Starting phenix.real_space_refine (version: dev) on Mon Feb 27 08:05:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vax_31869/02_2023/7vax_31869_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vax_31869/02_2023/7vax_31869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vax_31869/02_2023/7vax_31869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vax_31869/02_2023/7vax_31869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vax_31869/02_2023/7vax_31869_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vax_31869/02_2023/7vax_31869_updated.pdb" } resolution = 2.9 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= 0.004 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 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 325": "OD1" <-> "OD2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 302": "OE1" <-> "OE2" 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: 29553 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.83, per 1000 atoms: 0.54 Number of scatterers: 29553 At special positions: 0 Unit cell: (148.23, 147.42, 174.96, 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 105 16.00 P 8 15.00 Mg 2 11.99 O 5572 8.00 N 5131 7.00 C 18735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.92 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: 130 helices and 36 sheets defined 42.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 91 through 98 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 259 through 271 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 316 removed outlier: 3.901A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.181A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.584A 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: 4.072A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 531 Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.675A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.146A pdb=" N ARG A 552 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.723A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.518A pdb=" N VAL B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 296 through 315 removed outlier: 4.443A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.427A 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 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.624A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix removed outlier: 5.183A pdb=" N GLU B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 471 removed outlier: 4.477A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 493 removed outlier: 3.869A pdb=" N LEU B 482 " --> pdb=" O ASP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 544 through 553 removed outlier: 4.205A pdb=" N ARG B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR B 553 " --> pdb=" O GLY B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 577 Proline residue: B 560 - end of helix removed outlier: 4.027A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 577 " --> pdb=" O ALA B 573 " (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 296 through 316 removed outlier: 3.789A 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: 3.728A 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 Processing helix chain 'C' and resid 447 through 471 removed outlier: 3.829A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 509 through 532 Processing helix chain 'C' and resid 536 through 541 removed outlier: 3.645A pdb=" N GLN C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 4.496A pdb=" N ARG C 552 " --> pdb=" O ILE C 548 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N TYR C 553 " --> pdb=" O GLY C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 575 Proline residue: C 560 - end of helix removed outlier: 3.923A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (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 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 295 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 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.921A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.804A 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 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 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 214 through 216 No H-bonds generated for 'chain 'E' and resid 214 through 216' Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.545A 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: 3.628A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.748A 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 360 through 365 removed outlier: 4.357A pdb=" N ASN E 363 " --> pdb=" O ARG E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 398 removed outlier: 3.642A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 421 Processing helix chain 'E' and resid 432 through 443 removed outlier: 3.822A pdb=" N TRP E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.571A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 90' 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 198 through 211 Processing helix chain 'F' and resid 213 through 216 Processing helix chain 'F' and resid 229 through 249 removed outlier: 3.812A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.540A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.177A 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 285 through 297 removed outlier: 4.400A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLU F 296 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG F 297 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 346 removed outlier: 3.523A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) 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: 3.821A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 421 Processing helix chain 'F' and resid 432 through 445 removed outlier: 3.639A 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 Processing helix chain 'G' and resid 73 through 82 removed outlier: 3.564A pdb=" N GLY G 82 " --> pdb=" O GLY G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 206 removed outlier: 3.669A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 5.578A 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 16 Processing helix chain 'H' and resid 28 through 37 Processing helix chain 'H' and resid 