Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 08:37:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaw_31868/04_2023/7vaw_31868_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaw_31868/04_2023/7vaw_31868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaw_31868/04_2023/7vaw_31868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaw_31868/04_2023/7vaw_31868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaw_31868/04_2023/7vaw_31868_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaw_31868/04_2023/7vaw_31868_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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. Process input model Symmetric amino acids flipped Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 468": "OE1" <-> "OE2" Residue "F TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 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: 16.48, per 1000 atoms: 0.56 Number of scatterers: 29553 At special positions: 0 Unit cell: (148.23, 145.8, 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: 11.79 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: 133 helices and 36 sheets defined 42.0% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 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 268 Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 316 removed outlier: 4.135A 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: 4.148A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 394 through 400 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 471 removed outlier: 3.819A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 531 Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.940A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.515A pdb=" N ARG A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 5.252A 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: 3.549A 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 removed outlier: 3.560A 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 281 through 284 Processing helix chain 'B' and resid 296 through 316 removed outlier: 4.798A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.977A 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 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 478 through 493 Processing helix chain 'B' and resid 509 through 531 Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.889A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.642A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 4.897A 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 281 through 284 Processing helix chain 'C' and resid 296 through 315 removed outlier: 3.665A 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: 3.905A 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: 4.012A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 3.934A 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 540 Processing helix chain 'C' and resid 543 through 553 removed outlier: 4.023A pdb=" N ARG C 552 " --> pdb=" O GLY C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 576 Proline residue: C 560 - end of helix removed outlier: 3.524A 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 297 removed outlier: 4.516A 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: 3.850A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.350A 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: 3.721A 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 210 Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.543A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 287 through 297 removed outlier: 4.644A 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: 4.170A pdb=" N ASN E 363 " --> pdb=" O ARG E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 399 removed outlier: 3.549A 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: 4.302A pdb=" N GLY F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 228 through 249 removed outlier: 3.780A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.582A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.101A 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: 4.407A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU F 296 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 362 through 365 No H-bonds generated for 'chain 'F' and resid 362 through 365' Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.810A 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: 3.763A 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: 3.758A 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: 5.143A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix removed outlier: 3.647A pdb=" N GLU G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 16 removed outlier: 3.506A pdb=" N ALA H 16 " --> pdb=" O GLY H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 39 removed outlier: 3.510A pdb=" N THR H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 59 removed outlier: 3.596A pdb=" N VAL H 59 " --> pdb=" O GLU H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 removed outlier: 3.673A 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 104 Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'J' and resid 62 through 91 removed outlier: 3.538A pdb=" N ALA J 90 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU J 91 " --> pdb=" O ARG J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 100 through 114 removed outlier: 3.959A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA J 111 " --> pdb=" O LEU J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 127 No H-bonds generated for 'chain 'J' and resid 125 through 127' Processing helix chain 'J' and resid 129 through 138 removed outlier: 4.906A pdb=" N ALA J 133 " --> pdb=" O HIS J 130 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG J 138 " --> pdb=" O ALA J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.502A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 3.799A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU K 107 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) 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 98 through 114 Proline residue: L 101 - end of helix Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 4.078A pdb=" N GLU L 132 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ALA L 133 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 4.898A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 5 removed outlier: 4.035A pdb=" N ILE A 2 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 76 Processing sheet with id= C, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.362A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 223 through 227 removed outlier: 8.389A pdb=" N ALA A 224 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE A 380 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE A 226 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY A 382 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.683A 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 157 through 