Starting phenix.real_space_refine on Thu Mar 21 07:49:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaw_31868/03_2024/7vaw_31868_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaw_31868/03_2024/7vaw_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_31868/03_2024/7vaw_31868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaw_31868/03_2024/7vaw_31868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaw_31868/03_2024/7vaw_31868_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaw_31868/03_2024/7vaw_31868_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 14.72, per 1000 atoms: 0.50 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: 11.27 Conformation dependent library (CDL) restraints added in 5.1 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: 5.97 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: 10.59 Time building geometry restraints manager: 12.15 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: 17466 23.14 - 46.28: 748 46.28 - 69.42: 97 69.42 - 92.56: 43 92.56 - 115.70: 1 Dihedral angle restraints: 18355 sinusoidal: 7533 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 18352 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.690 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 77.020 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.220 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:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.530 ------------------------------------------------------------------------------- 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 : 13.298 115.702 11437 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 % Allowed : 0.16 % Favored : 99.81 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 119 HIS 0.007 0.001 HIS C 283 PHE 0.038 0.001 PHE B 269 TYR 0.013 0.001 TYR D 463 ARG 0.013 0.000 ARG B 364 *********************** 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 : 3.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7576 (tttm) REVERT: A 33 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6715 (mt-10) REVERT: A 114 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6780 (mt-10) REVERT: A 124 LYS cc_start: 0.7084 (mtmm) cc_final: 0.6666 (mttm) REVERT: A 128 GLU cc_start: 0.5704 (mt-10) cc_final: 0.5489 (mt-10) REVERT: A 158 LYS cc_start: 0.7191 (ttmt) cc_final: 0.6604 (tmtt) REVERT: A 169 GLU cc_start: 0.6911 (tp30) cc_final: 0.6688 (mm-30) REVERT: A 184 TYR cc_start: 0.8425 (p90) cc_final: 0.7955 (p90) REVERT: A 197 ARG cc_start: 0.7834 (ptm-80) cc_final: 0.7080 (ptp90) REVERT: A 209 MET cc_start: 0.7456 (mtp) cc_final: 0.7088 (mtp) REVERT: A 239 GLN cc_start: 0.7555 (mt0) cc_final: 0.7172 (mp10) REVERT: A 248 ASP cc_start: 0.7471 (m-30) cc_final: 0.7251 (m-30) REVERT: A 257 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7121 (mm-30) REVERT: A 271 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6470 (mm-30) REVERT: A 337 ILE cc_start: 0.7104 (mm) cc_final: 0.6897 (mm) REVERT: A 342 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6316 (mt-10) REVERT: A 343 GLU cc_start: 0.6596 (mt-10) cc_final: 0.5903 (mm-30) REVERT: A 393 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6452 (pp20) REVERT: A 460 ARG cc_start: 0.7046 (mtp180) cc_final: 0.6836 (mtp-110) REVERT: A 461 GLU cc_start: 0.7096 (tt0) cc_final: 0.6735 (pt0) REVERT: A 466 GLU cc_start: 0.6321 (mt-10) cc_final: 0.5404 (tp30) REVERT: A 485 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6311 (mm-30) REVERT: A 541 GLN cc_start: 0.5786 (mm110) cc_final: 0.5518 (mm110) REVERT: A 546 GLU cc_start: 0.6052 (mm-30) cc_final: 0.5370 (mt-10) REVERT: A 564 GLU cc_start: 0.5544 (mm-30) cc_final: 0.5124 (mm-30) REVERT: B 45 ASP cc_start: 0.7672 (t0) cc_final: 0.7326 (t0) REVERT: B 53 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6322 (mt-10) REVERT: B 114 GLU cc_start: 0.6506 (mp0) cc_final: 0.5830 (pt0) REVERT: B 128 GLU cc_start: 0.6123 (mm-30) cc_final: 0.5741 (mm-30) REVERT: B 156 ARG cc_start: 0.6613 (mtp180) cc_final: 0.6108 (ttt-90) REVERT: B 166 TYR cc_start: 0.7612 (m-80) cc_final: 0.7395 (m-80) REVERT: B 209 MET cc_start: 0.6450 (mtp) cc_final: 0.6241 (mtm) REVERT: B 257 GLU cc_start: 0.6358 (mm-30) cc_final: 0.6111 (mp0) REVERT: B 262 MET cc_start: 0.8026 (tpt) cc_final: 0.7811 (tpt) REVERT: B 271 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6287 (mp0) REVERT: B 397 GLN cc_start: 0.7321 (mm-40) cc_final: 0.7073 (tp40) REVERT: B 460 ARG cc_start: 0.6094 (mtp85) cc_final: 0.5105 (mmm160) REVERT: B 516 MET cc_start: 0.6317 (mtp) cc_final: 0.5918 (mtp) REVERT: B 517 LYS cc_start: 0.6535 (tttt) cc_final: 0.6128 (tppp) REVERT: B 520 LEU cc_start: 0.6274 (mm) cc_final: 0.5496 (pp) REVERT: B 547 ARG cc_start: 0.4702 (tpp-160) cc_final: 0.4445 (tpp-160) REVERT: B 567 MET cc_start: 0.5736 (mmm) cc_final: 0.5355 (mtp) REVERT: C 43 ASP cc_start: 0.7075 (t0) cc_final: 0.6842 (t0) REVERT: C 89 ARG cc_start: 0.7793 (mtm180) cc_final: 0.7339 (mtm-85) REVERT: C 114 GLU cc_start: 0.6889 (pt0) cc_final: 0.6592 (pp20) REVERT: C 127 ASP cc_start: 0.6758 (m-30) cc_final: 0.6297 (m-30) REVERT: C 130 ARG cc_start: 0.7142 (mmt-90) cc_final: 0.6917 (mmt180) REVERT: C 146 LYS cc_start: 0.8170 (mttt) cc_final: 0.7900 (mttp) REVERT: C 159 GLU cc_start: 0.6537 (mt-10) cc_final: 0.6140 (mt-10) REVERT: C 294 MET cc_start: 0.7715 (mtt) cc_final: 0.7441 (mtp) REVERT: C 323 MET cc_start: 0.8403 (mmp) cc_final: 0.8062 (mmt) REVERT: C 337 ILE cc_start: 0.7583 (mm) cc_final: 0.7331 (mp) REVERT: C 342 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7029 (mm-30) REVERT: C 424 TRP cc_start: 0.7642 (p90) cc_final: 0.7385 (p90) REVERT: C 441 GLU cc_start: 0.6930 (tt0) cc_final: 0.6458 (tp30) REVERT: C 461 GLU cc_start: 0.6109 (tm-30) cc_final: 0.5803 (tm-30) REVERT: C 485 GLU cc_start: 0.6352 (mm-30) cc_final: 0.6077 (tp30) REVERT: C 489 ILE cc_start: 0.7641 (mt) cc_final: 0.7301 (mt) REVERT: C 491 ARG cc_start: 0.6610 (mtm110) cc_final: 0.6208 (mtp180) REVERT: C 544 VAL cc_start: 0.7689 (t) cc_final: 0.7447 (p) REVERT: C 546 GLU cc_start: 0.6471 (mm-30) cc_final: 0.5267 (mt-10) REVERT: C 558 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6369 (mt-10) REVERT: D 7 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6765 (mm-30) REVERT: D 46 GLN cc_start: 0.8432 (tt0) cc_final: 0.8095 (tt0) REVERT: D 49 GLU cc_start: 0.7542 (tt0) cc_final: 0.7291 (tt0) REVERT: D 230 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7316 (mt-10) REVERT: D 274 ARG cc_start: 0.7221 (mtt180) cc_final: 0.6813 (mtt180) REVERT: D 353 ASP cc_start: 0.7264 (t0) cc_final: 0.7013 (t0) REVERT: D 407 ASN cc_start: 0.6289 (p0) cc_final: 0.4997 (m110) REVERT: D 409 ARG cc_start: 0.6660 (mtm-85) cc_final: 0.6415 (mtm-85) REVERT: D 410 ARG cc_start: 0.6498 (mtp180) cc_final: 0.6078 (mtt90) REVERT: D 420 ARG cc_start: 0.6670 (mtm-85) cc_final: 0.6466 (mtm-85) REVERT: D 428 GLN cc_start: 0.7493 (mt0) cc_final: 0.7174 (mt0) REVERT: D 452 LYS cc_start: 0.6659 (mttp) cc_final: 0.6260 (mtpt) REVERT: D 466 LYS cc_start: 0.5716 (ptpp) cc_final: 0.5385 (ptmt) REVERT: E 6 LYS cc_start: 0.7072 (tttt) cc_final: 0.6868 (ttpp) REVERT: E 26 ASP cc_start: 0.6543 (m-30) cc_final: 0.6065 (t70) REVERT: E 162 GLU cc_start: 0.6242 (mp0) cc_final: 0.5897 (mp0) REVERT: E 206 GLN cc_start: 0.6133 (tm-30) cc_final: 0.5931 (tp40) REVERT: E 209 GLU cc_start: 0.5859 (mt-10) cc_final: 0.5262 (pt0) REVERT: E 210 ARG cc_start: 0.6856 (ptt90) cc_final: 0.6609 (ppt-90) REVERT: E 243 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6416 (mt-10) REVERT: E 265 GLU cc_start: 0.6395 (mt-10) cc_final: 0.6142 (mm-30) REVERT: E 318 ASP cc_start: 0.6760 (m-30) cc_final: 0.6490 (m-30) REVERT: E 345 ARG cc_start: 0.6436 (mmt90) cc_final: 0.6170 (mmm-85) REVERT: E 364 ASN cc_start: 0.7108 (p0) cc_final: 0.6082 (t0) REVERT: E 377 GLN cc_start: 0.6071 (mp10) cc_final: 0.5301 (mt0) REVERT: E 409 ARG cc_start: 0.4404 (mpp80) cc_final: 0.4188 (mmp80) REVERT: E 434 GLU cc_start: 0.5655 (tt0) cc_final: 0.4759 (tp30) REVERT: E 437 GLN cc_start: 0.7089 (tt0) cc_final: 0.6872 (tt0) REVERT: E 461 LYS cc_start: 0.5699 (tttt) cc_final: 0.5054 (mptp) REVERT: F 61 GLU cc_start: 0.6893 (mp0) cc_final: 0.6631 (mp0) REVERT: F 103 LEU cc_start: 0.6919 (mm) cc_final: 0.6598 (mt) REVERT: F 380 ASP cc_start: 0.7325 (m-30) cc_final: 0.6842 (m-30) REVERT: F 395 LEU cc_start: 0.7316 (tp) cc_final: 0.7093 (tp) REVERT: F 409 ARG cc_start: 0.6796 (ttm110) cc_final: 0.6286 (ttm110) REVERT: F 421 PHE cc_start: 0.7751 (m-80) cc_final: 0.7430 (m-80) REVERT: F 447 PRO cc_start: 0.7995 (Cg_exo) cc_final: 0.7773 (Cg_endo) REVERT: G 19 ARG cc_start: 0.6848 (mtm-85) cc_final: 0.6065 (ttp-110) REVERT: G 23 LYS cc_start: 0.6221 (mttp) cc_final: 0.5946 (mtpp) REVERT: G 38 GLU cc_start: 0.6430 (tt0) cc_final: 0.6156 (tt0) REVERT: G 152 GLU cc_start: 0.6474 (tt0) cc_final: 0.5775 (tp30) REVERT: G 156 LYS cc_start: 0.6233 (tptp) cc_final: 0.5768 (mtmt) REVERT: G 196 ARG cc_start: 0.6078 (mtp-110) cc_final: 0.5646 (tpp80) REVERT: H 8 GLU cc_start: 0.3311 (mt-10) cc_final: 0.3076 (pt0) REVERT: J 92 GLU cc_start: 0.2555 (tp30) cc_final: 0.2282 (tt0) REVERT: J 164 GLU cc_start: 0.5049 (tt0) cc_final: 0.4628 (mp0) REVERT: L 76 ARG cc_start: 0.4871 (mtp85) cc_final: 0.4619 (ttt90) REVERT: L 78 GLU cc_start: 0.4814 (tt0) cc_final: 0.4097 (tt0) REVERT: L 86 ARG cc_start: 0.4877 (mtp85) cc_final: 0.4261 (mtp180) REVERT: L 88 ARG cc_start: 0.4815 (mtp-110) cc_final: 0.4141 (ptm160) REVERT: L 89 GLU cc_start: 0.4040 (mm-30) cc_final: 0.3685 (pt0) REVERT: L 140 VAL cc_start: 0.3913 (m) cc_final: 0.3702 (p) REVERT: L 141 GLU cc_start: 0.4827 (tt0) cc_final: 0.4436 (mp0) REVERT: L 170 ARG cc_start: 0.5370 (mtp85) cc_final: 0.4922 (mtp85) outliers start: 1 outliers final: 3 residues processed: 590 average time/residue: 1.7777 time to fit residues: 1187.2590 Evaluate side-chains 391 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 388 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 53 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 10.0000 chunk 282 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 292 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 217 optimal weight: 3.9990 chunk 338 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 283 HIS B 498 ASN ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 363 ASN E 166 GLN E 364 ASN F 364 ASN F 388 ASN G 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 30110 Z= 0.324 Angle : 0.650 9.746 40807 Z= 0.334 Chirality : 0.048 0.178 4576 Planarity : 0.006 0.054 5333 Dihedral : 6.684 105.583 4238 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.85 % Allowed : 8.11 % Favored : 90.04 % 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: 0.40 (0.14), residues: 3764 helix: 0.68 (0.13), residues: 1563 sheet: -0.11 (0.21), residues: 564 loop : 0.19 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 119 HIS 0.015 0.002 HIS C 283 PHE 0.017 0.002 PHE C 406 TYR 0.015 0.002 TYR A 304 ARG 0.009 0.001 ARG B 364 *********************** 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 444 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 387 time to evaluate : 3.