Starting phenix.real_space_refine (version: dev) on Mon Feb 27 06:14:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vay_31871/02_2023/7vay_31871_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vay_31871/02_2023/7vay_31871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vay_31871/02_2023/7vay_31871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vay_31871/02_2023/7vay_31871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vay_31871/02_2023/7vay_31871_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vay_31871/02_2023/7vay_31871_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 296": "OE1" <-> "OE2" Residue "F TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 130": "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: 29553 Number of models: 1 Model: "" Number of chains: 16 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: {'CIS': 1, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 441} 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: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" 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: 16.43, per 1000 atoms: 0.56 Number of scatterers: 29553 At special positions: 0 Unit cell: (149.04, 144.18, 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 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.29 Conformation dependent library (CDL) restraints added in 4.5 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: 133 helices and 37 sheets defined 42.3% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 91 through 98 Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' 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: 4.086A 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 352 through 364 removed outlier: 4.098A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 364 " --> pdb=" O PHE A 361 " (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: 3.833A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.263A 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 532 Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.600A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.468A pdb=" N ARG A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TYR A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.599A pdb=" N LYS B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 259 through 271 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 316 removed outlier: 4.631A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 316 " --> pdb=" O TYR B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.976A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 463 Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 478 through 493 Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.508A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.540A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR B 553 " --> pdb=" O GLY B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 576 Proline residue: B 560 - end of helix 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 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 296 through 316 removed outlier: 4.014A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 340 Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.959A 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 416 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 471 removed outlier: 4.154A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.116A 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 494 Processing helix chain 'C' and resid 509 through 531 Processing helix chain 'C' and resid 536 through 539 No H-bonds generated for 'chain 'C' and resid 536 through 539' Processing helix chain 'C' and resid 543 through 553 removed outlier: 4.087A pdb=" N ARG C 552 " --> pdb=" O GLY C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 577 Proline residue: C 560 - end of helix removed outlier: 3.641A 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 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' 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: 4.298A 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 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.837A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.465A 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: 3.825A 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 '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 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 198 through 209 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.808A 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 274 Processing helix chain 'E' and resid 287 through 297 removed outlier: 4.635A 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 364 removed outlier: 4.405A pdb=" N ASN E 363 " --> pdb=" O ARG E 360 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN E 364 " --> pdb=" O LEU E 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 360 through 364' Processing helix chain 'E' and resid 375 through 399 removed outlier: 3.682A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 442 Processing helix chain 'E' and resid 459 through 462 No H-bonds generated for 'chain 'E' and resid 459 through 462' Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.522A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 4.245A 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 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 213 through 216 Processing helix chain 'F' and resid 228 through 249 removed outlier: 3.691A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.543A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.206A 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 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: 4.164A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLU F 296 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.586A 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 345 Processing helix chain 'F' and resid 360 through 365 removed outlier: 4.390A pdb=" N ASN F 363 " --> pdb=" O ARG F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.802A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 406 through 421 Processing helix chain 'F' and resid 432 through 445 removed outlier: 3.795A 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: 3.601A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 123 through 208 removed outlier: 4.860A 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 removed outlier: 3.801A pdb=" N ALA H 16 " --> pdb=" O GLY H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 39 Processing helix chain 'H' and resid 55 through 59 removed outlier: 3.635A pdb=" N VAL H 59 " --> pdb=" O GLU H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 removed outlier: 3.979A pdb=" N GLN H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'I' and resid 82 through 118 removed outlier: 4.029A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 91 Processing helix chain 'J' and resid 98 through 114 Proline residue: J 101 - end of helix removed outlier: 3.506A pdb=" N VAL J 104 " --> pdb=" O PRO J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 130 Proline residue: J 129 - end of helix No H-bonds