160 removed outlier: 6.877A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 3 through 5 removed outlier: 6.549A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 72 through 76 Processing sheet with id= I, first strand: chain 'B' and resid 117 through 119 Processing sheet with id= J, first strand: chain 'B' and resid 405 through 407 removed outlier: 8.558A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 366 through 369 Processing sheet with id= L, first strand: chain 'B' and resid 134 through 139 removed outlier: 6.699A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.831A 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: 6.617A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.557A 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 82 through 84 removed outlier: 4.017A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 384 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 117 through 120 removed outlier: 3.603A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 197 through 199 removed outlier: 3.509A pdb=" N ARG C 197 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS C 367 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.686A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.541A 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: 6.649A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.364A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 77 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.623A 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: 5.246A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 81 through 84 Processing sheet with id= W, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.793A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.910A 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: 6.545A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.421A 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: 8.679A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (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: 6.502A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.388A 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: 7.831A pdb=" N PHE F 93 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU F 219 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.927A 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 89 through 96 Processing sheet with id= AH, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.805A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 141 through 144 removed outlier: 6.623A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 141 through 144 1228 hydrogen bonds defined for protein. 3234 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: 10.87 Time building geometry restraints manager: 12.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.34: 9891 1.34 - 1.49: 7177 1.49 - 1.64: 12846 1.64 - 1.80: 102 1.80 - 1.95: 94 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=" C PRO B 345 " pdb=" O PRO B 345 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.23e-02 6.61e+03 1.81e+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 1.67e+01 bond pdb=" C ILE B 226 " pdb=" O ILE B 226 " ideal model delta sigma weight residual 1.240 1.196 0.044 1.26e-02 6.30e+03 1.20e+01 bond pdb=" O3B ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sigma weight residual 1.510 1.576 -0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 30105 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.40: 1026 106.40 - 113.31: 16162 113.31 - 120.22: 10990 120.22 - 127.13: 12312 127.13 - 134.04: 317 Bond angle restraints: 40807 Sorted by residual: angle pdb=" N PRO B 345 " pdb=" CA PRO B 345 " pdb=" C PRO B 345 " ideal model delta sigma weight residual 114.35 122.73 -8.38 1.25e+00 6.40e-01 4.49e+01 angle pdb=" C PRO B 345 " pdb=" CA PRO B 345 " pdb=" CB PRO B 345 " ideal model delta sigma weight residual 110.88 103.43 7.45 1.41e+00 5.03e-01 2.79e+01 angle pdb=" O2B ADP A 602 " pdb=" PB ADP A 602 " pdb=" O3B ADP A 602 " ideal model delta sigma weight residual 119.90 105.16 14.74 3.00e+00 1.11e-01 2.41e+01 angle pdb=" C ALA B 346 " pdb=" CA ALA B 346 " pdb=" CB ALA B 346 " ideal model delta sigma weight residual 116.54 110.89 5.65 1.15e+00 7.56e-01 2.41e+01 angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 113.20 109.13 4.07 9.60e-01 1.09e+00 1.80e+01 ... (remaining 40802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 17463 23.14 - 46.28: 737 46.28 - 69.42: 89 69.42 - 92.56: 43 92.56 - 115.70: 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 55.71 -115.70 1 2.00e+01 2.50e-03 3.44e+01 dihedral pdb=" CA LEU F 257 " pdb=" C LEU F 257 " pdb=" N THR F 258 " pdb=" CA THR F 258 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ARG B 532 " pdb=" C ARG B 532 " pdb=" N GLY B 533 " pdb=" CA GLY B 533 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 18330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3889 0.063 - 0.125: 658 0.125 - 0.188: 25 0.188 - 0.251: 2 0.251 - 0.314: 2 Chirality restraints: 4576 Sorted by residual: chirality pdb=" CB ILE B 226 " pdb=" CA ILE B 226 " pdb=" CG1 ILE B 226 " pdb=" CG2 ILE B 226 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA LYS E 370 " pdb=" N LYS E 370 " pdb=" C LYS E 370 " pdb=" CB LYS E 370 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB THR E 371 " pdb=" CA THR E 371 " pdb=" OG1 THR E 371 " pdb=" CG2 THR E 371 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 4573 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 345 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.10e+00 pdb=" C PRO B 345 " -0.046 2.00e-02 2.50e+03 pdb=" O PRO B 345 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA B 346 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 225 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C ALA B 225 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA B 225 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 226 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 226 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C ILE B 226 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE B 226 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO B 227 " 0.013 2.00e-02 2.50e+03 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 172 2.55 - 3.14: 23326 3.14 - 3.72: 47607 3.72 - 4.31: 68129 4.31 - 4.90: 113346 Nonbonded interactions: 252580 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 601 " model vdw 1.960 2.170 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.062 2.440 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 2.165 2.440 nonbonded pdb=" OH TYR D 263 " pdb=" OD2 ASP D 290 " model vdw 2.200 2.440 nonbonded pdb=" OH TYR F 263 " pdb=" OD2 ASP F 290 " model vdw 2.212 2.440 ... (remaining 252575 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.510 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: 17.150 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 76.110 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 : 0.004 0.106 30110 Z= 0.250 Angle : 0.580 14.741 40807 Z= 0.308 Chirality : 0.044 0.314 4576 Planarity : 0.004 0.044 5333 Dihedral : 13.186 115.702 11415 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer Outliers : 0.03 % 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: 0.85 (0.14), residues: 3764 helix: 1.18 (0.13), residues: 1571 sheet: -0.19 (0.21), residues: 593 loop : 0.43 (0.16), residues: 1600 *********************** 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 590 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 589 time to evaluate : 4.