Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 08:21:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxu_34362/04_2023/8gxu_34362_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxu_34362/04_2023/8gxu_34362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxu_34362/04_2023/8gxu_34362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxu_34362/04_2023/8gxu_34362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxu_34362/04_2023/8gxu_34362_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxu_34362/04_2023/8gxu_34362_updated.pdb" } resolution = 2.5 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= 0.003 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 105 5.16 5 C 18715 2.51 5 N 5121 2.21 5 O 5559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 29503 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.56, per 1000 atoms: 0.49 Number of scatterers: 29503 At special positions: 0 Unit cell: (147.74, 149.4, 177.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 3 15.00 O 5559 8.00 N 5121 7.00 C 18715 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=0, symmetry=0 Time building additional restraints: 11.17 Conformation dependent library (CDL) restraints added in 4.4 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: 139 helices and 34 sheets defined 42.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 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 removed outlier: 3.540A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.123A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (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 401 removed outlier: 3.528A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 432 through 442 Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 447 through 471 removed outlier: 4.001A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (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 540 Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.567A pdb=" N ARG A 552 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.671A pdb=" N GLN A 571 " --> pdb=" O MET A 567 " (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: 4.977A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.948A 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: 3.544A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 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 removed outlier: 3.516A pdb=" N GLU B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 468 removed outlier: 3.728A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.867A 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 494 Processing helix chain 'B' and resid 509 through 531 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.592A pdb=" N ALA B 551 " --> pdb=" O ARG B 547 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N TYR B 553 " --> pdb=" O GLY B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 574 Proline residue: B 560 - end of helix removed outlier: 3.813A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (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 Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 297 through 315 removed outlier: 3.523A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 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: 3.677A 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 400 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 436 through 442 removed outlier: 3.606A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 471 removed outlier: 3.908A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (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 544 through 549 Processing helix chain 'C' and resid 556 through 577 Proline residue: C 560 - end of helix removed outlier: 3.685A 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 210 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 273 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 287 through 297 removed outlier: 4.371A pdb=" N ARG D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.809A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 removed outlier: 3.559A pdb=" N ASP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.891A 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 471 removed outlier: 3.533A pdb=" N TRP D 471 " --> pdb=" O GLU D 468 " (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 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 198 through 211 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 229 through 249 removed outlier: 3.775A pdb=" N THR E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.572A pdb=" N PHE E 247 " --> pdb=" O TYR E 244 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU E 248 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS E 249 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 274 Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.566A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG E 297 " --> 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 332 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 363 through 365 No H-bonds generated for 'chain 'E' and resid 363 through 365' Processing helix chain 'E' and resid 375 through 399 removed outlier: 3.776A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 403 No H-bonds generated for 'chain 'E' and resid 401 through 403' Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 445 removed outlier: 3.778A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) 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 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: 3.649A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.559A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.023A 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: 4.649A 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 346 Processing helix chain 'F' and resid 362 through 365 Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.870A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 4.216A 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: 3.790A 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 'F' and resid 467 through 469 No H-bonds generated for 'chain 'F' and resid 467 through 469' Processing helix chain 'G' and resid 8 through 70 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 166 removed outlier: 