56 through 61 removed outlier: 4.340A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 82 No H-bonds generated for 'chain 'H' and resid 79 through 82' Processing helix chain 'H' and resid 86 through 98 Processing helix chain 'I' and resid 83 through 118 removed outlier: 3.613A pdb=" N GLU I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA I 110 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 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 100 through 114 Processing helix chain 'J' and resid 125 through 138 Proline residue: J 129 - end of helix removed outlier: 4.727A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.612A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 105 removed outlier: 3.628A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'L' and resid 63 through 96 removed outlier: 3.556A pdb=" N ALA L 93 " --> pdb=" O GLU L 89 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Proline residue: L 95 - end of helix Processing helix chain 'L' and resid 98 through 114 Proline residue: L 101 - end of helix Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 3.582A pdb=" N GLU L 132 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 5.287A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 5 through 10 removed outlier: 6.561A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (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 117 through 119 Processing sheet with id= D, first strand: chain 'A' and resid 223 through 227 removed outlier: 8.261A pdb=" N ALA A 224 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE A 380 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE A 226 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY A 382 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A 251 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 366 through 369 Processing sheet with id= F, first strand: chain 'A' and resid 134 through 139 removed outlier: 6.614A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.954A 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: 4.092A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.595A 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 164 through 166 removed outlier: 5.648A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 223 through 227 removed outlier: 8.306A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (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: 7.039A 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: 6.643A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.483A 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 75 Processing sheet with id= P, first strand: chain 'C' and resid 117 through 120 Processing sheet with id= Q, first strand: chain 'C' and resid 197 through 199 removed outlier: 4.410A pdb=" N LYS C 367 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C 249 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N MET C 323 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 251 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 223 through 227 removed outlier: 6.359A pdb=" N ILE C 380 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE C 226 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLY C 382 " --> pdb=" O ILE C 226 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.607A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.642A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 7 through 9 removed outlier: 6.989A pdb=" N ILE D 32 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TYR D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR D 13 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU D 22 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE D 11 " --> pdb=" O GLU D 22 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.586A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 91 through 93 removed outlier: 4.088A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= Y, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.627A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 81 through 84 Processing sheet with id= AA, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= AB, first strand: chain 'E' and resid 217 through 221 removed outlier: 8.692A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.499A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 81 through 84 Processing sheet with id= AE, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.877A pdb=" N PHE F 93 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU F 219 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AG, first strand: chain 'G' and resid 91 through 96 Processing sheet with id= AH, first strand: chain 'H' and resid 44 through 48 removed outlier: 5.894A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'J' and resid 141 through 144 removed outlier: 6.610A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA J 154 " --> pdb=" O VAL J 163 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 141 through 144 1220 hydrogen bonds defined for protein. 3327 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: 10.90 Time building geometry restraints manager: 13.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 10022 1.36 - 1.50: 7393 1.50 - 1.65: 12499 1.65 - 1.80: 119 1.80 - 1.95: 77 Bond restraints: 30110 Sorted by residual: bond pdb=" C4 ADP A 602 " pdb=" C5 ADP A 602 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C5 ADP A 602 " pdb=" C6 ADP A 602 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" O3B ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sigma weight residual 1.510 1.582 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" N GLU E 184 " pdb=" CA GLU E 184 " ideal model delta sigma weight residual 1.452 1.490 -0.037 1.25e-02 6.40e+03 8.89e+00 bond pdb=" N GLU E 182 " pdb=" CA GLU E 182 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.29e-02 6.01e+03 8.00e+00 ... (remaining 30105 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.79: 1065 106.79 - 113.59: 16319 113.59 - 120.40: 11414 120.40 - 127.20: 11695 127.20 - 134.01: 314 Bond angle restraints: 40807 Sorted by residual: angle pdb=" N ALA E 188 " pdb=" CA ALA E 188 " pdb=" C ALA E 188 " ideal model delta sigma weight residual 110.17 101.72 8.45 1.61e+00 3.86e-01 2.75e+01 angle pdb=" O1B ADP A 602 " pdb=" PB ADP A 602 " pdb=" O3B ADP A 602 " ideal model delta sigma weight residual 119.90 106.44 13.46 3.00e+00 1.11e-01 2.01e+01 angle pdb=" CA ALA E 188 " pdb=" C ALA E 188 " pdb=" O ALA E 188 " ideal model delta sigma weight residual 121.28 116.47 4.81 1.18e+00 7.18e-01 1.66e+01 angle pdb=" C ALA E 188 " pdb=" N VAL E 189 " pdb=" CA VAL E 189 " ideal model delta sigma weight residual 123.17 118.47 4.70 1.28e+00 6.10e-01 1.35e+01 angle pdb=" CA GLU E 182 " pdb=" C GLU E 182 " pdb=" O GLU E 182 " ideal model delta sigma weight residual 121.40 117.39 4.01 1.13e+00 7.83e-01 1.26e+01 ... (remaining 40802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.16: 17596 26.16 - 52.32: 641 52.32 - 78.49: 76 78.49 - 104.65: 19 104.65 - 130.81: 1 Dihedral angle restraints: 18333 sinusoidal: 7511 harmonic: 10822 Sorted by residual: dihedral pdb=" C5' ADP A 602 " pdb=" O5' ADP A 602 " pdb=" PA ADP A 602 " pdb=" O2A ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 70.81 -130.81 1 2.00e+01 2.50e-03 3.97e+01 dihedral pdb=" CA THR E 371 " pdb=" C THR E 371 " pdb=" N ARG E 372 " pdb=" CA ARG E 372 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+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 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 18330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3677 0.051 - 0.102: 728 0.102 - 0.153: 162 0.153 - 0.204: 7 0.204 - 0.255: 2 Chirality restraints: 4576 Sorted by residual: chirality pdb=" CA GLU E 185 " pdb=" N GLU E 185 " pdb=" C GLU E 185 " pdb=" CB GLU E 185 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ALA E 188 " pdb=" N ALA E 188 " pdb=" C ALA E 188 " pdb=" CB ALA E 188 " both_signs ideal model delta sigma weight residual False 2.48 2.70 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE A 87 " pdb=" CA ILE A 87 " pdb=" CG1 ILE A 87 " pdb=" CG2 ILE A 87 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.61e-01 ... (remaining 4573 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 94 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO L 95 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 108 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO G 109 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO G 109 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 109 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO E 324 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.024 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 245 2.59 - 3.17: 24762 3.17 - 3.75: 47722 3.75 - 4.32: 66304 4.32 - 4.90: 110899 Nonbonded interactions: 249932 Sorted by model distance: nonbonded pdb=" OG SER A 235 " pdb="MG MG A 601 " model vdw 2.017 2.170 nonbonded pdb=" OG SER C 235 " pdb="MG MG C 601 " model vdw 2.027 2.170 nonbonded pdb="MG MG A 601 " pdb=" O3B ADP A 602 " model vdw 2.074 2.170 nonbonded pdb=" OH TYR F 263 " pdb=" OD2 ASP F 290 " model vdw 2.088 2.440 nonbonded pdb=" NH1 ARG A 258 " pdb="MG MG A 601 " model vdw 2.117 2.250 ... (remaining 249927 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 8 5.49 5 Mg 2 5.21 5 S 105 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5572 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: 4.230 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: 0.030 Extract box with map and model: 17.620 Check model and map are aligned: 0.420 Process input model: 74.730 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.250 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.106 30110 Z= 0.167 Angle : 0.509 13.456 40807 Z= 0.262 Chirality : 0.042 0.255 4576 Planarity : 0.004 0.047 5333 Dihedral : 13.456 130.812 11415 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.14), residues: 3764 helix: 1.97 (0.14), residues: 1547 sheet: -0.16 (0.22), residues: 573 loop : 0.53 (0.16), residues: 1644 *********************** 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 594 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 593 time to evaluate : 3.788 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 594 average time/residue: 1.8900 time to fit residues: 1271.3140 Evaluate side-chains 343 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 3.287 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5338 ------------------------------------------------------------------------------- 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: 4.9990 chunk 282 optimal weight: 0.0170 chunk 156 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 292 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 217 optimal weight: 5.9990 chunk 338 optimal weight: 0.0270 overall best weight: 3.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 202 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN C 571 GLN D 377 GLN D 437 GLN E 222 ASN E 364 ASN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN F 323 HIS G 22 GLN G 166 GLN G 181 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 30110 Z= 0.294 Angle : 0.590 7.557 40807 Z= 0.300 Chirality : 0.045 0.186 4576 Planarity : 0.005 0.050 5333 Dihedral : 5.062 104.858 4209 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 2.79 % 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: 0.94 (0.14), residues: 3764 helix: 1.43 (0.13), residues: 1555 sheet: -0.21 (0.22), residues: 557 loop : 0.29 (0.16), residues: 1652 *********************** 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 438 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 352 time to evaluate : 3.409 Fit side-chains revert: symmetry clash outliers start: 86 outliers final: 29 residues processed: 401 average time/residue: 1.7000 time to fit residues: 783.8261 Evaluate side-chains 343 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 314 time to evaluate : 3.508 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 18 residues processed: 11 average time/residue: 0.8909 time to fit residues: 17.4600 ------------------------------------------------------------------------------- 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: 5.9990 chunk 281 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 339 optimal weight: 20.0000 chunk 366 optimal weight: 0.0670 chunk 302 optimal weight: 7.9990 chunk 336 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 272 optimal weight: 10.0000 overall best weight: 5.