12407/09_2024/7njq_12407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njq_12407/09_2024/7njq_12407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njq_12407/09_2024/7njq_12407_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njq_12407/09_2024/7njq_12407_trim.cif" } resolution = 2.67 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= 0.002 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 23587 2.51 5 N 6408 2.21 5 O 7189 1.98 5 H 37357 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74669 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 7808 Classifications: {'peptide': 517} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 495} Chain: "B" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 7618 Classifications: {'peptide': 504} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 482} Chain breaks: 2 Chain: "C" Number of atoms: 7941 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 521, 7899 Classifications: {'peptide': 521} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 496} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 521, 7899 Classifications: {'peptide': 521} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 496} Chain breaks: 2 bond proxies already assigned to first conformer: 7914 Chain: "D" Number of atoms: 7143 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 467, 7125 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Conformer: "B" Number of residues, atoms: 467, 7125 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} bond proxies already assigned to first conformer: 7171 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: 7144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "G" Number of atoms: 4567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 4567 Classifications: {'peptide': 297} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 287} 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: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} 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: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "S" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "T" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} 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: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2161 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} 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: 2 residue: pdb=" N APHE C 354 " occ=0.80 ... (38 atoms not shown) pdb=" HZ BPHE C 354 " occ=0.20 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 33.93, per 1000 atoms: 0.45 Number of scatterers: 74669 At special positions: 0 Unit cell: (141.93, 126.99, 250.66, 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 7189 8.00 N 6408 7.00 C 23587 6.00 H 37357 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: 15.69 Conformation dependent library (CDL) restraints added in 5.9 seconds 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8892 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 0 sheets defined 55.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 removed outlier: 3.695A pdb=" N ILE A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 178 through 195 removed outlier: 4.276A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 243 through 263 Proline residue: A 250 - end of helix removed outlier: 3.688A pdb=" N ASN A 263 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.877A pdb=" N ARG A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 406 removed outlier: 4.993A pdb=" N SER A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 5.184A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 475 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.706A pdb=" N VAL B 19 " --> pdb=" O GLU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.789A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.771A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.606A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 384 through 406 removed outlier: 5.287A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 461 through 477 removed outlier: 4.654A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 467 " --> pdb=" O VAL B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 178 through 195 removed outlier: 3.720A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.695A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 301 through 311 removed outlier: 4.107A pdb=" N ARG C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 478 removed outlier: 5.121A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 176 Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 224 through 243 removed outlier: 4.864A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 270 removed outlier: 3.694A pdb=" N THR D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 318 through 326 removed outlier: 4.290A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS D 326 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 363 through 389 removed outlier: 4.491A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 412 Processing helix chain 'D' and resid 417 through 423 removed outlier: 3.590A pdb=" N GLU D 420 " --> pdb=" O MET D 417 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 444 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.855A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 269 Processing helix chain 'E' and resid 276 through 278 No H-bonds generated for 'chain 'E' and resid 276 through 278' Processing helix chain 'E' and resid 283 through 293 removed outlier: 4.236A pdb=" N ARG E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 318 through 325 removed outlier: 3.539A pdb=" N ALA E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 339 Processing