3.531A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 208 Processing helix chain 'H' and resid 7 through 15 removed outlier: 4.479A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 55 through 58 No H-bonds generated for 'chain 'H' and resid 55 through 58' Processing helix chain 'H' and resid 60 through 63 No H-bonds generated for 'chain 'H' and resid 60 through 63' Processing helix chain 'H' and resid 77 through 82 Processing helix chain 'H' and resid 86 through 98 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.922A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'J' and resid 63 through 92 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 98 through 114 Proline residue: J 101 - end of helix Processing helix chain 'J' and resid 125 through 137 Proline residue: J 129 - end of helix removed outlier: 5.345A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.854A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 3.835A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 92 Processing helix chain 'L' and resid 94 through 96 No H-bonds generated for 'chain 'L' and resid 94 through 96' Processing helix chain 'L' and resid 98 through 114 Proline residue: L 101 - end of helix Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 4.658A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 4.922A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.323A 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: 6.468A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.582A 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 75 Processing sheet with id= C, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.941A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.797A 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 138 through 140 Processing sheet with id= F, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.585A pdb=" N ARG A 197 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.868A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.006A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.605A 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 75 Processing sheet with id= J, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.010A pdb=" N GLY B 82 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA B 377 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU B 322 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR B 379 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA B 324 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 381 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA B 405 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N TRP B 407 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.653A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (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 157 through 160 removed outlier: 6.580A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.496A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 72 through 76 Processing sheet with id= P, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.861A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 384 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 164 through 166 removed outlier: 5.616A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 366 through 369 Processing sheet with id= S, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.669A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.273A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE D 60 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLY D 45 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.728A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 91 through 93 removed outlier: 4.032A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N MET D 194 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= X, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.482A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.621A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.953A pdb=" N ARG E 91 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 219 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN E 222 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ALA E 193 " --> pdb=" O ASN E 222 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET E 194 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE E 152 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.412A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.512A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.805A pdb=" N ARG F 91 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AE, first strand: chain 'G' and resid 90 through 96 removed outlier: 3.778A pdb=" N GLU G 92 " --> pdb=" O ARG G 103 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 19 through 22 removed outlier: 3.674A pdb=" N ALA H 46 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 141 through 144 removed outlier: 3.601A pdb=" N GLU J 141 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 120 through 123 1235 hydrogen bonds defined for protein. 3363 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: 10.57 Time building geometry restraints manager: 11.97 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: 9954 1.34 - 1.46: 4260 1.46 - 1.57: 15643 1.57 - 1.69: 5 1.69 - 1.81: 194 Bond restraints: 30056 Sorted by residual: bond pdb=" O4 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.448 0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" O1 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.498 1.449 0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" O2 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.498 1.449 0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" O3 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.450 0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" O3 SO4 C 600 " pdb=" S SO4 C 600 " ideal model delta sigma weight residual 1.499 1.452 0.047 2.00e-02 2.50e+03 5.47e+00 ... (remaining 30051 not shown) Histogram of bond angle deviations from ideal: 98.98 - 107.14: 1038 107.14 - 115.31: 18098 115.31 - 123.47: 20715 123.47 - 131.64: 832 131.64 - 139.81: 39 Bond angle restraints: 40722 Sorted by residual: angle pdb=" N VAL H 59 " pdb=" CA VAL H 59 " pdb=" C VAL H 59 " ideal model delta sigma weight residual 112.29 108.76 3.53 9.40e-01 1.13e+00 1.41e+01 angle pdb=" N ILE F 96 " pdb=" CA