Starting phenix.real_space_refine (version: dev) on Mon Feb 27 05:24:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/02_2023/8gxz_34366_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/02_2023/8gxz_34366.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/8gxz_34366/02_2023/8gxz_34366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/02_2023/8gxz_34366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/02_2023/8gxz_34366_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxz_34366/02_2023/8gxz_34366_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= 0.006 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 Process input model Symmetric amino acids flipped Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 408": "OD1" <-> "OD2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29499 Number of models: 1 Model: "" Number of chains: 14 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: "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: 16.04, per 1000 atoms: 0.54 Number of scatterers: 29499 At special positions: 0 Unit cell: (147.42, 148.23, 171.72, 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 104 16.00 P 3 15.00 Mg 1 11.99 O 5555 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: 11.94 Conformation dependent library (CDL) restraints added in 4.2 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: 135 helices and 35 sheets defined 42.4% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 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 269 removed outlier: 3.597A pdb=" N THR A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 316 removed outlier: 4.149A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.976A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.592A 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: 3.696A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) 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: 4.693A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 552 removed outlier: 4.678A pdb=" N ARG A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 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 269 Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 316 removed outlier: 4.760A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.032A 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 362 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 416 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: 3.741A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.568A 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: 3.503A 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: 4.264A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.751A pdb=" N ALA B 551 " --> pdb=" O ARG B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 575 removed outlier: 4.261A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 572 " --> pdb=" O LYS B 568 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 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 269 Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 315 removed outlier: 3.808A 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 354 through 364 removed outlier: 3.776A 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 432 through 442 removed outlier: 3.566A pdb=" N ASP C 436 " --> pdb=" O THR C 432 " (cutoff:3.500A) Proline residue: C 437 - end of helix removed outlier: 3.584A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 471 removed outlier: 3.992A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) 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 548 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 556 through 577 Proline residue: C 560 - end of helix removed outlier: 4.096A pdb=" N GLU C 564 " --> pdb=" O PRO C 560 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS C 575 " --> pdb=" O GLN C 571 " (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: 4.303A 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: 3.819A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 403 No H-bonds generated for 'chain 'D' and resid 401 through 403' Processing helix chain 'D' and resid 406 through 421 removed outlier: 3.593A pdb=" N ASP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.645A 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: 3.560A pdb=" N TRP D 471 " --> pdb=" O GLU D 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 26 No H-bonds generated for 'chain 'E' and resid 24 through 26' 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 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 209 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.785A 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 287 through 297 removed outlier: 4.658A 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 removed outlier: 3.557A pdb=" N ILE E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 360 through 365 removed outlier: 4.071A pdb=" N ASN E 363 " --> pdb=" O ARG E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 399 removed outlier: 4.179A pdb=" N LYS E 376 " --> pdb=" O GLU E 373 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN E 377 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE E 399 " --> pdb=" O VAL E 396 " (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: 3.806A 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 213 through 216 Processing helix chain 'F' and resid 229 through 249 Proline residue: F 235 - end of helix removed outlier: 3.554A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS F 249 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 274 Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.541A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 4.622A 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 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.596A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.918A 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: 4.057A 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 470 No H-bonds generated for 'chain 'F' and resid 467 through 470' Processing helix chain 'G' and resid 8 through 70 removed outlier: 3.726A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.588A 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 