helix chain 'E' and resid 358 through 361 No H-bonds generated for 'chain 'E' and resid 358 through 361' Processing helix chain 'E' and resid 363 through 389 removed outlier: 4.304A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 396 through 411 Processing helix chain 'E' and resid 418 through 420 No H-bonds generated for 'chain 'E' and resid 418 through 420' Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 461 through 469 Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 177 Processing helix chain 'F' and resid 194 through 206 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 243 removed outlier: 4.694A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 269 Processing helix chain 'F' and resid 276 through 278 No H-bonds generated for 'chain 'F' and resid 276 through 278' Processing helix chain 'F' and resid 283 through 293 Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.483A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 removed outlier: 3.595A pdb=" N LYS F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 361 No H-bonds generated for 'chain 'F' and resid 358 through 361' Processing helix chain 'F' and resid 363 through 389 removed outlier: 4.445A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 393 No H-bonds generated for 'chain 'F' and resid 391 through 393' Processing helix chain 'F' and resid 396 through 412 Processing helix chain 'F' and resid 418 through 423 removed outlier: 3.893A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 443 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 471 Processing helix chain 'G' and resid 4 through 59 Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 121 through 130 Processing helix chain 'G' and resid 147 through 164 removed outlier: 3.637A pdb=" N GLY G 164 " --> pdb=" O ALA G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 228 through 303 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 92 through 98 Processing helix chain 'H' and resid 104 through 117 Processing helix chain 'L' and resid 5 through 45 Processing helix chain 'L' and resid 47 through 80 removed outlier: 5.081A pdb=" N GLY L 51 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR L 55 " --> pdb=" O ARG L 52 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 3.557A pdb=" N ALA L 66 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE L 80 " --> pdb=" O LEU L 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 45 Processing helix chain 'M' and resid 47 through 80 removed outlier: 3.801A pdb=" N GLN M 50 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY M 51 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE M 54 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR M 55 " --> pdb=" O ARG M 52 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.876A pdb=" N PHE M 80 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 43 Processing helix chain 'N' and resid 47 through 80 removed outlier: 4.005A pdb=" N GLY N 51 " --> pdb=" O GLU N 48 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE N 54 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR N 55 " --> pdb=" O ARG N 52 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.531A pdb=" N GLU N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL N 79 " --> pdb=" O ALA N 76 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE N 80 " --> pdb=" O LEU N 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 45 Processing helix chain 'O' and resid 47 through 79 removed outlier: 3.916A pdb=" N GLY O 51 " --> pdb=" O GLU O 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE O 54 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 4.216A pdb=" N ALA O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 45 Processing helix chain 'P' and resid 50 through 80 removed outlier: 4.158A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix Processing helix chain 'Q' and resid 5 through 45 Processing helix chain 'Q' and resid 47 through 49 No H-bonds generated for 'chain 'Q' and resid 47 through 49' Processing helix chain 'Q' and resid 52 through 80 removed outlier: 3.864A pdb=" N THR Q 55 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) Proline residue: Q 56 - end of helix removed outlier: 4.059A pdb=" N PHE Q 80 " --> pdb=" O LEU Q 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 45 Processing helix chain 'R' and resid 47 through 80 removed outlier: 3.693A pdb=" N GLN R 50 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY R 51 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU R 53 " --> pdb=" O GLN R 50 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE R 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 3.549A pdb=" N GLU R 65 " --> pdb=" O GLY R 62 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA R 66 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE R 80 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 45 Processing helix chain 'S' and resid 48 through 80 removed outlier: 3.601A pdb=" N GLY S 51 " --> pdb=" O GLU S 48 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE S 54 " --> pdb=" O GLY S 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR S 55 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 4.166A pdb=" N ALA S 66 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE S 80 " --> pdb=" O LEU S 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 45 Processing helix chain 'T' and resid 47 through 80 removed outlier: 4.753A pdb=" N GLY T 51 " --> pdb=" O GLU T 48 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR T 55 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.531A pdb=" N GLU T 65 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA T 66 " --> pdb=" O LEU T 63 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL T 79 " --> pdb=" O