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 465 GLN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN C 425 ASN C 571 GLN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN F 363 ASN G 166 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.077 30110 Z= 0.479 Angle : 0.684 9.874 40807 Z= 0.349 Chirality : 0.049 0.214 4576 Planarity : 0.006 0.057 5333 Dihedral : 5.577 86.156 4209 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.25 (0.14), residues: 3764 helix: 0.77 (0.13), residues: 1545 sheet: -0.43 (0.21), residues: 565 loop : -0.04 (0.15), residues: 1654 *********************** 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 418 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 322 time to evaluate : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 38 residues processed: 385 average time/residue: 1.8108 time to fit residues: 802.1436 Evaluate side-chains 331 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 293 time to evaluate : 3.233 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 28 residues processed: 10 average time/residue: 0.8568 time to fit residues: 16.0854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 20.0000 chunk 255 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 161 optimal weight: 0.6980 chunk 227 optimal weight: 0.4980 chunk 340 optimal weight: 8.9990 chunk 360 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 322 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 469 GLN B 425 ASN B 498 ASN C 425 ASN C 571 GLN E 413 GLN ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN G 22 GLN G 166 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 30110 Z= 0.191 Angle : 0.535 7.989 40807 Z= 0.271 Chirality : 0.043 0.162 4576 Planarity : 0.004 0.052 5333 Dihedral : 5.099 76.928 4209 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 2.95 % 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: 0.53 (0.14), residues: 3764 helix: 1.11 (0.13), residues: 1551 sheet: -0.47 (0.21), residues: 562 loop : 0.06 (0.16), residues: 1651 *********************** 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 416 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 325 time to evaluate : 3.500 Fit side-chains outliers start: 91 outliers final: 43 residues processed: 392 average time/residue: 1.7165 time to fit residues: 777.5812 Evaluate side-chains 337 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 294 time to evaluate : 3.313 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 36 residues processed: 7 average time/residue: 0.4271 time to fit residues: 8.9937 ------------------------------------------------------------------------------- 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: 8.9990 chunk 204 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 307 optimal weight: 7.9990 chunk 249 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 425 ASN B 498 ASN C 238 GLN C 425 ASN C 571 GLN E 142 ASN E 364 ASN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN F 437 GLN F 465 GLN G 22 GLN G 166 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.091 30110 Z= 0.547 Angle : 0.726 9.798 40807 Z= 0.371 Chirality : 0.051 0.297 4576 Planarity : 0.007 0.059 5333 Dihedral : 5.719 70.093 4209 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.92 % Rotamer Outliers : 4.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.06 (0.13), residues: 3764 helix: 0.48 (0.13), residues: 1553 sheet: -0.54 (0.21), residues: 561 loop : -0.19 (0.15), residues: 1650 *********************** 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 437 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 308 time to evaluate : 3.802 Fit side-chains revert: symmetry clash outliers start: 129 outliers final: 64 residues processed: 397 average time/residue: 1.6921 time to fit residues: 776.5897 Evaluate side-chains 360 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 296 time to evaluate : 3.439 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 51 residues processed: 13 average time/residue: 0.7528 time to fit residues: 17.9518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 0.9990 chunk 324 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 360 optimal weight: 9.9990 chunk 299 optimal weight: 0.5980 chunk 167 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 425 ASN B 469 GLN B 498 ASN C 238 GLN C 425 ASN C 571 GLN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN F 437 GLN F 465 GLN G 22 GLN G 166 GLN G 175 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 30110 Z= 0.175 Angle : 0.537 8.695 40807 Z= 0.272 Chirality : 0.043 0.171 4576 Planarity : 0.004 0.054 5333 Dihedral : 5.114 63.582 4209 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 3.05 % 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: 0.38 (0.14), residues: 3764 helix: 0.97 (0.13), residues: 1552 sheet: -0.54 (0.21), residues: 568 loop : 0.01 (0.16), residues: 1644 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 319 time to evaluate : 3.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 60 residues processed: 394 average time/residue: 1.6851 time to fit residues: 770.3852 Evaluate side-chains 353 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 293 time to evaluate : 3.632 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 55 residues processed: 5 average time/residue: 0.3266 time to fit residues: 8.0847 ------------------------------------------------------------------------------- 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: 10.0000 chunk 40 optimal weight: 7.9990 chunk 205 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 chunk 204 optimal weight: 0.8980 chunk 303 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 359 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 219 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 425 ASN B 469 GLN B 498 ASN C 425 ASN C 571 GLN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN F 465 GLN G 22 GLN G 166 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 30110 Z= 0.372 Angle : 0.629 9.066 40807 Z= 0.320 Chirality : 0.047 0.233 4576 Planarity : 0.005 0.052 5333 Dihedral : 5.374 66.377 4209 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 3.67 % 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: 0.72 (0.13), residues: 1554 sheet: -0.64 (0.21), residues: 581 loop : -0.03 (0.16), residues: 