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 3 residues processed: 590 average time/residue: 1.8657 time to fit residues: 1246.7712 Evaluate side-chains 344 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 341 time to evaluate : 3.561 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.3079 time to fit residues: 5.4233 ------------------------------------------------------------------------------- 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: 9.9990 chunk 282 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 292 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 chunk 338 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 50 GLN B 283 HIS B 498 ASN C 283 HIS D 129 GLN D 363 ASN D 407 ASN E 166 GLN E 364 ASN F 364 ASN F 388 ASN G 162 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.095 30110 Z= 0.304 Angle : 0.639 9.621 40807 Z= 0.329 Chirality : 0.047 0.182 4576 Planarity : 0.006 0.054 5333 Dihedral : 5.963 105.839 4209 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 2.43 % 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: 0.46 (0.14), residues: 3764 helix: 0.72 (0.13), residues: 1562 sheet: -0.11 (0.22), residues: 568 loop : 0.25 (0.16), residues: 1634 *********************** 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 425 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 350 time to evaluate : 3.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 26 residues processed: 401 average time/residue: 1.8710 time to fit residues: 853.2177 Evaluate side-chains 350 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 324 time to evaluate : 3.402 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 6 average time/residue: 1.0309 time to fit residues: 12.3716 ------------------------------------------------------------------------------- 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: 0.0270 chunk 105 optimal weight: 6.9990 chunk 281 optimal weight: 10.0000 chunk 230 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 339 optimal weight: 30.0000 chunk 366 optimal weight: 0.0870 chunk 302 optimal weight: 10.0000 chunk 336 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 overall best weight: 4.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 GLN D 428 GLN E 166 GLN F 437 GLN G 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 30110 Z= 0.349 Angle : 0.657 9.047 40807 Z= 0.338 Chirality : 0.048 0.171 4576 Planarity : 0.006 0.054 5333 Dihedral : 6.099 104.569 4209 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.03 (0.14), residues: 3764 helix: 0.35 (0.13), residues: 1572 sheet: -0.26 (0.21), residues: 558 loop : -0.00 (0.15), residues: 1634 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 340 time to evaluate : 4.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 37 residues processed: 402 average time/residue: 1.8595 time to fit residues: 852.4906 Evaluate side-chains 360 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 323 time to evaluate : 3.595 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 28 residues processed: 10 average time/residue: 0.8959 time to fit residues: 16.3346 ------------------------------------------------------------------------------- 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: 9.9990 chunk 255 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 227 optimal weight: 0.2980 chunk 340 optimal weight: 6.9990 chunk 360 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 322 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN G 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 30110 Z= 0.273 Angle : 0.601 8.934 40807 Z= 0.308 Chirality : 0.046 0.164 4576 Planarity : 0.005 0.051 5333 Dihedral : 5.923 102.652 4209 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 2.82 % 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: 0.05 (0.14), residues: 3764 helix: 0.42 (0.13), residues: 1566 sheet: -0.31 (0.22), residues: 543 loop : -0.03 (0.15), residues: 1655 *********************** 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 420 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 333 time to evaluate : 3.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 39 residues processed: 402 average time/residue: 1.8963 time to fit residues: 872.3270 Evaluate side-chains 364 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 325 time to evaluate : 3.600 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 32 residues processed: 7 average time/residue: 0.7948 time to fit residues: 12.3406 ------------------------------------------------------------------------------- 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: 8.9990 chunk 5 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 chunk 148 optimal weight: 0.5980 chunk 307 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 323 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 HIS E 166 GLN G 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 30110 Z= 0.342 Angle : 0.651 8.982 40807 Z= 0.333 Chirality : 0.047 0.170 4576 Planarity : 0.006 0.064 5333 Dihedral : 6.072 102.796 4209 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 2.92 % 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: -0.10 (0.14), residues: 3764 helix: 0.25 (0.13), residues: 1567 sheet: -0.45 (0.20), residues: 616 loop : -0.02 (0.16), residues: 1581 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 330 time to evaluate : 3.