generated for 'chain 'J' and resid 125 through 130' Processing helix chain 'J' and resid 133 through 138 Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.394A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 106 removed outlier: 3.664A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 118 Processing helix chain 'L' and resid 63 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 125 through 138 Proline residue: L 129 - end of helix removed outlier: 3.962A pdb=" N GLU L 132 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ALA L 133 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 5.540A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.445A 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: 3.813A pdb=" N ILE A 2 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 Processing sheet with id= C, first strand: chain 'A' and resid 117 through 119 Processing sheet with id= D, first strand: chain 'A' and resid 223 through 227 removed outlier: 8.424A pdb=" N ALA A 224 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 380 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE A 226 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY A 382 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.827A 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: 6.630A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.654A 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: 6.940A 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: 3.979A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.400A 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 117 through 119 Processing sheet with id= K, first strand: chain 'B' and resid 405 through 407 removed outlier: 8.738A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.520A 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 removed outlier: 3.523A pdb=" N VAL B 378 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 134 through 139 removed outlier: 6.663A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.821A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.713A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 7.178A 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: 5.431A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= Q, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.084A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 384 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 117 through 120 removed outlier: 3.818A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 197 through 199 removed outlier: 3.557A pdb=" N ARG C 197 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS C 367 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.642A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.661A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL C 160 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL C 172 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU C 181 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.375A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 77 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.599A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.868A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= Z, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.433A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 81 through 84 Processing sheet with id= AB, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= AC, first strand: chain 'E' and resid 217 through 220 removed outlier: 8.749A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.414A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 81 through 84 Processing sheet with id= AF, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.853A pdb=" N PHE F 93 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU F 219 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AH, first strand: chain 'G' and resid 89 through 96 Processing sheet with id= AI, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.515A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 141 through 144 removed outlier: 3.733A pdb=" N GLU J 141 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 120 through 122 removed outlier: 3.925A pdb=" N ALA L 120 " --> pdb=" O VAL L 155 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL L 155 " --> pdb=" O ALA L 120 " (cutoff:3.500A) 1224 hydrogen bonds defined for protein. 3315 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: 11.83 Time building geometry restraints manager: 14.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 10094 1.37 - 1.51: 9463 1.51 - 1.66: 10357 1.66 - 1.80: 188 1.80 - 1.95: 8 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 2.83e+01 bond pdb=" C5 ADP A 602 " pdb=" C6 ADP A 602 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C HIS C 418 " pdb=" N PHE C 419 " ideal model delta sigma weight residual 1.327 1.273 0.054 1.71e-02 3.42e+03 9.87e+00 bond pdb=" O3B ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sigma weight residual 1.510 1.572 -0.062 2.00e-02 2.50e+03 9.75e+00 bond pdb=" CA GLU D 296 " pdb=" C GLU D 296 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.38e-02 5.25e+03 5.76e+00 ... (remaining 30105 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.54: 1035 106.54 - 113.40: 16397 113.40 - 120.26: 11073 120.26 - 127.13: 11984 127.13 - 133.99: 318 Bond angle restraints: 40807 Sorted by residual: angle pdb=" O2B ADP A 602 " pdb=" PB ADP A 602 " pdb=" O3B ADP A 602 " ideal model delta sigma weight residual 119.90 105.58 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" N ILE D 100 " pdb=" CA ILE D 100 " pdb=" C ILE D 100 " ideal model delta sigma weight residual 113.20 109.54 3.66 9.60e-01 1.09e+00 1.45e+01 angle pdb=" N ILE E 100 " pdb=" CA ILE E 100 " pdb=" C ILE E 100 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N ILE D 96 " pdb=" CA ILE D 96 " pdb=" C ILE D 96 " ideal model delta sigma weight residual 111.88 108.45 3.43 1.06e+00 8.90e-01 1.05e+01 angle pdb=" CA LEU L 148 " pdb=" CB LEU L 148 " pdb=" CG LEU L 148 " ideal model delta sigma weight residual 116.30 127.27 -10.97 3.50e+00 8.16e-02 9.82e+00 ... (remaining 40802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.88: 17527 24.88 - 49.76: 693 49.76 - 74.63: 76 74.63 - 99.51: 36 99.51 - 124.39: 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 64.39 -124.39 1 2.00e+01 2.50e-03 3.76e+01 dihedral pdb=" CA ARG K 87 " pdb=" C ARG K 87 " pdb=" N TYR K 88 " pdb=" CA TYR K 88 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" O2A ADP A 602 " pdb=" O3A ADP A 602 " pdb=" PA ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 -129.64 69.64 1 2.00e+01 2.50e-03 1.57e+01 ... (remaining 18330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2991 0.035 - 0.071: 1027 0.071 - 0.106: 432 0.106 - 0.142: 119 0.142 - 0.177: 7 Chirality restraints: 4576 Sorted by residual: chirality pdb=" C2' ADP A 602 " pdb=" C1' ADP A 602 " pdb=" C3' ADP A 602 " pdb=" O2' ADP A 602 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA ARG K 87 " pdb=" N ARG K 87 " pdb=" C ARG K 87 " pdb=" CB ARG K 87 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CA PHE B 269 " pdb=" N PHE B 269 " pdb=" C PHE B 269 " pdb=" CB PHE B 269 