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7519 (tttm) REVERT: A 33 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6732 (mt-10) REVERT: A 114 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6782 (mt-10) REVERT: A 124 LYS cc_start: 0.7138 (mtmm) cc_final: 0.6633 (mttm) REVERT: A 128 GLU cc_start: 0.5667 (mt-10) cc_final: 0.5446 (mt-10) REVERT: A 158 LYS cc_start: 0.7273 (ttmt) cc_final: 0.6604 (tmtt) REVERT: A 197 ARG cc_start: 0.7836 (ptm-80) cc_final: 0.7107 (ptp90) REVERT: A 209 MET cc_start: 0.7517 (mtp) cc_final: 0.7021 (mtp) REVERT: A 248 ASP cc_start: 0.7526 (m-30) cc_final: 0.7234 (m-30) REVERT: A 257 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7115 (mm-30) REVERT: A 271 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6785 (mp0) REVERT: A 342 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6319 (mt-10) REVERT: A 343 GLU cc_start: 0.6602 (mt-10) cc_final: 0.5902 (mm-30) REVERT: A 461 GLU cc_start: 0.7108 (tt0) cc_final: 0.6658 (pt0) REVERT: A 466 GLU cc_start: 0.6278 (mt-10) cc_final: 0.5385 (tp30) REVERT: A 470 LEU cc_start: 0.7370 (tp) cc_final: 0.7096 (tp) REVERT: A 485 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6318 (mm-30) REVERT: A 546 GLU cc_start: 0.6050 (mm-30) cc_final: 0.5423 (mt-10) REVERT: B 114 GLU cc_start: 0.6509 (mp0) cc_final: 0.6057 (mp0) REVERT: B 128 GLU cc_start: 0.6231 (mm-30) cc_final: 0.5765 (mm-30) REVERT: B 156 ARG cc_start: 0.6582 (mtp180) cc_final: 0.6082 (ttt180) REVERT: B 209 MET cc_start: 0.6605 (mtp) cc_final: 0.6228 (mtm) REVERT: B 257 GLU cc_start: 0.6697 (mm-30) cc_final: 0.6359 (tp30) REVERT: B 271 GLU cc_start: 0.6636 (mm-30) cc_final: 0.6185 (mp0) REVERT: B 323 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7901 (mtp) REVERT: B 348 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6744 (tt0) REVERT: B 424 TRP cc_start: 0.7677 (p90) cc_final: 0.7471 (p90) REVERT: B 460 ARG cc_start: 0.6282 (mtp85) cc_final: 0.5198 (mmm160) REVERT: B 481 ARG cc_start: 0.6045 (mmm-85) cc_final: 0.5791 (mmm-85) REVERT: B 516 MET cc_start: 0.6467 (mtp) cc_final: 0.6005 (mtp) REVERT: B 517 LYS cc_start: 0.6608 (tttt) cc_final: 0.6405 (tppp) REVERT: B 567 MET cc_start: 0.5506 (mmm) cc_final: 0.5204 (mtp) REVERT: C 43 ASP cc_start: 0.7129 (t0) cc_final: 0.6883 (t0) REVERT: C 114 GLU cc_start: 0.6954 (pt0) cc_final: 0.6603 (pp20) REVERT: C 159 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6227 (mt-10) REVERT: C 294 MET cc_start: 0.7536 (mtt) cc_final: 0.7275 (mtp) REVERT: C 337 ILE cc_start: 0.7488 (mm) cc_final: 0.7202 (mp) REVERT: C 342 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6997 (mm-30) REVERT: C 424 TRP cc_start: 0.7697 (p90) cc_final: 0.7446 (p90) REVERT: C 441 GLU cc_start: 0.6938 (tt0) cc_final: 0.6511 (tp30) REVERT: C 461 GLU cc_start: 0.5963 (tm-30) cc_final: 0.5557 (tm-30) REVERT: C 485 GLU cc_start: 0.6305 (mm-30) cc_final: 0.6005 (mm-30) REVERT: C 491 ARG cc_start: 0.6912 (mtm110) cc_final: 0.6399 (mtp180) REVERT: C 546 GLU cc_start: 0.6202 (mm-30) cc_final: 0.5127 (mt-10) REVERT: C 550 ARG cc_start: 0.6707 (mmm160) cc_final: 0.6363 (mmm160) REVERT: C 558 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6271 (mt-10) REVERT: D 7 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6776 (mm-30) REVERT: D 46 GLN cc_start: 0.8354 (tt0) cc_final: 0.8047 (tt0) REVERT: D 209 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: D 230 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7278 (mt-10) REVERT: D 274 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6816 (mtt180) REVERT: D 401 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6764 (mm-30) REVERT: D 407 ASN cc_start: 0.6334 (p0) cc_final: 0.5044 (m110) REVERT: D 410 ARG cc_start: 0.6456 (mtp180) cc_final: 0.5995 (mtt90) REVERT: D 428 GLN cc_start: 0.7579 (mt0) cc_final: 0.7227 (mt0) REVERT: D 452 LYS cc_start: 0.6787 (mttp) cc_final: 0.6403 (mtpt) REVERT: D 466 LYS cc_start: 0.5616 (ptpp) cc_final: 0.5274 (ptmt) REVERT: E 26 ASP cc_start: 0.6587 (m-30) cc_final: 0.6232 (t70) REVERT: E 36 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7750 (ttpp) REVERT: E 130 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6449 (p90) REVERT: E 209 GLU cc_start: 0.6274 (mt-10) cc_final: 0.5517 (pt0) REVERT: E 243 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6148 (mt-10) REVERT: E 259 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6755 (t70) REVERT: E 265 GLU cc_start: 0.6371 (mt-10) cc_final: 0.6109 (mm-30) REVERT: E 318 ASP cc_start: 0.6761 (m-30) cc_final: 0.6501 (m-30) REVERT: E 321 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6647 (ttt90) REVERT: E 345 ARG cc_start: 0.6506 (mmt90) cc_final: 0.6203 (mmm-85) REVERT: E 364 ASN cc_start: 0.6826 (p0) cc_final: 0.6070 (t0) REVERT: E 434 GLU cc_start: 0.5612 (tt0) cc_final: 0.4836 (tp30) REVERT: E 461 LYS cc_start: 0.5742 (tttt) cc_final: 0.5045 (mtmt) REVERT: F 61 GLU cc_start: 0.6892 (mp0) cc_final: 0.6660 (mp0) REVERT: F 230 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6522 (mt-10) REVERT: F 395 LEU cc_start: 0.7328 (tp) cc_final: 0.7044 (tp) REVERT: F 409 ARG cc_start: 0.6736 (ttm110) cc_final: 0.6350 (ttm110) REVERT: F 437 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: G 19 ARG cc_start: 0.6868 (mtm-85) cc_final: 0.6040 (ttp-110) REVERT: G 23 LYS cc_start: 0.6443 (mttp) cc_final: 0.6193 (mtpp) REVERT: G 38 GLU cc_start: 0.6496 (tt0) cc_final: 0.6248 (tt0) REVERT: G 152 GLU cc_start: 0.6642 (tt0) cc_final: 0.5899 (tp30) REVERT: G 156 LYS cc_start: 0.6199 (tptp) cc_final: 0.5704 (mtmt) REVERT: G 196 ARG cc_start: 0.6116 (mtp-110) cc_final: 0.5506 (tpp80) REVERT: H 1 MET cc_start: 0.3907 (OUTLIER) cc_final: 0.3309 (mmt) REVERT: J 92 GLU cc_start: 0.2635 (tp30) cc_final: 0.2420 (tt0) REVERT: J 164 GLU cc_start: 0.5166 (tt0) cc_final: 0.4613 (mp0) REVERT: L 78 GLU cc_start: 0.4886 (tt0) cc_final: 0.4167 (tt0) REVERT: L 88 ARG cc_start: 0.4726 (mtp-110) cc_final: 0.4241 (ptm160) REVERT: L 89 GLU cc_start: 0.3910 (mm-30) cc_final: 0.3661 (pt0) outliers start: 57 outliers final: 21 residues processed: 424 average time/residue: 1.8345 time to fit residues: 883.3786 Evaluate side-chains 383 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 353 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 461 LYS Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 281 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 339 optimal weight: 30.0000 chunk 366 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS E 166 GLN G 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 30110 Z= 0.239 Angle : 0.570 8.737 40807 Z= 0.293 Chirality : 0.045 0.161 4576 Planarity : 0.005 0.054 5333 Dihedral : 6.484 102.974 4236 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.04 % Allowed : 10.25 % Favored : 87.71 % 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: 0.66 (0.13), residues: 1564 sheet: -0.17 (0.21), residues: 553 loop : 0.14 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 119 HIS 0.010 0.001 HIS C 283 PHE 0.015 0.002 PHE B 415 TYR 0.014 0.002 TYR F 463 ARG 0.005 0.000 ARG A 93 *********************** 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 430 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 367 time to evaluate : 3.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7523 (tttm) REVERT: A 33 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6676 (mt-10) REVERT: A 114 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6783 (mt-10) REVERT: A 124 LYS cc_start: 0.7178 (mtmm) cc_final: 0.6662 (mttm) REVERT: A 128 GLU cc_start: 0.5614 (mt-10) cc_final: 0.5394 (mt-10) REVERT: A 158 LYS cc_start: 0.7244 (ttmt) cc_final: 0.6675 (tttm) REVERT: A 197 ARG cc_start: 0.7896 (ptm-80) cc_final: 0.7129 (ptp90) REVERT: A 209 MET cc_start: 0.7503 (mtp) cc_final: 0.7003 (mtp) REVERT: A 248 ASP cc_start: 0.7504 (m-30) cc_final: 0.7192 (m-30) REVERT: A 342 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6278 (mt-10) REVERT: A 343 GLU cc_start: 0.6622 (mt-10) cc_final: 0.5872 (mm-30) REVERT: A 347 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6323 (tp30) REVERT: A 450 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7519 (tp) REVERT: A 461 GLU cc_start: 0.7153 (tt0) cc_final: 0.6689 (pt0) REVERT: A 466 GLU cc_start: 0.6357 (mt-10) cc_final: 0.5308 (tp30) REVERT: A 485 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6350 (mm-30) REVERT: A 546 GLU cc_start: 0.6033 (mm-30) cc_final: 0.5392 (mt-10) REVERT: A 558 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6879 (pt0) REVERT: B 33 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6530 (mt-10) REVERT: B 114 GLU cc_start: 0.6551 (mp0) cc_final: 0.6114 (mp0) REVERT: B 128 GLU cc_start: 0.6241 (mm-30) cc_final: 0.5835 (mm-30) REVERT: B 156 ARG cc_start: 0.6666 (mtp180) cc_final: 0.6223 (ttt180) REVERT: B 159 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6786 (pt0) REVERT: B 190 ARG cc_start: 0.7956 (mtt180) cc_final: 0.7648 (mtt-85) REVERT: B 209 MET cc_start: 0.6585 (mtp) cc_final: 0.6180 (mtm) REVERT: B 257 GLU cc_start: 0.6567 (mm-30) cc_final: 0.6310 (tp30) REVERT: B 271 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6200 (mp0) REVERT: B 323 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7847 (mtp) REVERT: B 348 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6734 (tt0) REVERT: B 393 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6351 (pp20) REVERT: B 425 ASN cc_start: 0.7219 (m-40) cc_final: 0.6729 (m110) REVERT: B 460 ARG cc_start: 0.6262 (mtp85) cc_final: 0.5186 (mmm160) REVERT: B 481 ARG cc_start: 0.6056 (mmm-85) cc_final: 0.5817 (mmm-85) REVERT: B 516 MET cc_start: 0.6445 (mtp) cc_final: 0.6021 (mtp) REVERT: B 517 LYS cc_start: 0.6716 (tttt) cc_final: 0.6473 (tppp) REVERT: B 547 ARG cc_start: 0.4439 (tpp-160) cc_final: 0.4197 (tpp80) REVERT: B 567 MET cc_start: 0.5468 (mmm) cc_final: 0.5173 (mtp) REVERT: C 114 GLU cc_start: 0.6960 (pt0) cc_final: 0.6633 (pp20) REVERT: C 159 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6148 (mt-10) REVERT: C 201 PRO cc_start: 0.7654 (Cg_endo) cc_final: 0.7343 (Cg_exo) REVERT: C 257 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: C 294 MET cc_start: 0.7478 (mtt) cc_final: 0.7188 (mtp) REVERT: C 337 ILE cc_start: 0.7473 (mm) cc_final: 0.7194 (mp) REVERT: C 342 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6717 (mt-10) REVERT: C 344 MET cc_start: 0.7648 (ttp) cc_final: 0.7224 (tpp) REVERT: C 424 TRP cc_start: 0.7661 (p90) cc_final: 0.7431 (p90) REVERT: C 441 GLU cc_start: 0.6892 (tt0) cc_final: 0.6465 (tp30) REVERT: C 461 GLU cc_start: 0.5931 (tm-30) cc_final: 0.5465 (tm-30) REVERT: C 485 GLU cc_start: 0.6244 (mm-30) cc_final: 0.6036 (mm-30) REVERT: C 491 ARG cc_start: 0.7060 (mtm110) cc_final: 0.6647 (mtm-85) REVERT: C 493 ASP cc_start: 0.7059 (m-30) cc_final: 0.6790 (m-30) REVERT: C 546 GLU cc_start: 0.6272 (mm-30) cc_final: 0.5681 (mp0) REVERT: C 550 ARG cc_start: 0.6650 (mmm160) cc_final: 0.6314 (mmm160) REVERT: C 558 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6304 (mt-10) REVERT: D 7 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6751 (mm-30) REVERT: D 46 GLN cc_start: 0.8362 (tt0) cc_final: 0.8069 (tt0) REVERT: D 209 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: D 230 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7294 (mt-10) REVERT: D 274 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6826 (mtt180) REVERT: D 368 LYS cc_start: 0.7040 (ttpp) cc_final: 0.6590 (ptpt) REVERT: D 407 ASN cc_start: 0.6297 (p0) cc_final: 0.5059 (m-40) REVERT: D 410 ARG cc_start: 0.6460 (mtp180) cc_final: 0.6025 (mtt90) REVERT: D 428 GLN cc_start: 0.7558 (mt0) cc_final: 0.7189 (mt0) REVERT: D 452 LYS cc_start: 0.6790 (mttp) cc_final: 0.6416 (mtpt) REVERT: D 466 LYS cc_start: 0.5558 (ptpp) cc_final: 0.5249 (ptmt) REVERT: E 26 ASP cc_start: 0.6595 (m-30) cc_final: 0.6250 (t70) REVERT: E 36 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7747 (ttpp) REVERT: E 130 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.6407 (p90) REVERT: E 209 GLU cc_start: 0.6315 (mt-10) cc_final: 0.5530 (pt0) REVERT: E 243 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6066 (mt-10) REVERT: E 259 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6697 (t70) REVERT: E 265 GLU cc_start: 0.6381 (mt-10) cc_final: 0.6102 (mm-30) REVERT: E 318 ASP cc_start: 0.6708 (m-30) cc_final: 0.6498 (m-30) REVERT: E 321 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6590 (ttt90) REVERT: E 345 ARG cc_start: 0.6535 (mmt90) cc_final: 0.6179 (mmm-85) REVERT: E 434 GLU cc_start: 0.5651 (tt0) cc_final: 0.4850 (tp30) REVERT: E 461 LYS cc_start: 0.5903 (tttt) cc_final: 0.5123 (mtmt) REVERT: F 61 GLU cc_start: 0.6882 (mp0) cc_final: 0.6662 (mp0) REVERT: F 206 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6971 (mt0) REVERT: F 230 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6603 (mt-10) REVERT: F 406 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5460 (mt-10) REVERT: F 409 ARG cc_start: 0.6652 (ttm110) cc_final: 0.6262 (ttm110) REVERT: F 437 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: F 461 LYS cc_start: 0.6676 (tttm) cc_final: 0.6366 (ttmm) REVERT: G 19 ARG cc_start: 0.6852 (mtm-85) cc_final: 0.6019 (ttp-110) REVERT: G 23 LYS cc_start: 0.6483 (mttp) cc_final: 0.6219 (mtpp) REVERT: G 38 GLU cc_start: 0.6444 (tt0) cc_final: 0.6173 (tt0) REVERT: G 156 LYS cc_start: 0.6217 (tptp) cc_final: 0.5724 (mtmt) REVERT: G 196 ARG cc_start: 0.6196 (mtp-110) cc_final: 0.5552 (tpp80) REVERT: H 1 MET cc_start: 0.3871 (OUTLIER) cc_final: 0.3279 (mmt) REVERT: J 92 GLU cc_start: 0.2670 (tp30) cc_final: 0.2376 (tt0) REVERT: J 121 LEU cc_start: 0.4235 (mp) cc_final: 0.3869 (mm) REVERT: J 164 GLU cc_start: 0.5216 (tt0) cc_final: 0.4679 (mp0) REVERT: L 78 GLU cc_start: 0.4977 (tt0) cc_final: 0.4248 (tt0) REVERT: L 88 ARG cc_start: 0.4743 (mtp-110) cc_final: 0.4227 (ptm160) REVERT: L 89 GLU cc_start: 0.3967 (mm-30) cc_final: 0.3712 (pt0) REVERT: L 176 ASP cc_start: 0.5213 (OUTLIER) cc_final: 0.4797 (t70) outliers start: 63 outliers final: 28 residues processed: 406 average time/residue: 1.7742 time to fit residues: 817.2323 Evaluate side-chains 398 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 352 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 176 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 20.0000 chunk 255 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 340 optimal weight: 0.8980 chunk 360 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 GLN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 HIS E 166 GLN G 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 30110 Z= 0.469 Angle : 0.745 10.221 40807 Z= 0.384 Chirality : 0.051 0.187 4576 Planarity : 0.007 0.083 5333 Dihedral : 7.039 105.790 4236 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.11 % Allowed : 11.97 % Favored : 84.92 % 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: -0.26 (0.13), residues: 3764 helix: 0.11 (0.13), residues: 1556 sheet: -0.44 (0.21), residues: 579 loop : -0.15 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP L 175 HIS 0.008 0.002 HIS F 249 PHE 0.020 0.003 PHE A 205 TYR 0.025 0.003 TYR C 562 ARG 0.008 0.001 ARG G 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 371 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7529 (tttm) REVERT: A 33 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6602 (mt-10) REVERT: A 114 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7018 (mt-10) REVERT: A 124 LYS cc_start: 0.7173 (mtmm) cc_final: 0.6288 (pttm) REVERT: A 128 GLU cc_start: 0.5813 (mt-10) cc_final: 0.5496 (mt-10) REVERT: A 158 LYS cc_start: 0.7194 (ttmt) cc_final: 0.6600 (tttm) REVERT: A 197 ARG cc_start: 0.7915 (ptm-80) cc_final: 0.7091 (ptp90) REVERT: A 209 MET cc_start: 0.7566 (mtp) cc_final: 0.7075 (mtp) REVERT: A 248 ASP cc_start: 0.7529 (m-30) cc_final: 0.7172 (m-30) REVERT: A 342 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6160 (mt-10) REVERT: A 343 GLU cc_start: 0.6698 (mt-10) cc_final: 0.5930 (mm-30) REVERT: A 347 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6337 (tp30) REVERT: A 450 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7557 (tp) REVERT: A 461 GLU cc_start: 0.7181 (tt0) cc_final: 0.6719 (pt0) REVERT: A 466 GLU cc_start: 0.6443 (mt-10) cc_final: 0.5413 (tp30) REVERT: A 485 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6345 (mm-30) REVERT: A 546 GLU cc_start: 0.6106 (mm-30) cc_final: 0.5469 (mt-10) REVERT: A 556 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: A 558 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7012 (pt0) REVERT: B 33 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6509 (mt-10) REVERT: B 114 GLU cc_start: 0.6605 (mp0) cc_final: 0.6239 (mp0) REVERT: B 128 GLU cc_start: 0.6342 (mm-30) cc_final: 0.5982 (mm-30) REVERT: B 156 ARG cc_start: 0.6597 (mtp180) cc_final: 0.6219 (ttt-90) REVERT: B 159 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6737 (pt0) REVERT: B 209 MET cc_start: 0.6629 (mtp) cc_final: 0.6258 (mtm) REVERT: B 257 GLU cc_start: 0.6716 (mm-30) cc_final: 0.6469 (tp30) REVERT: B 323 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7857 (mtp) REVERT: B 348 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7068 (tt0) REVERT: B 393 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6086 (pp20) REVERT: B 425 ASN cc_start: 0.7084 (m-40) cc_final: 0.6807 (m110) REVERT: B 460 ARG cc_start: 0.6274 (mtp85) cc_final: 0.5274 (mmm160) REVERT: B 516 MET cc_start: 0.6562 (mtp) cc_final: 0.6160 (mtp) REVERT: B 517 LYS cc_start: 0.6685 (tttt) cc_final: 0.6462 (tppp) REVERT: C 159 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6123 (mt-10) REVERT: C 201 PRO cc_start: 0.7624 (Cg_endo) cc_final: 0.7307 (Cg_exo) REVERT: C 294 MET cc_start: 0.7612 (mtt) cc_final: 0.7389 (mtp) REVERT: C 344 MET cc_start: 0.7630 (ttp) cc_final: 0.7208 (tpp) REVERT: C 416 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7477 (ptm160) REVERT: C 441 GLU cc_start: 0.6903 (tt0) cc_final: 0.6476 (tp30) REVERT: C 461 GLU cc_start: 0.5928 (tm-30) cc_final: 0.5643 (tm-30) REVERT: C 485 GLU cc_start: 0.6389 (mm-30) cc_final: 0.6147 (mm-30) REVERT: C 502 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: C 546 GLU cc_start: 0.6242 (mm-30) cc_final: 0.5733 (mp0) REVERT: C 558 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6323 (mt-10) REVERT: D 7 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6773 (mm-30) REVERT: D 209 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: D 230 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7434 (mt-10) REVERT: D 407 ASN cc_start: 0.6542 (p0) cc_final: 0.5107 (m110) REVERT: D 428 GLN cc_start: 0.7507 (mt0) cc_final: 0.7161 (mt0) REVERT: D 452 LYS cc_start: 0.6815 (mttp) cc_final: 0.6470 (mtpt) REVERT: D 466 LYS cc_start: 0.5576 (ptpp) cc_final: 0.5241 (ptmt) REVERT: E 26 ASP cc_start: 0.6637 (m-30) cc_final: 0.6254 (t70) REVERT: E 36 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7807 (ttpp) REVERT: E 128 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6562 (pt0) REVERT: E 130 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.6462 (p90) REVERT: E 209 GLU cc_start: 0.6442 (mt-10) cc_final: 0.5706 (pt0) REVERT: E 243 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6118 (mt-10) REVERT: E 259 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6846 (t70) REVERT: E 265 GLU cc_start: 0.6491 (mt-10) cc_final: 0.6203 (mm-30) REVERT: E 318 ASP cc_start: 0.6618 (m-30) cc_final: 0.6418 (m-30) REVERT: E 321 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6628 (ttt90) REVERT: E 345 ARG cc_start: 0.6604 (mmt90) cc_final: 0.6162 (mmm-85) REVERT: E 409 ARG cc_start: 0.4485 (mpp80) cc_final: 0.4154 (mmp80) REVERT: E 461 LYS cc_start: 0.5926 (tttt) cc_final: 0.4920 (mppt) REVERT: F 61 GLU cc_start: 0.6999 (mp0) cc_final: 0.6749 (mp0) REVERT: F 206 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7085 (mt0) REVERT: F 230 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6740 (mt-10) REVERT: F 380 ASP cc_start: 0.7329 (m-30) cc_final: 0.6831 (m-30) REVERT: F 406 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5514 (mt-10) REVERT: F 409 ARG cc_start: 0.6874 (ttm110) cc_final: 0.6559 (ttm110) REVERT: F 461 LYS cc_start: 0.6743 (tttm) cc_final: 0.6350 (mtpp) REVERT: G 19 ARG cc_start: 0.6766 (mtm-85) cc_final: 0.5845 (ttp-110) REVERT: G 23 LYS cc_start: 0.6598 (mttp) cc_final: 0.6290 (mtpp) REVERT: G 38 GLU cc_start: 0.6473 (tt0) cc_final: 0.6226 (tt0) REVERT: G 156 LYS cc_start: 0.6195 (tptp) cc_final: 0.5728 (tptp) REVERT: G 196 ARG cc_start: 0.6253 (mtp-110) cc_final: 0.5559 (tpp80) REVERT: H 1 MET cc_start: 0.3980 (OUTLIER) cc_final: 0.3338 (mmt) REVERT: J 121 LEU cc_start: 0.4271 (mp) cc_final: 0.3921 (mm) REVERT: J 164 GLU cc_start: 0.5166 (tt0) cc_final: 0.4628 (mp0) REVERT: L 78 GLU cc_start: 0.5246 (tt0) cc_final: 0.4991 (mt-10) REVERT: L 89 GLU cc_start: 0.3882 (mm-30) cc_final: 0.3640 (pt0) REVERT: L 176 ASP cc_start: 0.5337 (OUTLIER) cc_final: 0.4927 (t0) REVERT: L 181 LYS cc_start: 0.4669 (mtmt) cc_final: 0.4444 (mtpt) outliers start: 96 outliers final: 42 residues processed: 447 average time/residue: 1.8099 time to fit residues: 918.6530 Evaluate side-chains 407 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 346 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 416 ARG Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 176 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 307 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 129 GLN G 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30110 Z= 0.151 Angle : 0.517 8.579 40807 Z= 0.264 Chirality : 0.043 0.167 4576 Planarity : 0.005 0.056 5333 Dihedral : 6.261 99.204 4236 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.95 % Allowed : 13.59 % Favored : 84.46 % 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: 0.24 (0.14), residues: 3764 helix: 0.61 (0.13), residues: 1569 sheet: -0.28 (0.21), residues: 576 loop : 0.07 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 119 HIS 0.002 0.001 HIS E 458 PHE 0.014 0.001 PHE B 415 TYR 0.013 0.001 TYR D 13 ARG 0.011 0.000 ARG L 88 *********************** 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 442 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 382 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7505 (tttm) REVERT: A 33 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6557 (mt-10) REVERT: A 53 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6113 (mm-30) REVERT: A 114 GLU cc_start: 0.7267 (mt-10) cc_final: 