ILE F 96 " pdb=" C ILE F 96 " ideal model delta sigma weight residual 111.77 108.58 3.19 1.04e+00 9.25e-01 9.41e+00 angle pdb=" N PRO C 420 " pdb=" CA PRO C 420 " pdb=" C PRO C 420 " ideal model delta sigma weight residual 112.10 119.54 -7.44 2.60e+00 1.48e-01 8.18e+00 angle pdb=" N PRO A 420 " pdb=" CA PRO A 420 " pdb=" C PRO A 420 " ideal model delta sigma weight residual 112.10 118.88 -6.78 2.60e+00 1.48e-01 6.80e+00 angle pdb=" N ASP B 177 " pdb=" CA ASP B 177 " pdb=" C ASP B 177 " ideal model delta sigma weight residual 113.01 110.08 2.93 1.20e+00 6.94e-01 5.96e+00 ... (remaining 40717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 16496 17.73 - 35.45: 1406 35.45 - 53.18: 296 53.18 - 70.91: 69 70.91 - 88.64: 40 Dihedral angle restraints: 18307 sinusoidal: 7485 harmonic: 10822 Sorted by residual: dihedral pdb=" CA LEU D 257 " pdb=" C LEU D 257 " pdb=" N THR D 258 " pdb=" CA THR D 258 " ideal model delta harmonic sigma weight residual -180.00 -154.36 -25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA TYR F 8 " pdb=" C TYR F 8 " pdb=" N THR F 9 " pdb=" CA THR F 9 " ideal model delta harmonic sigma weight residual 180.00 156.72 23.28 0 5.00e+00 4.00e-02 2.17e+01 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 -156.89 -23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 18304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3732 0.058 - 0.117: 762 0.117 - 0.175: 66 0.175 - 0.234: 1 0.234 - 0.292: 3 Chirality restraints: 4564 Sorted by residual: chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C3' ATP B 601 " pdb=" C2' ATP B 601 " pdb=" C4' ATP B 601 " pdb=" O3' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.90 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C4' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" C5' ATP B 601 " pdb=" O4' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.76 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 4561 not shown) Planarity restraints: 5331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " 0.056 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO B 229 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 364 " -0.228 9.50e-02 1.11e+02 1.02e-01 6.88e+00 pdb=" NE ARG A 364 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 364 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 364 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 364 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 294 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A 295 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.032 5.00e-02 4.00e+02 ... (remaining 5328 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 100 2.46 - 3.07: 20529 3.07 - 3.68: 43876 3.68 - 4.29: 68437 4.29 - 4.90: 114259 Nonbonded interactions: 247201 Sorted by model distance: nonbonded pdb=" OH TYR F 8 " pdb=" OD1 ASP F 26 " model vdw 1.855 2.440 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 1.923 2.440 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 1.946 2.440 nonbonded pdb=" OD2 ASP C 410 " pdb=" OG SER C 412 " model vdw 1.947 2.440 nonbonded pdb=" NH2 ARG D 91 " pdb=" O PRO D 104 " model vdw 2.007 2.520 ... (remaining 247196 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: 3.900 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: 15.490 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 71.450 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.007 0.090 30056 Z= 0.457 Angle : 0.575 7.435 40722 Z= 0.302 Chirality : 0.046 0.292 4564 Planarity : 0.005 0.102 5331 Dihedral : 14.467 88.636 11389 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: 0.82 (0.14), residues: 3764 helix: 1.48 (0.13), residues: 1576 sheet: -0.30 (0.21), residues: 574 loop : 0.05 (0.16), residues: 1614 *********************** 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 796 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 796 time to evaluate : 3.602 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 796 average time/residue: 1.9187 time to fit residues: 1719.1708 Evaluate side-chains 420 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 419 time to evaluate : 3.371 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 4.8249 ------------------------------------------------------------------------------- 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: 1.9990 chunk 282 optimal weight: 2.9990 chunk 156 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 292 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 338 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN A 498 ASN B 397 GLN B 418 HIS B 496 GLN B 501 HIS C 238 GLN C 397 GLN C 496 GLN C 571 GLN D 129 GLN D 166 GLN D 206 GLN ** D 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 142 ASN E 364 ASN E 427 GLN E 428 GLN E 437 GLN F 413 GLN G 10 ASN G 180 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 30056 Z= 0.186 Angle : 0.531 6.889 40722 Z= 0.277 Chirality : 0.043 0.194 4564 Planarity : 0.005 0.058 5331 Dihedral : 4.410 24.047 4183 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 2.53 % 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: 1.20 (0.14), residues: 3764 helix: 1.75 (0.14), residues: 1581 sheet: 0.00 (0.22), residues: 560 loop : 0.26 (0.16), residues: 1623 *********************** 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 520 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 442 time to evaluate : 3.785 Fit side-chains outliers start: 78 outliers final: 21 residues processed: 495 average time/residue: 1.8540 time to fit residues: 1041.6213 Evaluate side-chains 409 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 388 time to evaluate : 3.573 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 8 average time/residue: 0.7793 time to fit residues: 13.0048 ------------------------------------------------------------------------------- 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: 0.0370 chunk 230 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 339 optimal weight: 6.9990 chunk 366 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 336 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 272 optimal weight: 0.8980 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 GLN C 541 GLN C 571 GLN D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 413 GLN E 58 GLN E 428 GLN E 458 HIS ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 