121 through 208 removed outlier: 3.822A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 5.293A 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 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 65 Processing helix chain 'H' and resid 78 through 82 removed outlier: 3.966A pdb=" N GLN H 82 " --> pdb=" O GLU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'I' and resid 82 through 118 removed outlier: 3.568A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 96 Proline residue: J 95 - end of helix 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: 4.282A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 186 removed outlier: 3.741A pdb=" N LEU J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP J 172 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG J 173 " --> pdb=" O ALA J 169 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 3.676A pdb=" N ARG K 87 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET K 104 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA K 105 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP K 108 " --> 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 100 through 114 Processing helix chain 'L' and resid 129 through 138 removed outlier: 4.858A pdb=" N ALA L 133 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 3.799A pdb=" N ASP L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG L 173 " --> pdb=" O ALA L 169 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 5 removed outlier: 4.163A pdb=" N ILE A 2 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.690A 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 164 through 166 removed outlier: 5.677A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.747A pdb=" N ARG A 197 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 251 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 223 through 227 removed outlier: 6.313A pdb=" N ILE A 380 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A 226 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLY A 382 " --> pdb=" O ILE A 226 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.924A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.392A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 72 through 75 Processing sheet with id= I, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.839A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 223 through 227 removed outlier: 8.698A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP B 325 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 253 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 366 through 369 removed outlier: 3.546A pdb=" N VAL B 378 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.671A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.467A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 72 through 76 Processing sheet with id= O, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.257A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 117 through 119 Processing sheet with id= Q, first strand: chain 'C' and resid 366 through 369 Processing sheet with id= R, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.658A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.682A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL C 160 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL C 172 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU C 181 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.382A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 5.489A 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: 7.211A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.655A 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: 3.564A 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: 4.192A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.751A 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: 7.823A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.515A pdb=" N LEU D 314 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 11 through 15 removed outlier: 3.517A pdb=" N THR E 12 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.762A 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 Processing sheet with id= Z, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= AA, first strand: chain 'E' and resid 307 through 310 removed outlier: 3.583A pdb=" N MET E 194 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 72 through 77 removed outlier: 6.838A pdb=" N ILE F 32 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL F 56 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.815A pdb=" N ARG F 91 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (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 'F' and resid 11 through 15 removed outlier: 6.416A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 91 through 96 removed outlier: 3.508A pdb=" N SER G 99 " --> pdb=" O VAL G 96 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 19 through 23 removed outlier: 3.500A pdb=" N ALA H 5 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ASP H 6 " --> pdb=" O ASP H 48 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 141 through 144 removed outlier: 3.846A pdb=" N GLU J 141 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA J 123 " --> pdb=" O GLN J 143 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 120 through 122 removed outlier: 3.779A pdb=" N ALA L 120 " --> pdb=" O VAL L 155 " (cutoff:3.500A) 1227 hydrogen bonds defined for protein. 