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 4573 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO E 324 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 277 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO E 278 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO E 278 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 278 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 323 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO F 324 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " 0.024 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 200 2.54 - 3.13: 23220 3.13 - 3.72: 47411 3.72 - 4.31: 66371 4.31 - 4.90: 112017 Nonbonded interactions: 249219 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 601 " model vdw 1.949 2.170 nonbonded pdb=" OE2 GLU G 59 " pdb=" NH2 ARG G 132 " model vdw 2.062 2.520 nonbonded pdb=" OH TYR E 411 " pdb=" OE1 GLU E 450 " model vdw 2.107 2.440 nonbonded pdb=" OH TYR F 263 " pdb=" OD2 ASP F 290 " model vdw 2.110 2.440 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.140 2.440 ... (remaining 249214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 17.110 Check model and map are aligned: 0.440 Process input model: 78.640 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.270 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 : 0.005 0.106 30110 Z= 0.297 Angle : 0.585 14.315 40807 Z= 0.308 Chirality : 0.044 0.177 4576 Planarity : 0.004 0.045 5333 Dihedral : 13.520 124.388 11415 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3764 helix: 1.53 (0.14), residues: 1545 sheet: -0.29 (0.23), residues: 534 loop : 0.43 (0.16), residues: 1685 *********************** 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 639 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 639 time to evaluate : 3.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 639 average time/residue: 0.5220 time to fit residues: 490.4626 Evaluate side-chains 318 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 3.296 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0043 ------------------------------------------------------------------------------- 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: 3.9990 chunk 96 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 292 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 217 optimal weight: 0.0980 chunk 338 optimal weight: 10.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 81 ASN C 571 GLN D 413 GLN ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 30110 Z= 0.299 Angle : 0.585 8.767 40807 Z= 0.297 Chirality : 0.045 0.175 4576 Planarity : 0.005 0.051 5333 Dihedral : 5.377 106.679 4209 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.78 (0.14), residues: 3764 helix: 1.21 (0.13), residues: 1555 sheet: -0.41 (0.22), residues: 593 loop : 0.38 (0.16), residues: 1616 *********************** 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 365 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 329 time to evaluate : 3.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 26 residues processed: 353 average time/residue: 0.4698 time to fit residues: 256.3830 Evaluate side-chains 296 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 270 time to evaluate : 3.755 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3307 time to fit residues: 20.1450 ------------------------------------------------------------------------------- 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: 10.0000 chunk 105 optimal weight: 6.9990 chunk 281 optimal weight: 0.1980 chunk 230 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 339 optimal weight: 30.0000 chunk 366 optimal weight: 20.0000 chunk 302 optimal weight: 7.9990 chunk 336 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS B 425 ASN C 571 GLN D 170 GLN D 413 GLN ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 30110 Z= 0.362 Angle : 0.600 9.938 40807 Z= 0.302 Chirality : 0.046 0.167 4576 Planarity : 0.005 0.053 5333 Dihedral : 5.369 95.106 4209 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3764 helix: 0.93 (0.13), residues: 1566 sheet: -0.44 (0.21), residues: 620 loop : 0.13 (0.16), residues: 1578 *********************** 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 326 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 294 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 322 average time/residue: 0.4922 time to fit residues: 246.2152 Evaluate side-chains 283 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 265 time to evaluate : 3.401 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3169 time to fit residues: 15.2314 ------------------------------------------------------------------------------- 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: 40.0000 chunk 255 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 227 optimal weight: 0.0270 chunk 340 optimal weight: 10.0000 chunk 360 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 322 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN F 206 GLN F 437 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 30110 Z= 0.369 Angle : 0.595 7.288 40807 Z= 0.302 Chirality : 0.046 0.169 4576 Planarity : 0.005 0.049 5333 Dihedral : 5.364 88.117 4209 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.21 (0.14), residues: 3764 helix: 0.75 (0.13), residues: 1566 sheet: -0.53 (0.21), residues: 618 loop : -0.02 (0.16), residues: 1580 *********************** 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 327 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 283 time to evaluate : 3.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 23 residues processed: 321 average time/residue: 0.4623 time to fit residues: 235.8090 Evaluate side-chains 268 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 3.721 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2898 time to fit residues: 17.0270 ------------------------------------------------------------------------------- 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: 6.9990 chunk 204 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 268 optimal weight: 8.9990 chunk 148 optimal weight: 0.9980 chunk 307 optimal weight: 0.6980 chunk 249 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 323 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN F 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 30110 Z= 0.346 Angle : 0.581 7.682 40807 Z= 0.294 Chirality : 0.046 0.167 4576 Planarity : 0.005 0.049 5333 Dihedral : 5.318 87.015 4209 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.13 (0.14), residues: 3764 helix: 0.72 (0.13), residues: 1569 sheet: -0.62 (0.20), residues: 625 loop : -0.08 (0.16), residues: 1570 *********************** 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 297 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 268 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 293 average time/residue: 0.4851 time to fit residues: 224.6522 Evaluate side-chains 256 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 244 time to evaluate : 3.639 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2899 time to fit residues: 11.5520 ------------------------------------------------------------------------------- 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: 6.9990 chunk 324 optimal weight: 5.9990 chunk 71 optimal weight: 0.0570 chunk 211 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 360 optimal weight: 4.9990 chunk 299 optimal weight: 0.2980 chunk 167 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 overall best weight: 2.