30056 Z= 0.324 Angle : 0.645 8.959 40722 Z= 0.336 Chirality : 0.048 0.275 4564 Planarity : 0.006 0.060 5331 Dihedral : 4.934 25.006 4183 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 3.02 % 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: 0.86 (0.14), residues: 3764 helix: 1.37 (0.13), residues: 1574 sheet: -0.10 (0.22), residues: 546 loop : 0.16 (0.16), residues: 1644 *********************** 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 488 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 395 time to evaluate : 3.660 Fit side-chains revert: symmetry clash outliers start: 93 outliers final: 35 residues processed: 456 average time/residue: 1.8685 time to fit residues: 967.7013 Evaluate side-chains 403 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 368 time to evaluate : 3.511 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 27 residues processed: 8 average time/residue: 0.7841 time to fit residues: 13.0535 ------------------------------------------------------------------------------- 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: 10.0000 chunk 255 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 340 optimal weight: 0.4980 chunk 360 optimal weight: 0.3980 chunk 177 optimal weight: 0.6980 chunk 322 optimal weight: 9.9990 chunk 97 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 465 GLN B 469 GLN C 571 GLN D 206 GLN D 413 GLN E 58 GLN E 428 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN G 175 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 30056 Z= 0.157 Angle : 0.507 8.436 40722 Z= 0.262 Chirality : 0.042 0.213 4564 Planarity : 0.005 0.056 5331 Dihedral : 4.430 23.162 4183 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 2.72 % 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: 1.11 (0.14), residues: 3764 helix: 1.61 (0.14), residues: 1585 sheet: -0.07 (0.22), residues: 548 loop : 0.28 (0.16), residues: 1631 *********************** 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 467 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 383 time to evaluate : 3.570 Fit side-chains revert: symmetry clash outliers start: 84 outliers final: 35 residues processed: 441 average time/residue: 1.8883 time to fit residues: 945.1523 Evaluate side-chains 388 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 353 time to evaluate : 3.696 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 26 residues processed: 9 average time/residue: 0.7427 time to fit residues: 13.8212 ------------------------------------------------------------------------------- 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: 1.9990 chunk 204 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 323 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 283 HIS D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN E 428 GLN F 252 HIS F 323 HIS F 413 GLN G 10 ASN G 166 GLN G 175 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 30056 Z= 0.298 Angle : 0.615 8.889 40722 Z= 0.319 Chirality : 0.046 0.182 4564 Planarity : 0.006 0.062 5331 Dihedral : 4.869 26.242 4183 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 2.82 % 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: 0.87 (0.14), residues: 3764 helix: 1.36 (0.13), residues: 1577 sheet: -0.16 (0.21), residues: 557 loop : 0.21 (0.16), residues: 1630 *********************** 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 460 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 373 time to evaluate : 3.816 Fit side-chains revert: symmetry clash outliers start: 87 outliers final: 46 residues processed: 430 average time/residue: 1.8353 time to fit residues: 898.1664 Evaluate side-chains 404 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 358 time to evaluate : 3.316 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 35 residues processed: 11 average time/residue: 0.8181 time to fit residues: 16.1177 ------------------------------------------------------------------------------- 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: 7.9990 chunk 324 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 360 optimal weight: 5.9990 chunk 299 optimal weight: 2.9990 chunk 167 optimal weight: 0.0010 chunk 30 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 465 GLN B 469 GLN C 571 GLN D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN E 428 GLN F 413 GLN G 10 ASN G 175 GLN ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 30056 Z= 0.331 Angle : 0.645 8.964 40722 Z= 0.336 Chirality : 0.047 0.168 4564 Planarity : 0.006 0.064 5331 Dihedral : 5.065 27.595 4183 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 3.02 % 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: 0.62 (0.14), residues: 3764 helix: 1.11 (0.13), residues: 1571 sheet: -0.26 (0.21), residues: 585 loop : 0.13 (0.16), residues: 1608 *********************** 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 465 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 372 time to evaluate : 3.719 Fit side-chains revert: symmetry clash outliers start: 93 outliers final: 47 residues processed: 436 average time/residue: 1.9266 time to fit residues: 960.0349 Evaluate side-chains 403 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 356 time to evaluate : 3.648 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 37 residues processed: 10 average time/residue: 0.6511 time to fit residues: 13.6455 ------------------------------------------------------------------------------- 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: 0.6980 chunk 40 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 303 optimal weight: 0.0170 chunk 201 optimal weight: 0.5980 chunk 359 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 469 GLN C 571 GLN D 206 GLN D 388 ASN D 413 GLN E 23 ASN F 413 GLN G 10 ASN J 130 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 30056 Z= 0.170 Angle : 0.513 8.866 40722 Z= 0.266 Chirality : 0.043 0.144 4564 Planarity : 0.005 0.060 5331 Dihedral : 4.505 23.302 4183 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 2.08 % 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: 0.97 (0.14), residues: 3764 helix: 1.45 (0.14), residues: 1581 sheet: -0.18 (0.21), residues: 570 loop : 0.29 (0.16), residues: 1613 *********************** 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 