3165 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: 11.13 Time building geometry restraints manager: 12.86 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: 9960 1.34 - 1.46: 4580 1.46 - 1.57: 15313 1.57 - 1.69: 5 1.69 - 1.81: 194 Bond restraints: 30052 Sorted by residual: bond pdb=" CB ARG C 95 " pdb=" CG ARG C 95 " ideal model delta sigma weight residual 1.520 1.399 0.121 3.00e-02 1.11e+03 1.62e+01 bond pdb=" CG ARG C 95 " pdb=" CD ARG C 95 " ideal model delta sigma weight residual 1.520 1.405 0.115 3.00e-02 1.11e+03 1.47e+01 bond pdb=" O4 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.455 0.044 2.00e-02 2.50e+03 4.90e+00 bond pdb=" O3 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.455 0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" CA ARG C 95 " pdb=" CB ARG C 95 " ideal model delta sigma weight residual 1.531 1.498 0.034 1.57e-02 4.06e+03 4.60e+00 ... (remaining 30047 not shown) Histogram of bond angle deviations from ideal: 99.81 - 107.78: 1258 107.78 - 115.76: 18399 115.76 - 123.74: 20356 123.74 - 131.72: 664 131.72 - 139.70: 39 Bond angle restraints: 40716 Sorted by residual: angle pdb=" CG ARG C 95 " pdb=" CD ARG C 95 " pdb=" NE ARG C 95 " ideal model delta sigma weight residual 112.00 104.50 7.50 2.20e+00 2.07e-01 1.16e+01 angle pdb=" N HIS E 375 " pdb=" CA HIS E 375 " pdb=" C HIS E 375 " ideal model delta sigma weight residual 111.07 114.08 -3.01 1.07e+00 8.73e-01 7.89e+00 angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 113.20 110.56 2.64 9.60e-01 1.09e+00 7.54e+00 angle pdb=" C2' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O3' ATP C 601 " ideal model delta sigma weight residual 111.83 104.97 6.86 2.67e+00 1.40e-01 6.61e+00 angle pdb=" C GLU B 347 " pdb=" CA GLU B 347 " pdb=" CB GLU B 347 " ideal model delta sigma weight residual 110.42 115.22 -4.80 1.99e+00 2.53e-01 5.81e+00 ... (remaining 40711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 16678 17.91 - 35.82: 1330 35.82 - 53.73: 208 53.73 - 71.63: 53 71.63 - 89.54: 38 Dihedral angle restraints: 18307 sinusoidal: 7485 harmonic: 10822 Sorted by residual: dihedral pdb=" CA LEU F 257 " pdb=" C LEU F 257 " pdb=" N THR F 258 " pdb=" CA THR F 258 " ideal model delta harmonic sigma weight residual 180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.00e+01 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 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU L 128 " pdb=" C LEU L 128 " pdb=" N PRO L 129 " pdb=" CA PRO L 129 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 18304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3899 0.058 - 0.116: 593 0.116 - 0.174: 69 0.174 - 0.232: 0 0.232 - 0.290: 3 Chirality restraints: 4564 Sorted by residual: chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ATP C 601 " pdb=" C2' ATP C 601 " pdb=" C4' ATP C 601 " pdb=" O3' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C4' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" C5' ATP C 601 " pdb=" O4' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4561 not shown) Planarity restraints: 5331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 394 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 355 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO D 356 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 356 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 356 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 229 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " 0.022 5.00e-02 4.00e+02 ... (remaining 5328 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 118 2.44 - 3.06: 20636 3.06 - 3.67: 42792 3.67 - 4.29: 64635 4.29 - 4.90: 111334 Nonbonded interactions: 239515 Sorted by model distance: nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 1.826 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 1.888 2.170 nonbonded pdb=" O3B ATP C 601 " pdb="MG MG C 602 " model vdw 1.893 2.170 nonbonded pdb=" OG SER H 24 " pdb=" OE1 GLU H 28 " model vdw 1.939 2.440 nonbonded pdb=" O LYS D 370 " pdb=" OG1 THR D 371 " model vdw 1.953 2.440 ... (remaining 239510 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' 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 18715 2.51 5 N 5121 2.21 5 O 5555 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 7.070 Check model and map are aligned: 0.430 Process input model: 73.570 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.240 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 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 : 0.006 0.121 30052 Z= 0.371 Angle : 0.536 7.501 40716 Z= 0.283 Chirality : 0.043 0.290 4564 Planarity : 0.004 0.058 5331 Dihedral : 13.807 89.543 11389 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % 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: 0.46 (0.14), residues: 3764 helix: 1.46 (0.13), residues: 1571 sheet: -1.06 (0.21), residues: 594 loop : -0.19 (0.16), residues: 1599 *********************** 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 823 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 823 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 823 average time/residue: 0.5535 time to fit residues: 666.9081 Evaluate side-chains 446 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 3.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6908 ------------------------------------------------------------------------------- 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: 8.9990 chunk 282 optimal weight: 7.9990 chunk 156 optimal weight: 0.6980 chunk 96 optimal weight: 0.1980 chunk 190 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 292 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 chunk 338 optimal weight: 10.0000 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 442 ASN A 571 GLN B 145 HIS B 185 HIS B 246 ASN B 571 GLN C 81 ASN C 283 HIS ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 GLN D 170 GLN D 252 HIS D 323 HIS D 375 HIS D 448 GLN E 58 GLN E 148 GLN E 249 HIS E 364 ASN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS F 142 ASN F 206 GLN F 249 HIS F 388 ASN F 413 GLN F 427 GLN G 68 GLN G 180 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.155 30052 Z= 0.431 Angle : 0.702 13.373 40716 Z= 0.364 Chirality : 0.050 0.239 4564 Planarity : 0.007 0.065 5331 Dihedral : 4.892 45.857 4183 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.24 % 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: 0.11 (0.14), residues: 3764 helix: 0.82 (0.13), residues: 1565 sheet: -0.84 (0.21), residues: 600 loop : -0.14 (0.16), residues: 1599 *********************** 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 516 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 452 time to evaluate : 3.568 Fit side-chains outliers start: 64 outliers final: 45 residues processed: 492 average time/residue: 0.5139 time to fit residues: 384.3450 Evaluate side-chains 433 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 388 time to evaluate : 3.511 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3129 time to fit residues: 30.8829 ------------------------------------------------------------------------------- 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: 0.8980 chunk 281 optimal weight: 5.9990 chunk 230 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 339 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 302 optimal weight: 0.9980 chunk 336 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 272 optimal weight: 2.