Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 08:12:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7val_31849/04_2023/7val_31849_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7val_31849/04_2023/7val_31849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7val_31849/04_2023/7val_31849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7val_31849/04_2023/7val_31849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7val_31849/04_2023/7val_31849_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7val_31849/04_2023/7val_31849_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 53": "OE1" <-> "OE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "E TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 207": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 29558 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 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} Time building chain proxies: 14.81, per 1000 atoms: 0.50 Number of scatterers: 29558 At special positions: 0 Unit cell: (151.36, 148.72, 178.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 9 15.00 Mg 2 11.99 O 5578 8.00 N 5131 7.00 C 18735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.37 Conformation dependent library (CDL) restraints added in 4.3 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 36 sheets defined 42.7% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 259 through 271 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 315 removed outlier: 3.663A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 303 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.315A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 394 through 400 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 471 removed outlier: 3.997A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 532 Processing helix chain 'A' and resid 536 through 541 removed outlier: 5.087A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 4.937A pdb=" N ARG A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.687A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 259 through 271 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 315 removed outlier: 4.955A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 354 through 364 removed outlier: 4.231A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 470 removed outlier: 3.878A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 478 through 493 removed outlier: 3.568A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.683A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 559 through 576 removed outlier: 3.539A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 259 through 271 removed outlier: 3.553A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 315 removed outlier: 3.578A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 340 Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.988A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 394 through 401 removed outlier: 3.607A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 414 No H-bonds generated for 'chain 'C' and resid 411 through 414' Processing helix chain 'C' and resid 433 through 442 removed outlier: 3.775A pdb=" N ASP C 436 " --> pdb=" O SER C 433 " (cutoff:3.500A) Proline residue: C 437 - end of helix Processing helix chain 'C' and resid 447 through 471 removed outlier: 3.930A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 509 through 531 Processing helix chain 'C' and resid 536 through 540 Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 559 through 577 removed outlier: 3.547A pdb=" N GLN C 571 " --> pdb=" O MET C 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 198 through 211 removed outlier: 4.114A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 216 Processing helix chain 'D' and resid 228 through 249 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 285 through 297 removed outlier: 4.468A pdb=" N TYR D 288 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU D 296 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 297 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 removed outlier: 3.597A pdb=" N TYR D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.889A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.879A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'D' and resid 467 through 473 removed outlier: 3.614A pdb=" N TRP D 471 " --> pdb=" O GLU D 468 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLY D 472 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.852A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 285 through 297 removed outlier: 4.398A pdb=" N TYR E 288 " --> pdb=" O GLY E 285 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU E 296 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 330 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 375 through 399 removed outlier: 4.174A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 445 removed outlier: 3.900A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 456 through 462 Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 229 through 249 removed outlier: 3.837A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.611A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N HIS F 249 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.682A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 362 through 365 No H-bonds generated for 'chain 'F' and resid 362 through 365' Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.550A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 406 through 421 Processing helix chain 'F' and resid 432 through 445 removed outlier: 3.984A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 456 through 462 Processing helix chain 'G' and resid 8 through 70 removed outlier: 3.814A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 123 through 207 removed outlier: 3.797A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 7 through 15 Processing helix chain 'H' and resid 26 through 38 removed outlier: 3.779A pdb=" N LEU H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 63 removed outlier: 6.125A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 removed outlier: 4.037A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 77 through 82' Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'I' and resid 82 through 118 removed outlier: 3.698A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 92 removed outlier: 4.126A pdb=" N LEU J 67 " --> pdb=" O ALA