444 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 380 time to evaluate : 3.615 Fit side-chains outliers start: 64 outliers final: 36 residues processed: 430 average time/residue: 1.8901 time to fit residues: 923.0651 Evaluate side-chains 395 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 359 time to evaluate : 3.557 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 29 residues processed: 7 average time/residue: 0.7177 time to fit residues: 11.7959 ------------------------------------------------------------------------------- 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: 0.9990 chunk 143 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 228 optimal weight: 0.0060 chunk 244 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 469 GLN C 571 GLN D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN F 413 GLN G 10 ASN G 175 GLN J 143 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 30056 Z= 0.172 Angle : 0.510 9.044 40722 Z= 0.264 Chirality : 0.042 0.148 4564 Planarity : 0.005 0.061 5331 Dihedral : 4.398 24.083 4183 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 1.75 % 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: 1.07 (0.14), residues: 3764 helix: 1.54 (0.14), residues: 1573 sheet: -0.05 (0.22), residues: 560 loop : 0.32 (0.16), residues: 1631 *********************** 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 422 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 368 time to evaluate : 3.553 Fit side-chains outliers start: 54 outliers final: 39 residues processed: 413 average time/residue: 1.9225 time to fit residues: 907.0372 Evaluate side-chains 380 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 341 time to evaluate : 3.628 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 34 residues processed: 5 average time/residue: 1.2209 time to fit residues: 12.5671 ------------------------------------------------------------------------------- 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: 0.0010 chunk 344 optimal weight: 6.9990 chunk 314 optimal weight: 6.9990 chunk 335 optimal weight: 0.6980 chunk 201 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 302 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 333 optimal weight: 10.0000 overall best weight: 1.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN F 413 GLN G 10 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 30056 Z= 0.306 Angle : 0.619 9.401 40722 Z= 0.321 Chirality : 0.046 0.182 4564 Planarity : 0.006 0.064 5331 Dihedral : 4.884 26.008 4183 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 1.88 % 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: 0.80 (0.14), residues: 3764 helix: 1.27 (0.13), residues: 1565 sheet: -0.14 (0.22), residues: 576 loop : 0.21 (0.16), residues: 1623 *********************** 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 413 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 355 time to evaluate : 3.310 Fit side-chains outliers start: 58 outliers final: 39 residues processed: 405 average time/residue: 1.8568 time to fit residues: 857.8853 Evaluate side-chains 388 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 349 time to evaluate : 3.456 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 36 residues processed: 3 average time/residue: 0.3322 time to fit residues: 6.3642 ------------------------------------------------------------------------------- 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: 1.9990 chunk 354 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 168 optimal weight: 0.0570 chunk 246 optimal weight: 0.5980 chunk 371 optimal weight: 1.9990 chunk 342 optimal weight: 0.7980 chunk 295 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 228 optimal weight: 0.0000 chunk 181 optimal weight: 0.8980 overall best weight: 0.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN D 166 GLN D 206 GLN D 413 GLN E 58 GLN F 413 GLN G 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 30056 Z= 0.163 Angle : 0.506 9.137 40722 Z= 0.262 Chirality : 0.042 0.146 4564 Planarity : 0.005 0.059 5331 Dihedral : 4.385 24.342 4183 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 1.39 % 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: 1.05 (0.14), residues: 3764 helix: 1.52 (0.14), residues: 1570 sheet: -0.07 (0.22), residues: 560 loop : 0.31 (0.16), residues: 1634 ********************** 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 397 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 354 time to evaluate : 3.572 Fit side-chains outliers start: 43 outliers final: 34 residues processed: 393 average time/residue: 1.9457 time to fit residues: 875.9746 Evaluate side-chains 382 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 348 time to evaluate : 3.667 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 32 residues processed: 2 average time/residue: 0.8510 time to fit residues: 7.3058 ------------------------------------------------------------------------------- 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: 5.9990 chunk 315 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 272 optimal weight: 0.0270 chunk 43 optimal weight: 0.0970 chunk 82 optimal weight: 8.9990 chunk 296 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 304 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 0.0470 overall best weight: 0.8336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN D 166 GLN D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN F 413 GLN G 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.157279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125318 restraints weight = 34168.640| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.33 r_work: 0.3249 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 30056 Z= 0.188 Angle : 0.521 9.276 40722 Z= 0.270 Chirality : 0.043 0.154 4564 Planarity : 0.005 0.060 5331 Dihedral : 4.419 24.038 4183 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 1.23 % 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: 1.06 (0.14), residues: 3764 helix: 1.51 (0.14), residues: 1577 sheet: -0.03 (0.22), residues: 560 loop : 0.32 (0.16), residues: 1627 =============================================================================== Job complete usr+sys time: 14188.96 seconds wall clock time: 250 minutes 48.59 seconds (15048.59 seconds total)