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN C 3 GLN ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 ASN G 166 GLN G 180 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.105 30052 Z= 0.264 Angle : 0.547 7.031 40716 Z= 0.286 Chirality : 0.044 0.210 4564 Planarity : 0.005 0.046 5331 Dihedral : 4.591 51.279 4183 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.69 % Rotamer Outliers : 1.20 % 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: 0.20 (0.14), residues: 3764 helix: 0.88 (0.13), residues: 1571 sheet: -0.74 (0.20), residues: 590 loop : -0.11 (0.16), residues: 1603 *********************** 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 457 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 420 time to evaluate : 3.579 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 20 residues processed: 445 average time/residue: 0.5236 time to fit residues: 352.0500 Evaluate side-chains 406 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 386 time to evaluate : 3.787 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3520 time to fit residues: 17.0911 ------------------------------------------------------------------------------- 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: 6.9990 chunk 255 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 340 optimal weight: 0.5980 chunk 360 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 322 optimal weight: 0.2980 chunk 97 optimal weight: 5.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN A 498 ASN B 145 HIS B 246 ASN B 316 GLN ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 GLN F 413 GLN G 180 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.133 30052 Z= 0.436 Angle : 0.669 10.765 40716 Z= 0.348 Chirality : 0.049 0.240 4564 Planarity : 0.006 0.064 5331 Dihedral : 5.095 53.926 4183 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % 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: -0.29 (0.13), residues: 3764 helix: 0.39 (0.13), residues: 1561 sheet: -0.91 (0.20), residues: 590 loop : -0.32 (0.16), residues: 1613 *********************** 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 455 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 398 time to evaluate : 3.614 Fit side-chains outliers start: 57 outliers final: 35 residues processed: 440 average time/residue: 0.5316 time to fit residues: 351.2737 Evaluate side-chains 411 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 376 time to evaluate : 3.285 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2615 time to fit residues: 21.8475 ------------------------------------------------------------------------------- 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: 0.8980 chunk 204 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 307 optimal weight: 0.9980 chunk 249 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 323 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN B 290 ASN C 397 GLN E 377 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.099 30052 Z= 0.246 Angle : 0.539 6.896 40716 Z= 0.282 Chirality : 0.044 0.203 4564 Planarity : 0.005 0.049 5331 Dihedral : 4.681 45.565 4183 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer Outliers : 1.07 % 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: -0.05 (0.14), residues: 3764 helix: 0.64 (0.13), residues: 1545 sheet: -0.81 (0.20), residues: 579 loop : -0.23 (0.15), residues: 1640 *********************** 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 420 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 387 time to evaluate : 3.608 Fit side-chains outliers start: 33 outliers final: 15 residues processed: 412 average time/residue: 0.5253 time to fit residues: 325.6577 Evaluate side-chains 388 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 373 time to evaluate : 3.649 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3062 time to fit residues: 13.5651 ------------------------------------------------------------------------------- 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: 9.9990 chunk 324 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 360 optimal weight: 4.9990 chunk 299 optimal weight: 0.0770 chunk 167 optimal weight: 10.0000 chunk 30 optimal weight: 0.4980 chunk 119 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS A 397 GLN A 423 ASN E 161 ASN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 ASN F 413 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 30052 Z= 0.200 Angle : 0.500 7.023 40716 Z= 0.261 Chirality : 0.043 0.272 4564 Planarity : 0.005 0.048 5331 Dihedral : 4.421 44.503 4183 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.32 % 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: 0.16 (0.14), residues: 3764 helix: 0.86 (0.14), residues: 1557 sheet: -0.76 (0.20), residues: 611 loop : -0.13 (0.16), residues: 1596 *********************** 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 420 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 391 time to evaluate : 3.141 Fit side-chains outliers start: 29 outliers final: 18 residues processed: 412 average time/residue: 0.5455 time to fit residues: 337.3829 Evaluate side-chains 392 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 374 time to evaluate : 3.443 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2863 time to fit residues: 14.4500 ------------------------------------------------------------------------------- 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: 4.9990 chunk 40 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 263 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 chunk 303 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 359 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 219 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 