ALA T 76 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE T 80 " --> pdb=" O LEU T 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 52 Processing helix chain 'a' and resid 61 through 80 Processing helix chain 'a' and resid 88 through 108 removed outlier: 4.074A pdb=" N ALA a 107 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL a 108 " --> pdb=" O ASN a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 129 No H-bonds generated for 'chain 'a' and resid 127 through 129' Processing helix chain 'a' and resid 131 through 164 removed outlier: 6.377A pdb=" N ILE a 155 " --> pdb=" O TRP a 151 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N VAL a 156 " --> pdb=" O ARG a 152 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS a 158 " --> pdb=" O GLY a 154 " (cutoff:3.500A) Proline residue: a 159 - end of helix Processing helix chain 'a' and resid 168 through 205 Proline residue: a 172 - end of helix removed outlier: 4.073A pdb=" N LYS a 181 " --> pdb=" O GLU a 178 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 4.060A pdb=" N LEU a 187 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG a 188 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA a 195 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL a 200 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 244 removed outlier: 5.804A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.821A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 48 Processing helix chain 'b' and resid 50 through 145 removed outlier: 3.560A pdb=" N ALA b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLN b 82 " --> pdb=" O VAL b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 160 Processing helix chain 'd' and resid 2 through 138 removed outlier: 4.494A pdb=" N VAL d 23 " --> pdb=" O VAL d 19 " (cutoff:3.500A) Proline residue: d 24 - end of helix removed outlier: 3.651A pdb=" N ALA d 138 " --> pdb=" O ARG d 134 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 155 Processing helix chain 'd' and resid 174 through 215 removed outlier: 3.536A pdb=" N SER d 189 " --> pdb=" O GLU d 185 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY d 193 " --> pdb=" O SER d 189 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA d 196 " --> pdb=" O GLY d 192 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ASP d 197 " --> pdb=" O GLY d 193 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY d 198 " --> pdb=" O LEU d 194 " (cutoff:3.500A) Processing helix chain 'd' and resid 217 through 224 Processing helix chain 'd' and resid 231 through 241 Processing helix chain 'd' and resid 247 through 257 Processing helix chain 'd' and resid 264 through 286 Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 307 through 314 Processing helix chain 'd' and resid 320 through 330 Processing helix chain 'd' and resid 339 through 350 Processing helix chain 'd' and resid 357 through 372 removed outlier: 4.273A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 401 Processing helix chain 'd' and resid 432 through 441 1908 hydrogen bonds defined for protein. 4893 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: 25.11 Time building geometry restraints manager: 19.23 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: 37337 1.03 - 1.23: 83 1.23 - 1.42: 15288 1.42 - 1.62: 22364 1.62 - 1.81: 194 Bond restraints: 75266 Sorted by residual: bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" CG PRO F 344 " pdb=" CD PRO F 344 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.60e+00 bond pdb=" CB GLU G 250 " pdb=" CG GLU G 250 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.41e+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 1.35e+00 bond pdb=" CG1 ILE Q 20 " pdb=" CD1 ILE Q 20 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.33e+00 ... (remaining 75261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 134106 1.49 - 2.97: 2009 2.97 - 4.46: 213 4.46 - 5.94: 30 5.94 - 7.43: 13 Bond angle restraints: 136371 Sorted by residual: angle pdb=" C ASP F 254 " pdb=" N ASN F 255 " pdb=" CA ASN F 255 " ideal model delta sigma weight residual 121.70 127.62 -5.92 1.80e+00 3.09e-01 1.08e+01 angle pdb=" C ASP E 254 " pdb=" N ASN E 255 " pdb=" CA ASN E 255 " ideal model delta sigma weight residual 121.70 127.57 -5.87 1.80e+00 3.09e-01 1.07e+01 angle pdb=" C ASP D 254 " pdb=" N ASN D 255 " pdb=" CA ASN D 255 " ideal model delta sigma weight residual 121.70 127.16 -5.46 1.80e+00 3.09e-01 9.21e+00 angle pdb=" C ALA L 49 " pdb=" N GLN L 50 " pdb=" CA GLN L 50 " ideal model delta sigma weight residual 120.65 124.37 -3.72 1.32e+00 5.74e-01 7.94e+00 angle pdb=" C LEU L 53 " pdb=" N PHE L 54 " pdb=" CA PHE L 54 " ideal model delta sigma weight residual 120.38 116.52 3.86 1.37e+00 5.33e-01 7.93e+00 ... (remaining 136366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.91: 33454 28.91 - 57.82: 1591 57.82 - 86.73: 144 86.73 - 115.64: 4 115.64 - 144.56: 3 Dihedral angle restraints: 35196 sinusoidal: 19502 harmonic: 15694 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 84.56 -144.56 1 2.00e+01 2.50e-03 4.36e+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 300.00 177.14 122.85 1 2.00e+01 2.50e-03 3.70e+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 -179.48 119.48 1 2.00e+01 2.50e-03 3.58e+01 ... (remaining 35193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5135 0.058 - 0.116: 738 0.116 - 0.174: 84 0.174 - 0.232: 3 0.232 - 0.290: 9 Chirality restraints: 5969 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 -2.97 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C3' ATP B 600 " pdb=" C2' ATP B 600 " pdb=" C4' ATP B 600 " pdb=" O3' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C2' ATP F 600 " pdb=" C1' ATP F 600 " pdb=" C3' ATP F 600 " pdb=" O2' ATP