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 52 residues processed: 399 average time/residue: 1.8278 time to fit residues: 830.9992 Evaluate side-chains 375 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 323 time to evaluate : 3.683 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 41 residues processed: 11 average time/residue: 0.7568 time to fit residues: 15.9577 ------------------------------------------------------------------------------- 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: 0.9980 chunk 324 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 360 optimal weight: 20.0000 chunk 299 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 189 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.067 30110 Z= 0.151 Angle : 0.516 8.429 40807 Z= 0.262 Chirality : 0.043 0.154 4576 Planarity : 0.005 0.052 5333 Dihedral : 5.450 96.499 4209 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 2.27 % 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: 0.30 (0.14), residues: 3764 helix: 0.68 (0.13), residues: 1581 sheet: -0.39 (0.20), residues: 597 loop : 0.14 (0.16), residues: 1586 *********************** 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 422 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 352 time to evaluate : 4.081 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 37 residues processed: 410 average time/residue: 1.8453 time to fit residues: 869.9922 Evaluate side-chains 371 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 334 time to evaluate : 3.614 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 35 residues processed: 3 average time/residue: 0.7291 time to fit residues: 8.0575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 263 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 303 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 359 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 30110 Z= 0.208 Angle : 0.556 8.233 40807 Z= 0.281 Chirality : 0.044 0.177 4576 Planarity : 0.005 0.047 5333 Dihedral : 5.528 96.203 4209 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 2.17 % 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: 0.34 (0.14), residues: 3764 helix: 0.71 (0.13), residues: 1570 sheet: -0.31 (0.21), residues: 576 loop : 0.14 (0.16), residues: 1618 *********************** 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 409 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 342 time to evaluate : 3.616 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 43 residues processed: 392 average time/residue: 1.7939 time to fit residues: 805.0076 Evaluate side-chains 371 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 328 time to evaluate : 3.552 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 39 residues processed: 5 average time/residue: 0.6757 time to fit residues: 9.5115 ------------------------------------------------------------------------------- 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: 9.9990 chunk 143 optimal weight: 0.0970 chunk 214 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 228 optimal weight: 0.0040 chunk 244 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 282 optimal weight: 6.9990 overall best weight: 3.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 30110 Z= 0.269 Angle : 0.602 8.648 40807 Z= 0.306 Chirality : 0.046 0.183 4576 Planarity : 0.005 0.055 5333 Dihedral : 5.747 98.451 4209 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 2.34 % 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: 0.19 (0.14), residues: 3764 helix: 0.55 (0.13), residues: 1579 sheet: -0.31 (0.21), residues: 573 loop : 0.06 (0.16), residues: 1612 *********************** 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 402 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 330 time to evaluate : 3.644 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 49 residues processed: 385 average time/residue: 1.7790 time to fit residues: 786.2279 Evaluate side-chains 374 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 325 time to evaluate : 3.825 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 44 residues processed: 6 average time/residue: 0.6312 time to fit residues: 10.6414 ------------------------------------------------------------------------------- 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: 7.9990 chunk 344 optimal weight: 0.8980 chunk 314 optimal weight: 10.0000 chunk 335 optimal weight: 2.9990 chunk 201 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 263 optimal weight: 0.0010 chunk 102 optimal weight: 6.9990 chunk 302 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 chunk 333 optimal weight: 10.0000 overall best weight: 3.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 30110 Z= 0.266 Angle : 0.600 9.032 40807 Z= 0.305 Chirality : 0.046 0.179 4576 Planarity : 0.005 0.055 5333 Dihedral : 5.770 99.482 4209 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 1.95 % 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: 0.51 (0.13), residues: 1578 sheet: -0.34 (0.21), residues: 573 loop : 0.02 (0.16), residues: 1613 *********************** 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 387 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 327 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 46 residues processed: 377 average time/residue: 1.8468 time to fit residues: 798.4687 Evaluate side-chains 362 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 316 time to evaluate : 3.524 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 44 residues processed: 3 average time/residue: 0.3422 time to fit residues: 6.6464 ------------------------------------------------------------------------------- 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: 3.9990 chunk 354 optimal weight: 9.9990 chunk 216 optimal weight: 0.8980 chunk 168 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 371 optimal weight: 0.9990 chunk 342 optimal weight: 7.9990 chunk 295 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 181 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 30110 Z= 0.160 Angle : 0.528 8.846 40807 Z= 0.267 Chirality : 0.043 0.168 4576 Planarity : 0.004 0.049 5333 Dihedral : 5.408 94.863 4209 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 1.69 % 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: 0.39 (0.14), residues: 3764 helix: 0.75 (0.13), residues: 1587 sheet: -0.30 (0.21), residues: 583 loop : 0.18 (0.16), residues: 1594 ********************** 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: 52 poor density : 325 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 44 residues processed: 370 average time/residue: 1.7381 time to fit residues: 740.9011 Evaluate side-chains 364 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 320 time to evaluate : 3.560 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 43 residues processed: 3 average time/residue: 1.2983 time to fit residues: 9.4288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 0.3980 chunk 315 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 296 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 37 optimal weight: 0.0050 chunk 54 optimal weight: 2.9990 overall best weight: 2.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.156884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123462 restraints weight = 36245.329| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.50 r_work: 0.3249 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 30110 Z= 0.237 Angle : 0.576 8.477 40807 Z= 0.292 Chirality : 0.045 0.185 4576 Planarity : 0.005 0.055 5333 Dihedral : 5.596 96.483 4209 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 1.52 % 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: 0.30 (0.14), residues: 3764 helix: 0.66 (0.13), residues: 1584 sheet: -0.35 (0.20), residues: 610 loop : 0.16 (0.16), residues: 1570 =============================================================================== Job complete usr+sys time: 12420.65 seconds wall clock time: 220 minutes 23.25 seconds (13223.25 seconds total)