238 GLN ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.085 30052 Z= 0.389 Angle : 0.628 10.578 40716 Z= 0.327 Chirality : 0.048 0.278 4564 Planarity : 0.006 0.050 5331 Dihedral : 4.940 53.751 4183 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer Outliers : 1.17 % 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: -0.17 (0.14), residues: 3764 helix: 0.49 (0.13), residues: 1556 sheet: -0.77 (0.21), residues: 583 loop : -0.29 (0.16), residues: 1625 *********************** 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 418 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 382 time to evaluate : 3.544 Fit side-chains outliers start: 36 outliers final: 20 residues processed: 400 average time/residue: 0.5383 time to fit residues: 322.6544 Evaluate side-chains 390 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 370 time to evaluate : 3.700 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3338 time to fit residues: 16.5318 ------------------------------------------------------------------------------- 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: 5.9990 chunk 143 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 177 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 282 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 459 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 30052 Z= 0.184 Angle : 0.501 7.177 40716 Z= 0.262 Chirality : 0.042 0.229 4564 Planarity : 0.005 0.050 5331 Dihedral : 4.436 43.090 4183 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 0.49 % 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: 0.10 (0.14), residues: 3764 helix: 0.81 (0.14), residues: 1557 sheet: -0.76 (0.20), residues: 601 loop : -0.18 (0.16), residues: 1606 *********************** 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 401 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 386 time to evaluate : 3.463 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 397 average time/residue: 0.5514 time to fit residues: 328.6030 Evaluate side-chains 383 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 373 time to evaluate : 3.698 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2777 time to fit residues: 10.2405 ------------------------------------------------------------------------------- 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: 0.6980 chunk 344 optimal weight: 5.9990 chunk 314 optimal weight: 5.9990 chunk 335 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 302 optimal weight: 10.0000 chunk 316 optimal weight: 1.9990 chunk 333 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 459 GLN E 427 GLN E 429 ASN F 413 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 30052 Z= 0.322 Angle : 0.583 9.257 40716 Z= 0.303 Chirality : 0.046 0.243 4564 Planarity : 0.006 0.059 5331 Dihedral : 4.726 50.366 4183 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.45 % 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: -0.05 (0.14), residues: 3764 helix: 0.61 (0.13), residues: 1558 sheet: -0.74 (0.20), residues: 598 loop : -0.23 (0.16), residues: 1608 *********************** 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 383 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 369 time to evaluate : 3.268 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 376 average time/residue: 0.5390 time to fit residues: 303.2583 Evaluate side-chains 372 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 361 time to evaluate : 3.509 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3279 time to fit residues: 11.6921 ------------------------------------------------------------------------------- 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: 0.2980 chunk 354 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 chunk 371 optimal weight: 10.0000 chunk 342 optimal weight: 5.9990 chunk 295 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 228 optimal weight: 5.9990 chunk 181 optimal weight: 0.0020 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 459 GLN E 161 ASN E 429 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 30052 Z= 0.155 Angle : 0.478 7.475 40716 Z= 0.249 Chirality : 0.042 0.192 4564 Planarity : 0.005 0.050 5331 Dihedral : 4.224 40.522 4183 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: 0.28 (0.14), residues: 3764 helix: 0.99 (0.14), residues: 1555 sheet: -0.66 (0.21), residues: 593 loop : -0.12 (0.16), residues: 1616 ********************** 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 387 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 380 time to evaluate : 3.348 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 386 average time/residue: 0.5482 time to fit residues: 319.6822 Evaluate side-chains 365 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 360 time to evaluate : 3.796 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2988 time to fit residues: 7.9337 ------------------------------------------------------------------------------- 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: 7.9990 chunk 315 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 296 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 304 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 0.0040 overall best weight: 3.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 GLN ** C 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN E 429 ASN G 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.150194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.113215 restraints weight = 34711.975| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.52 r_work: 0.3015 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 30052 Z= 0.339 Angle : 0.594 9.757 40716 Z= 0.307 Chirality : 0.046 0.253 4564 Planarity : 0.006 0.063 5331 Dihedral : 4.679 49.944 4183 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.19 % 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: 0.03 (0.14), residues: 3764 helix: 0.68 (0.13), residues: 1556 sheet: -0.62 (0.21), residues: 585 loop : -0.23 (0.16), residues: 1623 =============================================================================== Job complete usr+sys time: 7271.10 seconds wall clock time: 132 minutes 29.71 seconds (7949.71 seconds total)