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN F 23 ASN F 206 GLN ** F 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 30110 Z= 0.225 Angle : 0.518 7.426 40807 Z= 0.263 Chirality : 0.043 0.190 4576 Planarity : 0.004 0.050 5333 Dihedral : 5.099 90.157 4209 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.35 (0.14), residues: 3764 helix: 0.92 (0.14), residues: 1568 sheet: -0.55 (0.21), residues: 604 loop : 0.01 (0.16), residues: 1592 *********************** 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 297 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 273 time to evaluate : 3.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 295 average time/residue: 0.4784 time to fit residues: 223.9968 Evaluate side-chains 259 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 250 time to evaluate : 3.603 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3072 time to fit residues: 9.7126 ------------------------------------------------------------------------------- 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: 9.9990 chunk 40 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 303 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 359 optimal weight: 20.0000 chunk 224 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS B 81 ASN ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 30110 Z= 0.352 Angle : 0.579 7.138 40807 Z= 0.294 Chirality : 0.046 0.196 4576 Planarity : 0.005 0.051 5333 Dihedral : 5.197 86.781 4209 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.18 (0.14), residues: 3764 helix: 0.78 (0.13), residues: 1568 sheet: -0.60 (0.20), residues: 626 loop : -0.07 (0.16), residues: 1570 *********************** 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 280 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 257 time to evaluate : 3.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 277 average time/residue: 0.4826 time to fit residues: 209.6696 Evaluate side-chains 262 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 248 time to evaluate : 3.443 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2751 time to fit residues: 12.0004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 69 optimal weight: 0.0770 chunk 228 optimal weight: 0.0050 chunk 244 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 282 optimal weight: 2.9990 overall best weight: 1.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3186 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= 0.199 Angle : 0.507 7.352 40807 Z= 0.258 Chirality : 0.043 0.193 4576 Planarity : 0.004 0.051 5333 Dihedral : 4.925 90.463 4209 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.37 (0.14), residues: 3764 helix: 0.96 (0.14), residues: 1567 sheet: -0.58 (0.21), residues: 609 loop : 0.03 (0.16), residues: 1588 *********************** 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 269 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 259 time to evaluate : 3.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 269 average time/residue: 0.5013 time to fit residues: 211.5801 Evaluate side-chains 247 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 242 time to evaluate : 3.836 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2938 time to fit residues: 8.0960 ------------------------------------------------------------------------------- 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: 0.9990 chunk 344 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 chunk 335 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 302 optimal weight: 8.9990 chunk 316 optimal weight: 20.0000 chunk 333 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 30110 Z= 0.255 Angle : 0.532 7.505 40807 Z= 0.270 Chirality : 0.044 0.197 4576 Planarity : 0.005 0.051 5333 Dihedral : 4.946 89.242 4209 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.34 (0.14), residues: 3764 helix: 0.90 (0.13), residues: 1567 sheet: -0.53 (0.21), residues: 604 loop : 0.02 (0.16), residues: 1593 *********************** 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 265 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 253 time to evaluate : 3.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 263 average time/residue: 0.4974 time to fit residues: 204.9323 Evaluate side-chains 250 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 243 time to evaluate : 3.701 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3356 time to fit residues: 9.0850 ------------------------------------------------------------------------------- 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: 0.7980 chunk 354 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 168 optimal weight: 0.0980 chunk 246 optimal weight: 0.6980 chunk 371 optimal weight: 5.9990 chunk 342 optimal weight: 0.7980 chunk 295 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 228 optimal weight: 2.9990 chunk 181 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 496 GLN D 381 GLN ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN E 465 GLN ** F 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 30110 Z= 0.138 Angle : 0.481 7.569 40807 Z= 0.244 Chirality : 0.042 0.199 4576 Planarity : 0.004 0.050 5333 Dihedral : 4.650 94.544 4209 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 3764 helix: 1.12 (0.14), residues: 1561 sheet: -0.49 (0.21), residues: 600 loop : 0.23 (0.17), residues: 1603 ********************** 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 274 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 3.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 274 average time/residue: 0.5008 time to fit residues: 216.6297 Evaluate side-chains 250 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 3.792 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3259 time to fit residues: 6.1862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 0.0270 chunk 315 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 296 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 304 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 overall best weight: 4.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 425 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103755 restraints weight = 46390.086| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.62 r_work: 0.3171 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 30110 Z= 0.404 Angle : 0.613 9.189 40807 Z= 0.310 Chirality : 0.047 0.209 4576 Planarity : 0.005 0.057 5333 Dihedral : 5.094 86.305 4209 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.22 (0.14), residues: 3764 helix: 0.80 (0.13), residues: 1562 sheet: -0.53 (0.21), residues: 610 loop : -0.06 (0.16), residues: 1592 =============================================================================== Job complete usr+sys time: 6111.70 seconds wall clock time: 112 minutes 25.32 seconds (6745.32 seconds total)