J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 100 through 114 Processing helix chain 'J' and resid 125 through 138 Proline residue: J 129 - end of helix removed outlier: 4.357A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.788A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 4.061A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 96 removed outlier: 3.981A pdb=" N ALA L 93 " --> pdb=" O GLU L 89 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Proline residue: L 95 - end of helix Processing helix chain 'L' and resid 98 through 114 Proline residue: L 101 - end of helix removed outlier: 3.561A pdb=" N ARG L 105 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 138 removed outlier: 3.721A pdb=" N GLU L 132 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA L 133 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU L 134 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA L 135 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 5.323A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 6.593A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 76 Processing sheet with id= C, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.129A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 249 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 117 through 119 Processing sheet with id= E, first strand: chain 'A' and resid 197 through 199 removed outlier: 4.657A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 134 through 140 removed outlier: 6.605A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 7.019A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 3 through 5 removed outlier: 6.636A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 72 through 76 Processing sheet with id= J, first strand: chain 'B' and resid 117 through 119 Processing sheet with id= K, first strand: chain 'B' and resid 405 through 407 removed outlier: 8.659A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP B 325 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 253 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 366 through 369 Processing sheet with id= M, first strand: chain 'B' and resid 134 through 140 removed outlier: 6.883A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.789A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.502A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 72 through 76 Processing sheet with id= Q, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.083A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 384 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 117 through 119 removed outlier: 3.538A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 197 through 199 removed outlier: 3.670A pdb=" N ARG C 197 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS C 367 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.679A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.927A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.417A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.785A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.991A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= Z, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.630A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 81 through 84 Processing sheet with id= AB, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.971A pdb=" N ARG E 91 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE E 152 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.468A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.536A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 92 through 94 removed outlier: 8.297A pdb=" N PHE F 93 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU F 219 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AG, first strand: chain 'G' and resid 91 through 96 Processing sheet with id= AH, first strand: chain 'H' and resid 19 through 22 removed outlier: 3.539A pdb=" N ALA H 5 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 141 through 144 removed outlier: 6.750A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 141 through 144 removed outlier: 3.547A pdb=" N GLU L 141 " --> pdb=" O LYS L 119 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL L 155 " --> pdb=" O LYS L 119 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU L 121 " --> pdb=" O ARG L 153 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG L 153 " --> pdb=" O LEU L 121 " (cutoff:3.500A) 1209 hydrogen bonds defined for protein. 3267 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: 11.29 Time building geometry restraints manager: 13.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9953 1.34 - 1.46: 4219 1.46 - 1.57: 15736 1.57 - 1.69: 12 1.69 - 1.81: 194 Bond restraints: 30114 Sorted by residual: bond pdb=" O3 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.569 1.512 0.057 2.00e-02 2.50e+03 8.01e+00 bond pdb=" O4 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.568 1.513 0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" O2 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.567 1.513 0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" O1 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.565 1.513 0.052 2.00e-02 2.50e+03 6.78e+00 bond pdb=" C MET F 445 " pdb=" N LEU F 446 " ideal model delta sigma weight residual 1.331 1.304 0.027 1.48e-02 4.57e+03 3.34e+00 ... (remaining 30109 not shown) Histogram of bond angle deviations from ideal: 100.08 - 108.04: 1282 108.04 - 116.01: 18596 116.01 - 123.97: 20229 123.97 - 131.94: 661 131.94 - 139.91: 45 Bond angle restraints: 40813 Sorted by residual: angle pdb=" C GLU B 347 " pdb=" CA GLU B 347 " pdb=" CB GLU B 347 " ideal model delta sigma weight residual 116.54 110.60 5.94 1.15e+00 7.56e-01 2.67e+01 angle pdb=" N ILE D 470 " pdb=" CA ILE D 470 " pdb=" C ILE D 470 " ideal model delta sigma weight residual 113.53 108.67 4.86 9.80e-01 1.04e+00 2.46e+01 angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 113.20 109.51 3.69 9.60e-01 1.09e+00 1.48e+01 angle pdb=" C ASN B 442 " pdb=" N VAL B 443 " pdb=" CA VAL B 443 " ideal model delta sigma weight residual 123.16 119.60 3.56 1.06e+00 8.90e-01 1.13e+01 angle pdb=" N GLY C 142 " pdb=" CA GLY C 142 " pdb=" C GLY C 142 " ideal model delta sigma weight residual 114.67 110.09 4.58 1.41e+00 5.03e-01 1.05e+01 ... (remaining 40808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16951 17.98 - 35.97: 1110 35.97 - 53.95: 176 53.95 - 71.94: 55 71.94 - 89.92: 29 Dihedral angle restraints: 18321 sinusoidal: 7499 