F 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 5966 not shown) Planarity restraints: 11442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS a 158 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO a 159 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO a 159 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO a 159 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 54 " -0.018 2.00e-02 2.50e+03 1.11e-02 3.72e+00 pdb=" CG PHE L 54 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE L 54 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE L 54 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE L 54 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE L 54 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE L 54 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE L 54 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE L 54 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE L 54 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE L 54 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE L 54 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 245 " 0.019 2.00e-02 2.50e+03 9.97e-03 2.98e+00 pdb=" CG PHE C 245 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 245 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 245 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 245 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 245 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 245 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE C 245 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE C 245 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE C 245 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE C 245 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE C 245 " 0.001 2.00e-02 2.50e+03 ... (remaining 11439 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.00: 821 2.00 - 2.65: 106418 2.65 - 3.30: 235993 3.30 - 3.95: 309549 3.95 - 4.60: 484672 Nonbonded interactions: 1137453 Sorted by model distance: nonbonded pdb="HD22 ASN B 335 " pdb=" HG SER B 357 " model vdw 1.347 2.100 nonbonded pdb=" H PHE G 190 " pdb=" OE2 GLU G 250 " model vdw 1.435 2.450 nonbonded pdb=" O PRO a 207 " pdb=" H GLN a 211 " model vdw 1.544 2.450 nonbonded pdb=" HH TYR B 281 " pdb=" OD2 ASP B 300 " model vdw 1.548 2.450 nonbonded pdb=" H GLY D 165 " pdb=" O1B ADP D 600 " model vdw 1.551 2.450 ... (remaining 1137448 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 21 or (resid 30 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 or name HB2 \ or name HB3 or name HG2 or name HG3)) or resid 31 through 173 or resid 175 thro \ ugh 353 or resid 356 through 407 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 name HA or name HB2 o \ r name HB3)) or resid 415 through 515 or resid 518 through 519 or resid 521 or r \ esid 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 21 or (resid 30 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 or name HB2 \ or name HB3 or name HG2 or name HG3)) or resid 31 through 173 or resid 175 thro \ ugh 353 or resid 356 through 515 or resid 518 through 519 or resid 521 or resid \ 600 through 601)) selection = (chain 'C' and (resid 6 through 173 or resid 175 through 353 or resid 356 throug \ h 407 or (resid 414 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 415 t \ hrough 514 or resid 532 or resid 537 through 538 or resid 540 or resid 600 throu \ gh 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 through 452 or resid 455 through 471)) } ncs_group { reference = chain 'L' selection = (chain 'M' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = (chain 'R' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = (chain 'S' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = (chain 'T' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) } 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=0.20 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: 141.520 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: 1.110 Extract box with map and model: 3.400 Check model and map are aligned: 0.450 Set scattering table: 0.560 Process input model: 130.410 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.310 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: 0.030 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 292.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 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 0.048 37909 Z= 0.252 Angle : 0.518 7.425 51423 Z= 0.280 Chirality : 0.042 0.290 5969 Planarity : 0.003 0.050 6732 Dihedral : 14.818 144.555 13879 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 1.78 (0.12), residues: 4891 helix: 1.98 (0.10), residues: 2648 sheet: -0.17 (0.21), residues: 550 loop : 0.52 (0.16), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.004 0.001 HIS C 43 PHE 0.033 0.001 PHE L 54 TYR 0.011 0.001 TYR a 145 ARG 0.008 0.000 ARG d 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 407 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 4.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 177 ILE cc_start: 0.7864 (pt) cc_final: 0.7624 (pt) REVERT: L 75 MET cc_start: 0.8595 (tmm) cc_final: 0.8242 (tmt) REVERT: T 72 LEU cc_start: 0.9364 (tp) cc_final: 0.9150 (tp) REVERT: T 86 GLN cc_start: 0.8284 (pt0) cc_final: 0.8003 (pt0) REVERT: a 161 LYS cc_start: 0.8647 (tptt) cc_final: 0.8269 (tppt) REVERT: d 127 ASN cc_start: 0.8450 (m110) cc_final: 0.8246 (m-40) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 2.8828 time to fit residues: 1424.3237 Evaluate side-chains 292 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 4.