1629 *********************** 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 405 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 292 time to evaluate : 3.322 Fit side-chains revert: symmetry clash outliers start: 113 outliers final: 69 residues processed: 380 average time/residue: 1.6276 time to fit residues: 718.7535 Evaluate side-chains 351 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 282 time to evaluate : 3.682 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 57 residues processed: 12 average time/residue: 0.7014 time to fit residues: 16.5932 ------------------------------------------------------------------------------- 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: 6.9990 chunk 143 optimal weight: 0.0670 chunk 214 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 425 ASN C 238 GLN C 425 ASN C 571 GLN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN F 465 GLN G 17 GLN G 166 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 30110 Z= 0.420 Angle : 0.660 9.172 40807 Z= 0.336 Chirality : 0.048 0.254 4576 Planarity : 0.006 0.094 5333 Dihedral : 5.535 68.427 4209 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 3.18 % 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: 0.55 (0.13), residues: 1554 sheet: -0.70 (0.21), residues: 580 loop : -0.14 (0.16), residues: 1630 *********************** 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 389 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 291 time to evaluate : 3.858 Fit side-chains revert: symmetry clash outliers start: 98 outliers final: 72 residues processed: 370 average time/residue: 1.6368 time to fit residues: 710.3635 Evaluate side-chains 348 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 276 time to evaluate : 3.524 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 61 residues processed: 11 average time/residue: 0.3114 time to fit residues: 10.8998 ------------------------------------------------------------------------------- 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: 5.9990 chunk 344 optimal weight: 0.0570 chunk 314 optimal weight: 5.9990 chunk 335 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 263 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 302 optimal weight: 0.7980 chunk 316 optimal weight: 8.9990 chunk 333 optimal weight: 30.0000 overall best weight: 1.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 469 GLN B 425 ASN B 498 ASN C 425 ASN C 571 GLN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN F 465 GLN G 166 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 30110 Z= 0.206 Angle : 0.556 9.433 40807 Z= 0.282 Chirality : 0.044 0.178 4576 Planarity : 0.005 0.053 5333 Dihedral : 5.144 64.392 4209 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 2.66 % 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: 0.27 (0.14), residues: 3764 helix: 0.88 (0.13), residues: 1555 sheet: -0.68 (0.21), residues: 595 loop : 0.00 (0.16), residues: 1614 *********************** 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 382 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 300 time to evaluate : 3.501 Fit side-chains revert: symmetry clash outliers start: 82 outliers final: 62 residues processed: 370 average time/residue: 1.6408 time to fit residues: 709.2220 Evaluate side-chains 350 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 288 time to evaluate : 3.532 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 56 residues processed: 6 average time/residue: 0.6919 time to fit residues: 10.7276 ------------------------------------------------------------------------------- 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: 0.9990 chunk 354 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 371 optimal weight: 10.0000 chunk 342 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 228 optimal weight: 0.0570 chunk 181 optimal weight: 0.4980 overall best weight: 1.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 425 ASN C 425 ASN C 571 GLN E 132 GLN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN F 465 GLN G 166 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 30110 Z= 0.171 Angle : 0.539 10.176 40807 Z= 0.271 Chirality : 0.043 0.172 4576 Planarity : 0.004 0.052 5333 Dihedral : 4.916 59.804 4209 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 2.11 % 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: 0.50 (0.14), residues: 3764 helix: 1.09 (0.14), residues: 1555 sheet: -0.58 (0.21), residues: 583 loop : 0.10 (0.16), residues: 1626 ********************** 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 377 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 312 time to evaluate : 3.483 Fit side-chains revert: symmetry clash outliers start: 65 outliers final: 57 residues processed: 372 average time/residue: 1.6891 time to fit residues: 730.8104 Evaluate side-chains 345 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 288 time to evaluate : 3.462 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 54 residues processed: 4 average time/residue: 0.7983 time to fit residues: 9.3255 ------------------------------------------------------------------------------- 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: 1.9990 chunk 315 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 272 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 296 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 304 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN B 425 ASN B 498 ASN C 425 ASN C 571 GLN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.109529 restraints weight = 39698.753| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.82 r_work: 0.3180 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 30110 Z= 0.181 Angle : 0.539 9.835 40807 Z= 0.271 Chirality : 0.043 0.168 4576 Planarity : 0.004 0.054 5333 Dihedral : 4.878 59.486 4209 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 2.17 % 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: 0.57 (0.14), residues: 3764 helix: 1.16 (0.14), residues: 1554 sheet: -0.53 (0.21), residues: 583 loop : 0.11 (0.16), residues: 1627 =============================================================================== Job complete usr+sys time: 11680.18 seconds wall clock time: 208 minutes 29.61 seconds (12509.61 seconds total)