harmonic: 10822 Sorted by residual: dihedral pdb=" CA ARG E 372 " pdb=" C ARG E 372 " pdb=" N GLU E 373 " pdb=" CA GLU E 373 " ideal model delta harmonic sigma weight residual -180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA VAL F 21 " pdb=" C VAL F 21 " pdb=" N GLU F 22 " pdb=" CA GLU F 22 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PRO G 120 " pdb=" C PRO G 120 " pdb=" N ALA G 121 " pdb=" CA ALA G 121 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 18318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3022 0.034 - 0.068: 1005 0.068 - 0.102: 382 0.102 - 0.136: 155 0.136 - 0.170: 8 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA THR G 119 " pdb=" N THR G 119 " pdb=" C THR G 119 " pdb=" CB THR G 119 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO E 324 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 394 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 323 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO F 324 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " -0.021 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 39 2.40 - 3.03: 17194 3.03 - 3.65: 43275 3.65 - 4.28: 66123 4.28 - 4.90: 113720 Nonbonded interactions: 240351 Sorted by model distance: nonbonded pdb=" O3B ADP A 601 " pdb=" O2 PO4 A 603 " model vdw 1.776 3.040 nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 1.954 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.959 2.170 nonbonded pdb=" OG SER A 235 " pdb="MG MG A 602 " model vdw 1.980 2.170 nonbonded pdb=" PB ADP A 601 " pdb=" O2 PO4 A 603 " model vdw 2.017 3.400 ... (remaining 240346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.880 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 74.290 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.450 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: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.003 0.057 30114 Z= 0.223 Angle : 0.549 8.032 40813 Z= 0.308 Chirality : 0.043 0.170 4572 Planarity : 0.004 0.046 5333 Dihedral : 12.971 89.923 11403 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.14), residues: 3764 helix: 1.91 (0.14), residues: 1545 sheet: 0.42 (0.22), residues: 563 loop : 0.34 (0.16), residues: 1656 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 569 time to evaluate : 3.576 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 569 average time/residue: 0.5351 time to fit residues: 442.7440 Evaluate side-chains 354 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 3.556 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 5.9990 chunk 282 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 190 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 217 optimal weight: 5.9990 chunk 338 optimal weight: 8.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN B 246 ASN B 260 ASN C 541 GLN D 170 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS F 23 ASN F 222 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 30114 Z= 0.297 Angle : 0.611 12.036 40813 Z= 0.315 Chirality : 0.047 0.193 4572 Planarity : 0.006 0.048 5333 Dihedral : 5.056 64.284 4197 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3764 helix: 1.39 (0.13), residues: 1551 sheet: 0.33 (0.22), residues: 566 loop : 0.07 (0.15), residues: 1647 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 340 time to evaluate : 3.695 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 27 residues processed: 363 average time/residue: 0.5093 time to fit residues: 277.7025 Evaluate side-chains 341 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 314 time to evaluate : 3.823 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2859 time to fit residues: 18.4998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 281 optimal weight: 10.0000 chunk 230 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 339 optimal weight: 20.0000 chunk 366 optimal weight: 0.9990 chunk 302 optimal weight: 1.9990 chunk 336 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 23 ASN F 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 30114 Z= 0.144 Angle : 0.479 10.912 40813 Z= 0.246 Chirality : 0.042 0.166 4572 Planarity : 0.004 0.047 5333 Dihedral : 4.591 64.746 4197 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.14), residues: 3764 helix: 1.56 (0.14), residues: 1556 sheet: 0.46 (0.22), residues: 574 loop : 0.20 (0.15), residues: 1634 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 344 time to evaluate : 3.573 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 359 average time/residue: 0.5147 time to fit residues: 279.1163 Evaluate side-chains 313 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 300 time to evaluate : 3.595 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2999 time to fit residues: 12.0910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 20.0000 chunk 255 optimal weight: 20.0000 chunk 176 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 227 optimal weight: 6.9990 chunk 340 optimal weight: 20.0000 chunk 360 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 322 optimal weight: 40.0000 chunk 97 optimal weight: 10.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS B 316 GLN B 477 GLN C 283 HIS F 323 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.057 30114 Z= 0.441 Angle : 0.668 11.184 40813 Z= 0.344 Chirality : 0.050 0.227 4572 Planarity : 0.006 0.059 5333 Dihedral : 5.358 66.949 4197 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3764 helix: 0.98 (0.13), residues: 1542 sheet: 0.19 (0.22), residues: 576 loop : -0.22 (0.15), residues: 1646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 306 time to evaluate : 3.789 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 35 residues processed: 349 average time/residue: 0.4954 time to fit residues: 263.5270 Evaluate side-chains 325 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 290 time to evaluate : 3.808 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3417 time to fit residues: 26.2751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 268 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 307 optimal weight: 6.9990 chunk 249 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 323 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 30114 Z= 0.293 Angle : 0.574 11.546 40813 Z= 0.296 Chirality : 0.046 0.187 4572 Planarity : 0.005 0.051 5333 Dihedral : 5.172 66.893 4197 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3764 helix: 0.97 (0.13), residues: 1564 sheet: 0.25 (0.22), residues: 554 loop : -0.25 (0.15), residues: 1646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 303 time to evaluate : 3.375 Fit side-chains outliers start: 28 outliers final: 17 residues processed: 320 average time/residue: 0.5053 time to fit residues: 244.8827 Evaluate side-chains 303 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 286 time to evaluate : 3.636 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2692 time to fit residues: 13.6248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 0.4980 chunk 324 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 360 optimal weight: 6.9990 chunk 299 optimal weight: 0.3980 chunk 167 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 119 optimal weight: 0.0870 chunk 189 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 GLN D 166 GLN D 170 GLN E 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 30114 Z= 0.127 Angle : 0.466 11.576 40813 Z= 0.238 Chirality : 0.042 0.180 4572 Planarity : 0.004 0.049 5333 Dihedral : 4.510 67.409 4197 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3764 helix: 1.42 (0.14), residues: 1569 sheet: 0.47 (0.22), residues: 551 loop : -0.01 (0.15), residues: 1644 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 327 time to evaluate : 3.859 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 338 average time/residue: 0.5060 time to fit residues: 259.8837 Evaluate side-chains 309 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 299 time to evaluate : 3.561 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2641 time to fit residues: 9.7164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 205 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 chunk 359 optimal weight: 9.9990 chunk 224 optimal weight: 0.0000 chunk 219 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 GLN D 166 GLN D 170 GLN E 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 30114 Z= 0.274 Angle : 0.562 12.508 40813 Z= 0.286 Chirality : 0.045 0.182 4572 Planarity : 0.005 0.049 5333 Dihedral : 4.880 67.659 4197 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.14), residues: 3764 helix: 1.23 (0.14), residues: 1569 sheet: 0.33 (0.22), residues: 560 loop : -0.11 (0.15), residues: 1635 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 303 time to evaluate : 3.932 Fit side-chains outliers start: 29 outliers final: 23 residues processed: 318 average time/residue: 0.5198 time to fit residues: 250.8914 Evaluate side-chains 313 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 290 time to evaluate : 3.449 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3122 time to fit residues: 17.7366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 282 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 30114 Z= 0.425 Angle : 0.667 14.007 40813 Z= 0.342 Chirality : 0.049 0.224 4572 Planarity : 0.006 0.059 5333 Dihedral : 5.452 71.446 4197 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.13), residues: 3764 helix: 0.78 (0.13), residues: 1552 sheet: 0.23 (0.23), residues: 521 loop : -0.47 (0.14), residues: 1691 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 300 time to evaluate : 3.764 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 310 average time/residue: 0.5117 time to fit residues: 240.2105 Evaluate side-chains 298 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 286 time to evaluate : 3.317 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2977 time to fit residues: 11.1157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 9.9990 chunk 344 optimal weight: 0.9980 chunk 314 optimal weight: 10.0000 chunk 335 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 263 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 302 optimal weight: 3.9990 chunk 316 optimal weight: 20.0000 chunk 333 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 30114 Z= 0.266 Angle : 0.565 17.999 40813 Z= 0.289 Chirality : 0.045 0.181 4572 Planarity : 0.005 0.051 5333 Dihedral : 5.163 72.264 4197 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3764 helix: 0.94 (0.14), residues: 1561 sheet: 0.26 (0.23), residues: 540 loop : -0.42 (0.15), residues: 1663 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 297 time to evaluate : 3.468 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 301 average time/residue: 0.5168 time to fit residues: 233.5217 Evaluate side-chains 297 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 292 time to evaluate : 3.409 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2681 time to fit residues: 7.1904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 8.9990 chunk 354 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 246 optimal weight: 0.7980 chunk 371 optimal weight: 5.9990 chunk 342 optimal weight: 10.0000 chunk 295 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 30114 Z= 0.184 Angle : 0.526 21.468 40813 Z= 0.267 Chirality : 0.043 0.176 4572 Planarity : 0.005 0.051 5333 Dihedral : 4.897 68.418 4197 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3764 helix: 1.10 (0.14), residues: 1575 sheet: 0.39 (0.23), residues: 534 loop : -0.33 (0.15), residues: 1655 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 303 time to evaluate : 3.918 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 304 average time/residue: 0.5132 time to fit residues: 236.5916 Evaluate side-chains 300 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 297 time to evaluate : 3.631 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2920 time to fit residues: 6.4538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 0.3980 chunk 315 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 272 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 296 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 304 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.135532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.100797 restraints weight = 38173.727| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.46 r_work: 0.2842 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 30114 Z= 0.220 Angle : 0.546 23.068 40813 Z= 0.276 Chirality : 0.044 0.168 4572 Planarity : 0.005 0.050 5333 Dihedral : 4.909 67.497 4197 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3764 helix: 1.14 (0.14), residues: 1564 sheet: 0.36 (0.23), residues: 540 loop : -0.30 (0.15), residues: 1660 =============================================================================== Job complete usr+sys time: 6272.35 seconds wall clock time: 114 minutes 22.14 seconds (6862.14 seconds total)