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 5.9990 chunk 366 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 195 optimal weight: 0.3980 chunk 378 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 230 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN O 86 GLN Q 46 GLN R 86 GLN S 50 GLN a 166 HIS ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 71 ASN b 128 GLN b 165 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 37909 Z= 0.254 Angle : 0.525 7.853 51423 Z= 0.281 Chirality : 0.041 0.170 5969 Planarity : 0.005 0.052 6732 Dihedral : 7.433 128.415 5415 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 0.78 % Allowed : 5.95 % Favored : 93.27 % 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: 1.44 (0.12), residues: 4891 helix: 1.64 (0.10), residues: 2670 sheet: -0.43 (0.21), residues: 574 loop : 0.53 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.018 0.001 PHE M 58 TYR 0.027 0.001 TYR a 145 ARG 0.007 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 336 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 306 time to evaluate : 5.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 173 MET cc_start: 0.8744 (mmt) cc_final: 0.8431 (mmt) REVERT: E 466 LYS cc_start: 0.8489 (mptm) cc_final: 0.8281 (ptpp) REVERT: G 177 ILE cc_start: 0.7796 (pt) cc_final: 0.7574 (pt) REVERT: H 4 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8153 (pp) REVERT: L 75 MET cc_start: 0.8650 (tmm) cc_final: 0.8411 (tmt) REVERT: M 46 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7687 (mm-40) REVERT: O 63 LEU cc_start: 0.9489 (mm) cc_final: 0.9176 (mm) REVERT: P 86 GLN cc_start: 0.7997 (pp30) cc_final: 0.7420 (pp30) REVERT: a 161 LYS cc_start: 0.8670 (tptt) cc_final: 0.8253 (tppt) outliers start: 30 outliers final: 9 residues processed: 327 average time/residue: 2.9041 time to fit residues: 1181.8637 Evaluate side-chains 295 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 285 time to evaluate : 4.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain F residue 462 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain T residue 59 ILE Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain d residue 197 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 365 optimal weight: 4.9990 chunk 298 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 439 optimal weight: 4.9990 chunk 474 optimal weight: 4.9990 chunk 391 optimal weight: 3.9990 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: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN O 86 GLN P 46 GLN Q 46 GLN R 86 GLN b 128 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 37909 Z= 0.362 Angle : 0.541 8.742 51423 Z= 0.289 Chirality : 0.042 0.179 5969 Planarity : 0.004 0.053 6732 Dihedral : 7.438 120.507 5415 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 0.70 % Allowed : 7.54 % Favored : 91.76 % 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: 1.20 (0.12), residues: 4891 helix: 1.43 (0.10), residues: 2674 sheet: -0.58 (0.20), residues: 580 loop : 0.47 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.005 0.001 HIS C 43 PHE 0.017 0.001 PHE C 245 TYR 0.025 0.002 TYR a 145 ARG 0.006 0.001 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 320 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 293 time to evaluate : 4.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 220 MET cc_start: 0.8858 (mmt) cc_final: 0.8630 (mmt) REVERT: E 466 LYS cc_start: 0.8495 (mptm) cc_final: 0.8276 (ptpp) REVERT: G 177 ILE cc_start: 0.7850 (pt) cc_final: 0.7640 (pt) REVERT: L 75 MET cc_start: 0.8621 (tmm) cc_final: 0.8329 (tmt) REVERT: M 46 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7777 (mm-40) REVERT: O 63 LEU cc_start: 0.9449 (mm) cc_final: 0.9130 (mm) REVERT: P 86 GLN cc_start: 0.8045 (pp30) cc_final: 0.7579 (pp30) REVERT: a 73 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8744 (mpp) REVERT: a 80 SER cc_start: 0.8058 (p) cc_final: 0.7842 (p) REVERT: a 161 LYS cc_start: 0.8672 (tptt) cc_final: 0.8255 (tppt) REVERT: b 89 MET cc_start: 0.6958 (mmm) cc_final: 0.6605 (mmm) outliers start: 27 outliers final: 14 residues processed: 308 average time/residue: 2.7607 time to fit residues: 1039.4723 Evaluate side-chains 296 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 281 time to evaluate : 4.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain F residue 462 ASP Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 73 MET Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain b residue 88 GLU Chi-restraints excluded: chain d residue 55 ASP Chi-restraints excluded: chain d residue 197 ASP 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: 5.9990 chunk 228 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 209 optimal weight: 0.9990 chunk 295 optimal weight: 2.9990 chunk 440 optimal weight: 1.9990 chunk 466 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 417 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN L 71 ASN O 86 GLN P 46 GLN Q 46 GLN R 86 GLN b 128 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 37909 Z= 0.282 Angle : 0.518 8.468 51423 Z= 0.275 Chirality : 0.041 0.182 5969 Planarity : 0.004 0.053 6732 Dihedral : 7.245 120.735 5415 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Rotamer: Outliers : 0.83 % Allowed : 8.22 % Favored : 90.95 % 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: 1.19 (0.12), residues: 4891 helix: 1.43 (0.10), residues: 2673 sheet: -0.69 (0.20), residues: 569 loop : 0.48 (0.16), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.004 0.001 HIS C 43 PHE 0.015 0.001 PHE F 257 TYR 0.024 0.001 TYR a 145 ARG 0.007 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 328 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 296 time to evaluate : 4.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.8809 (mtm) cc_final: 0.8584 (mtm) REVERT: E 466 LYS cc_start: 0.8500 (mptm) cc_final: 0.8279 (ptpp) REVERT: G 177 ILE cc_start: 0.7827 (pt) cc_final: 0.7627 (pt) REVERT: H 4 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8283 (pp) REVERT: L 75 MET cc_start: 0.8569 (tmm) cc_final: 0.8233 (tmt) REVERT: M 46 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7776 (mm-40) REVERT: O 63 LEU cc_start: 0.9409 (mm) cc_final: 0.9092 (mm) REVERT: P 86 GLN cc_start: 0.7954 (pp30) cc_final: 0.7537 (pp30) REVERT: a 80 SER cc_start: 0.8099 (p) cc_final: 0.7890 (p) REVERT: a 161 LYS cc_start: 0.8662 (tptt) cc_final: 0.8240 (tppt) outliers start: 32 outliers final: 16 residues processed: 317 average time/residue: 2.7715 time to fit residues: 1075.1738 Evaluate side-chains 299 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 282 time to evaluate : 4.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain F residue 462 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain b residue 88 GLU Chi-restraints excluded: chain b residue 89 MET Chi-restraints excluded: chain b residue 128 GLN Chi-restraints excluded: chain d residue 57 MET Chi-restraints excluded: chain d residue 197 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 347 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 398 optimal weight: 3.9990 chunk 322 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 238 optimal weight: 3.9990 chunk 419 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN O 86 GLN P 46 GLN P 71 ASN Q 46 GLN R 86 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 37909 Z= 0.322 Angle : 0.529 8.622 51423 Z= 0.281 Chirality : 0.041 0.182 5969 Planarity : 0.004 0.058 6732 Dihedral : 7.216 120.804 5415 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.09 % Rotamer: Outliers : 0.86 % Allowed : 9.18 % Favored : 89.96 % 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: 1.14 (0.12), residues: 4891 helix: 1.40 (0.10), residues: 2674 sheet: -0.67 (0.20), residues: 548 loop : 0.40 (0.16), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.004 0.001 HIS C 43 PHE 0.015 0.001 PHE F 257 TYR 0.023 0.001 TYR a 145 ARG 0.007 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 325 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 292 time to evaluate : 4.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 466 LYS cc_start: 0.8510 (mptm) cc_final: 0.8284 (ptpp) REVERT: H 4 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8265 (pp) REVERT: L 75 MET cc_start: 0.8555 (tmm) cc_final: 0.8215 (tmt) REVERT: M 46 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7788 (mm-40) REVERT: O 63 LEU cc_start: 0.9410 (mm) cc_final: 0.9108 (mm) REVERT: P 86 GLN cc_start: 0.7964 (pp30) cc_final: 0.7514 (pp30) REVERT: a 161 LYS cc_start: 0.8680 (tptt) cc_final: 0.8242 (tppt) outliers start: 33 outliers final: 14 residues processed: 310 average time/residue: 2.8034 time to fit residues: 1062.7060 Evaluate side-chains 294 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 279 time to evaluate : 4.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain F residue 462 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain b residue 88 GLU Chi-restraints excluded: chain b residue 89 MET Chi-restraints excluded: chain d residue 197 ASP 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: 0.8980 chunk 92 optimal weight: 2.9990 chunk 274 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 467 optimal weight: 0.9990 chunk 387 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN O 86 GLN P 46 GLN P 71 ASN Q 46 GLN R 86 GLN ** b 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 37909 Z= 0.252 Angle : 0.509 8.291 51423 Z= 0.269 Chirality : 0.040 0.179 5969 Planarity : 0.004 0.068 6732 Dihedral : 7.039 120.211 5415 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.64 % Favored : 97.30 % Rotamer: Outliers : 0.88 % Allowed : 9.46 % 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: 1.21 (0.12), residues: 4891 helix: 1.46 (0.10), residues: 2674 sheet: -0.69 (0.21), residues: 525 loop : 0.44 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 218 HIS 0.003 0.001 HIS C 259 PHE 0.016 0.001 PHE M 58 TYR 0.023 0.001 TYR a 145 ARG 0.009 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 324 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 290 time to evaluate : 4.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 173 MET cc_start: 0.8738 (mmt) cc_final: 0.8458 (mmt) REVERT: E 466 LYS cc_start: 0.8510 (mptm) cc_final: 0.8283 (ptpp) REVERT: H 4 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8272 (pp) REVERT: L 75 MET cc_start: 0.8508 (tmm) cc_final: 0.8158 (tmt) REVERT: M 46 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7763 (mm-40) REVERT: O 63 LEU cc_start: 0.9385 (mm) cc_final: 0.9074 (mm) REVERT: P 86 GLN cc_start: 0.7957 (pp30) cc_final: 0.7532 (pp30) REVERT: a 21 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: a 161 LYS cc_start: 0.8684 (tptt) cc_final: 0.8241 (tppt) outliers start: 34 outliers final: 15 residues processed: 309 average time/residue: 2.8020 time to fit residues: 1060.0979 Evaluate side-chains 297 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 280 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain F residue 462 ASP Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain a residue 21 GLU Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain b residue 88 GLU Chi-restraints excluded: chain b residue 89 MET Chi-restraints excluded: chain d residue 55 ASP Chi-restraints excluded: chain d residue 197 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 chunk 341 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 393 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 465 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN N 6 ASN O 86 GLN P 46 GLN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 GLN R 86 GLN ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 128 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 37909 Z= 0.366 Angle : 0.543 8.857 51423 Z= 0.288 Chirality : 0.041 0.183 5969 Planarity : 0.004 0.058 6732 Dihedral : 7.137 121.238 5415 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.97 % Favored : 96.97 % Rotamer: Outliers : 1.01 % Allowed : 9.93 % Favored : 89.05 % 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: 1.09 (0.12), residues: 4891 helix: 1.37 (0.10), residues: 2675 sheet: -0.70 (0.21), residues: 542 loop : 0.38 (0.16), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.006 0.001 HIS C 43 PHE 0.015 0.001 PHE M 58 TYR 0.022 0.002 TYR a 145 ARG 0.009 0.000 ARG b 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 329 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 290 time to evaluate : 4.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.8788 (mtm) cc_final: 0.8572 (mtm) REVERT: E 456 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8389 (m-80) REVERT: E 466 LYS cc_start: 0.8502 (mptm) cc_final: 0.8271 (ptpp) REVERT: H 4 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8286 (pp) REVERT: H 76 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8163 (t) REVERT: L 75 MET cc_start: 0.8556 (tmm) cc_final: 0.8156 (tmt) REVERT: M 46 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7796 (mm-40) REVERT: M 48 GLU cc_start: 0.8001 (pm20) cc_final: 0.7782 (pm20) REVERT: O 63 LEU cc_start: 0.9403 (mm) cc_final: 0.9099 (mm) REVERT: P 86 GLN cc_start: 0.7990 (pp30) cc_final: 0.7457 (pp30) REVERT: a 21 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: a 161 LYS cc_start: 0.8719 (tptt) cc_final: 0.8257 (tppt) outliers start: 39 outliers final: 21 residues processed: 316 average time/residue: 2.7651 time to fit residues: 1076.4338 Evaluate side-chains 299 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 274 time to evaluate : 4.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain F residue 462 ASP Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain a residue 21 GLU Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain b residue 88 GLU Chi-restraints excluded: chain b residue 89 MET Chi-restraints excluded: chain d residue 55 ASP Chi-restraints excluded: chain d residue 197 ASP Chi-restraints excluded: chain d residue 409 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 278 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 295 optimal weight: 0.7980 chunk 317 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 365 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN O 86 GLN P 46 GLN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 GLN R 86 GLN ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 128 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 37909 Z= 0.206 Angle : 0.506 8.142 51423 Z= 0.265 Chirality : 0.040 0.176 5969 Planarity : 0.004 0.059 6732 Dihedral : 6.903 119.788 5415 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.74 % Favored : 97.19 % Rotamer: Outliers : 0.75 % Allowed : 10.61 % Favored : 88.64 % 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: 1.24 (0.12), residues: 4891 helix: 1.49 (0.10), residues: 2678 sheet: -0.80 (0.21), residues: 527 loop : 0.50 (0.16), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 218 HIS 0.003 0.001 HIS E 97 PHE 0.018 0.001 PHE S 74 TYR 0.022 0.001 TYR a 145 ARG 0.008 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 322 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 293 time to evaluate : 4.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 173 MET cc_start: 0.8757 (mmt) cc_final: 0.8483 (mmt) REVERT: E 456 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8373 (m-80) REVERT: E 466 LYS cc_start: 0.8511 (mptm) cc_final: 0.8281 (ptpp) REVERT: H 4 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8331 (pp) REVERT: M 46 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7782 (mm-40) REVERT: O 63 LEU cc_start: 0.9371 (mm) cc_final: 0.9063 (mm) REVERT: P 86 GLN cc_start: 0.7962 (pp30) cc_final: 0.7576 (pp30) REVERT: a 21 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: a 161 LYS cc_start: 0.8715 (tptt) cc_final: 0.8251 (tppt) REVERT: d 1 MET cc_start: 0.8378 (tpt) cc_final: 0.8144 (tpt) outliers start: 29 outliers final: 19 residues processed: 311 average time/residue: 2.6994 time to fit residues: 1029.7253 Evaluate side-chains 302 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 280 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain F residue 462 ASP Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain a residue 21 GLU Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain b residue 88 GLU Chi-restraints excluded: chain b residue 89 MET Chi-restraints excluded: chain b residue 128 GLN Chi-restraints excluded: chain d residue 55 ASP Chi-restraints excluded: chain d residue 197 ASP Chi-restraints excluded: chain d residue 409 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 0.5980 chunk 445 optimal weight: 4.9990 chunk 406 optimal weight: 3.9990 chunk 433 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 340 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 392 optimal weight: 2.9990 chunk 410 optimal weight: 0.2980 chunk 432 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN O 86 GLN P 46 GLN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 GLN R 86 GLN ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 127 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 37909 Z= 0.220 Angle : 0.508 8.120 51423 Z= 0.266 Chirality : 0.040 0.169 5969 Planarity : 0.004 0.058 6732 Dihedral : 6.825 118.633 5415 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 0.75 % Allowed : 10.56 % Favored : 88.69 % 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: 1.28 (0.12), residues: 4891 helix: 1.51 (0.10), residues: 2679 sheet: -0.81 (0.21), residues: 518 loop : 0.53 (0.16), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.020 0.001 PHE S 74 TYR 0.022 0.001 TYR a 145 ARG 0.009 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 315 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 286 time to evaluate : 4.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 173 MET cc_start: 0.8751 (mmt) cc_final: 0.8475 (mmt) REVERT: E 456 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8372 (m-80) REVERT: E 466 LYS cc_start: 0.8511 (mptm) cc_final: 0.8281 (ptpp) REVERT: H 4 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8375 (pp) REVERT: M 46 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7792 (mm-40) REVERT: O 21 MET cc_start: 0.8786 (mmm) cc_final: 0.8290 (mmm) REVERT: O 63 LEU cc_start: 0.9370 (mm) cc_final: 0.9075 (mm) REVERT: P 86 GLN cc_start: 0.7961 (pp30) cc_final: 0.7586 (pp30) REVERT: a 21 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: a 161 LYS cc_start: 0.8712 (tptt) cc_final: 0.8250 (tppt) REVERT: d 1 MET cc_start: 0.8400 (tpt) cc_final: 0.8181 (tpt) outliers start: 29 outliers final: 17 residues processed: 306 average time/residue: 2.7892 time to fit residues: 1051.8182 Evaluate side-chains 299 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 279 time to evaluate : 4.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain F residue 462 ASP Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain a residue 21 GLU Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain b residue 88 GLU Chi-restraints excluded: chain b residue 89 MET Chi-restraints excluded: chain d residue 55 ASP Chi-restraints excluded: chain d residue 197 ASP Chi-restraints excluded: chain d residue 409 LEU 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: 6.9990 chunk 279 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 318 optimal weight: 1.9990 chunk 481 optimal weight: 3.9990 chunk 442 optimal weight: 0.7980 chunk 383 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN O 86 GLN P 46 GLN P 71 ASN Q 46 GLN R 86 GLN ** b 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 127 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 37909 Z= 0.256 Angle : 0.516 8.243 51423 Z= 0.271 Chirality : 0.040 0.173 5969 Planarity : 0.004 0.061 6732 Dihedral : 6.835 119.744 5415 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.70 % Favored : 97.24 % Rotamer: Outliers : 0.73 % Allowed : 10.82 % Favored : 88.46 % 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: 1.27 (0.12), residues: 4891 helix: 1.51 (0.10), residues: 2679 sheet: -0.79 (0.21), residues: 519 loop : 0.51 (0.16), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.004 0.001 HIS C 43 PHE 0.019 0.001 PHE S 74 TYR 0.022 0.001 TYR a 145 ARG 0.008 0.000 ARG D 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 317 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 289 time to evaluate : 4.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 173 MET cc_start: 0.8746 (mmt) cc_final: 0.8465 (mmt) REVERT: E 456 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: E 466 LYS cc_start: 0.8518 (mptm) cc_final: 0.8275 (ptpp) REVERT: H 4 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8415 (pp) REVERT: H 76 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8166 (t) REVERT: M 46 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7791 (mm-40) REVERT: O 63 LEU cc_start: 0.9369 (mm) cc_final: 0.9079 (mm) REVERT: P 86 GLN cc_start: 0.7965 (pp30) cc_final: 0.7598 (pp30) REVERT: a 21 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: a 161 LYS cc_start: 0.8734 (tptt) cc_final: 0.8256 (tppt) REVERT: a 178 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8013 (mm-30) outliers start: 28 outliers final: 18 residues processed: 309 average time/residue: 2.7709 time to fit residues: 1058.8751 Evaluate side-chains 299 residues out of total 3839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 277 time to evaluate : 4.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain F residue 462 ASP Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain a residue 21 GLU Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain b residue 88 GLU Chi-restraints excluded: chain b residue 89 MET Chi-restraints excluded: chain d residue 55 ASP Chi-restraints excluded: chain d residue 197 ASP Chi-restraints excluded: chain d residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 2.9990 chunk 408 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 353 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 383 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 394 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN O 86 GLN P 46 GLN Q 46 GLN R 86 GLN ** b 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.073321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.055036 restraints weight = 275759.723| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.63 r_work: 0.2736 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 37909 Z= 0.297 Angle : 0.526 8.496 51423 Z= 0.278 Chirality : 0.040 0.180 5969 Planarity : 0.004 0.060 6732 Dihedral : 6.904 120.910 5415 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 0.65 % Allowed : 11.00 % Favored : 88.35 % 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: 1.22 (0.12), residues: 4891 helix: 1.45 (0.10), residues: 2681 sheet: -0.83 (0.21), residues: 515 loop : 0.51 (0.16), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.004 0.001 HIS C 43 PHE 0.019 0.001 PHE S 74 TYR 0.021 0.001 TYR a 145 ARG 0.009 0.000 ARG D 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19640.66 seconds wall clock time: 340 minutes 56.70 seconds (20456.70 seconds total)