0.7002 (mt-10) REVERT: A 124 LYS cc_start: 0.7287 (mtmm) cc_final: 0.6793 (mttm) REVERT: A 128 GLU cc_start: 0.5709 (mt-10) cc_final: 0.5444 (mt-10) REVERT: A 152 ASP cc_start: 0.6617 (OUTLIER) cc_final: 0.6295 (p0) REVERT: A 158 LYS cc_start: 0.7186 (ttmt) cc_final: 0.6557 (tttm) REVERT: A 197 ARG cc_start: 0.7861 (ptm-80) cc_final: 0.7037 (ptp90) REVERT: A 209 MET cc_start: 0.7433 (mtp) cc_final: 0.6969 (mtp) REVERT: A 248 ASP cc_start: 0.7472 (m-30) cc_final: 0.7097 (m-30) REVERT: A 342 GLU cc_start: 0.6630 (mt-10) cc_final: 0.6154 (mt-10) REVERT: A 343 GLU cc_start: 0.6607 (mt-10) cc_final: 0.5846 (mm-30) REVERT: A 348 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7335 (mt-10) REVERT: A 393 GLU cc_start: 0.6945 (tm-30) cc_final: 0.6448 (pp20) REVERT: A 450 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7447 (tp) REVERT: A 461 GLU cc_start: 0.7148 (tt0) cc_final: 0.6670 (pt0) REVERT: A 466 GLU cc_start: 0.6361 (mt-10) cc_final: 0.5316 (tp30) REVERT: A 485 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6338 (mm-30) REVERT: A 546 GLU cc_start: 0.6062 (mm-30) cc_final: 0.5450 (mt-10) REVERT: A 567 MET cc_start: 0.6530 (mmm) cc_final: 0.6301 (mmp) REVERT: B 114 GLU cc_start: 0.6603 (mp0) cc_final: 0.6239 (mp0) REVERT: B 128 GLU cc_start: 0.6265 (mm-30) cc_final: 0.5957 (mm-30) REVERT: B 156 ARG cc_start: 0.6617 (mtp180) cc_final: 0.6245 (ttt-90) REVERT: B 159 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6773 (pt0) REVERT: B 209 MET cc_start: 0.6630 (mtp) cc_final: 0.6141 (mtm) REVERT: B 271 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6203 (mp0) REVERT: B 323 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7803 (mtp) REVERT: B 348 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6996 (tt0) REVERT: B 393 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6019 (pp20) REVERT: B 460 ARG cc_start: 0.6459 (mtp85) cc_final: 0.5307 (mmm160) REVERT: B 481 ARG cc_start: 0.6044 (mmm-85) cc_final: 0.5720 (mmm-85) REVERT: B 516 MET cc_start: 0.6413 (mtp) cc_final: 0.5994 (mtp) REVERT: B 517 LYS cc_start: 0.6460 (tttt) cc_final: 0.6254 (tppp) REVERT: B 548 ILE cc_start: 0.5920 (mt) cc_final: 0.5425 (mt) REVERT: C 159 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6119 (mt-10) REVERT: C 201 PRO cc_start: 0.7609 (Cg_endo) cc_final: 0.7218 (Cg_exo) REVERT: C 294 MET cc_start: 0.7312 (mtt) cc_final: 0.7052 (mtp) REVERT: C 337 ILE cc_start: 0.7380 (mm) cc_final: 0.7087 (mp) REVERT: C 342 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6824 (mt-10) REVERT: C 344 MET cc_start: 0.7467 (ttp) cc_final: 0.7153 (tpp) REVERT: C 433 SER cc_start: 0.8094 (t) cc_final: 0.7605 (m) REVERT: C 441 GLU cc_start: 0.6840 (tt0) cc_final: 0.6402 (tp30) REVERT: C 461 GLU cc_start: 0.5859 (tm-30) cc_final: 0.5494 (tm-30) REVERT: C 485 GLU cc_start: 0.6260 (mm-30) cc_final: 0.6035 (mm-30) REVERT: C 491 ARG cc_start: 0.7015 (mtm110) cc_final: 0.6807 (mtm-85) REVERT: C 493 ASP cc_start: 0.7078 (m-30) cc_final: 0.6764 (m-30) REVERT: C 546 GLU cc_start: 0.6238 (mm-30) cc_final: 0.5273 (mt-10) REVERT: C 558 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6248 (mt-10) REVERT: D 7 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6728 (mm-30) REVERT: D 368 LYS cc_start: 0.7032 (ttpp) cc_final: 0.6554 (ptpt) REVERT: D 407 ASN cc_start: 0.6321 (p0) cc_final: 0.5085 (m110) REVERT: D 410 ARG cc_start: 0.6883 (mmm-85) cc_final: 0.6531 (mtp85) REVERT: D 428 GLN cc_start: 0.7461 (mt0) cc_final: 0.7111 (mt0) REVERT: D 452 LYS cc_start: 0.6784 (mttp) cc_final: 0.6405 (mtpt) REVERT: D 466 LYS cc_start: 0.5467 (ptpp) cc_final: 0.5214 (ptmt) REVERT: E 26 ASP cc_start: 0.6555 (m-30) cc_final: 0.6154 (t70) REVERT: E 128 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6548 (pt0) REVERT: E 130 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6356 (p90) REVERT: E 209 GLU cc_start: 0.6389 (mt-10) cc_final: 0.5615 (pt0) REVERT: E 237 MET cc_start: 0.7751 (mmm) cc_final: 0.7255 (mtt) REVERT: E 243 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6034 (mt-10) REVERT: E 265 GLU cc_start: 0.6381 (mt-10) cc_final: 0.6113 (mm-30) REVERT: E 318 ASP cc_start: 0.6601 (m-30) cc_final: 0.6380 (m-30) REVERT: E 345 ARG cc_start: 0.6569 (mmt90) cc_final: 0.6235 (mmm-85) REVERT: E 377 GLN cc_start: 0.6082 (mp10) cc_final: 0.5311 (mt0) REVERT: E 434 GLU cc_start: 0.5665 (tt0) cc_final: 0.4844 (tp30) REVERT: E 446 LEU cc_start: 0.6005 (mm) cc_final: 0.5657 (mm) REVERT: E 461 LYS cc_start: 0.5902 (tttt) cc_final: 0.4931 (mppt) REVERT: F 61 GLU cc_start: 0.6881 (mp0) cc_final: 0.6644 (mp0) REVERT: F 141 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8245 (mtp) REVERT: F 206 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6922 (mt0) REVERT: F 230 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6535 (mt-10) REVERT: F 406 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5743 (mm-30) REVERT: F 409 ARG cc_start: 0.6848 (ttm110) cc_final: 0.6561 (ttm110) REVERT: F 437 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: F 461 LYS cc_start: 0.6830 (tttm) cc_final: 0.6471 (tttp) REVERT: G 19 ARG cc_start: 0.6714 (mtm-85) cc_final: 0.5963 (ttp-110) REVERT: G 23 LYS cc_start: 0.6374 (mttp) cc_final: 0.6123 (mtpp) REVERT: G 38 GLU cc_start: 0.6265 (tt0) cc_final: 0.5991 (tt0) REVERT: G 156 LYS cc_start: 0.6200 (tptp) cc_final: 0.5761 (tptp) REVERT: G 196 ARG cc_start: 0.6150 (mtp-110) cc_final: 0.5572 (tpp80) REVERT: H 1 MET cc_start: 0.3935 (OUTLIER) cc_final: 0.3316 (mmt) REVERT: J 121 LEU cc_start: 0.4144 (mp) cc_final: 0.3759 (mm) REVERT: J 164 GLU cc_start: 0.5102 (tt0) cc_final: 0.4604 (mp0) REVERT: J 186 LEU cc_start: 0.2792 (tt) cc_final: 0.2135 (mp) REVERT: L 78 GLU cc_start: 0.5026 (tt0) cc_final: 0.4769 (mt-10) REVERT: L 88 ARG cc_start: 0.4468 (mtp-110) cc_final: 0.4181 (ptm160) outliers start: 60 outliers final: 17 residues processed: 422 average time/residue: 1.7546 time to fit residues: 841.4709 Evaluate side-chains 389 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 360 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain L residue 140 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 3.9990 chunk 324 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 360 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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** G 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 30110 Z= 0.307 Angle : 0.616 9.182 40807 Z= 0.314 Chirality : 0.047 0.186 4576 Planarity : 0.006 0.053 5333 Dihedral : 6.545 100.138 4236 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.40 % Allowed : 14.50 % Favored : 83.10 % 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: 0.09 (0.14), residues: 3764 helix: 0.47 (0.13), residues: 1558 sheet: -0.32 (0.21), residues: 566 loop : -0.02 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 187 HIS 0.005 0.001 HIS F 249 PHE 0.016 0.002 PHE C 559 TYR 0.018 0.002 TYR C 562 ARG 0.005 0.001 ARG L 88 *********************** 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 434 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 360 time to evaluate : 3.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7466 (tttm) REVERT: A 33 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6642 (mt-10) REVERT: A 124 LYS cc_start: 0.7286 (mtmm) cc_final: 0.6803 (mttm) REVERT: A 128 GLU cc_start: 0.5778 (mt-10) cc_final: 0.5511 (mt-10) REVERT: A 152 ASP cc_start: 0.6628 (OUTLIER) cc_final: 0.6309 (p0) REVERT: A 158 LYS cc_start: 0.7195 (ttmt) cc_final: 0.6582 (tttm) REVERT: A 197 ARG cc_start: 0.7906 (ptm-80) cc_final: 0.7086 (ptp90) REVERT: A 209 MET cc_start: 0.7503 (mtp) cc_final: 0.6956 (mtp) REVERT: A 248 ASP cc_start: 0.7536 (m-30) cc_final: 0.7169 (m-30) REVERT: A 342 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6199 (mt-10) REVERT: A 343 GLU cc_start: 0.6662 (mt-10) cc_final: 0.5872 (mm-30) REVERT: A 347 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6327 (tp30) REVERT: A 348 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7581 (mt-10) REVERT: A 450 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7496 (tp) REVERT: A 461 GLU cc_start: 0.7169 (tt0) cc_final: 0.6721 (pt0) REVERT: A 466 GLU cc_start: 0.6427 (mt-10) cc_final: 0.5405 (tp30) REVERT: A 538 GLU cc_start: 0.5843 (OUTLIER) cc_final: 0.5631 (tm-30) REVERT: A 546 GLU cc_start: 0.6123 (mm-30) cc_final: 0.5503 (mt-10) REVERT: A 558 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7018 (pt0) REVERT: B 114 GLU cc_start: 0.6618 (mp0) cc_final: 0.6321 (mp0) REVERT: B 128 GLU cc_start: 0.6304 (mm-30) cc_final: 0.5992 (mm-30) REVERT: B 156 ARG cc_start: 0.6592 (mtp180) cc_final: 0.6207 (ttt-90) REVERT: B 209 MET cc_start: 0.6634 (mtp) cc_final: 0.6151 (mtm) REVERT: B 271 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6185 (mp0) REVERT: B 323 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7817 (mtp) REVERT: B 348 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7027 (tt0) REVERT: B 393 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6183 (pp20) REVERT: B 460 ARG cc_start: 0.6472 (mtp85) cc_final: 0.5420 (mmm160) REVERT: B 481 ARG cc_start: 0.6054 (mmm-85) cc_final: 0.5716 (mmm-85) REVERT: B 517 LYS cc_start: 0.6481 (tttt) cc_final: 0.6146 (tppp) REVERT: C 159 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6143 (mt-10) REVERT: C 201 PRO cc_start: 0.7665 (Cg_endo) cc_final: 0.7257 (Cg_exo) REVERT: C 294 MET cc_start: 0.7514 (mtt) cc_final: 0.7275 (mtp) REVERT: C 337 ILE cc_start: 0.7483 (mm) cc_final: 0.7196 (mp) REVERT: C 342 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6881 (mt-10) REVERT: C 344 MET cc_start: 0.7587 (ttp) cc_final: 0.7237 (tpp) REVERT: C 416 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7487 (ptm160) REVERT: C 441 GLU cc_start: 0.6916 (tt0) cc_final: 0.6446 (tp30) REVERT: C 461 GLU cc_start: 0.5900 (tm-30) cc_final: 0.5487 (tm-30) REVERT: C 485 GLU cc_start: 0.6405 (mm-30) cc_final: 0.6149 (mm-30) REVERT: C 546 GLU cc_start: 0.6236 (mm-30) cc_final: 0.5766 (mp0) REVERT: C 558 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6272 (mt-10) REVERT: D 7 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6738 (mm-30) REVERT: D 209 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: D 407 ASN cc_start: 0.6340 (p0) cc_final: 0.5162 (m110) REVERT: D 410 ARG cc_start: 0.6865 (mmm-85) cc_final: 0.6633 (mtp85) REVERT: D 428 GLN cc_start: 0.7500 (mt0) cc_final: 0.7147 (mt0) REVERT: D 452 LYS cc_start: 0.6827 (mttp) cc_final: 0.6476 (mtpt) REVERT: D 466 LYS cc_start: 0.5570 (ptpp) cc_final: 0.5287 (ptmt) REVERT: E 26 ASP cc_start: 0.6647 (m-30) cc_final: 0.6216 (t70) REVERT: E 36 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7719 (ttpp) REVERT: E 128 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6521 (pt0) REVERT: E 130 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6372 (p90) REVERT: E 209 GLU cc_start: 0.6443 (mt-10) cc_final: 0.5722 (pt0) REVERT: E 243 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6021 (mt-10) REVERT: E 259 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6631 (t70) REVERT: E 265 GLU cc_start: 0.6444 (mt-10) cc_final: 0.6177 (mm-30) REVERT: E 345 ARG cc_start: 0.6581 (mmt90) cc_final: 0.6191 (mmm-85) REVERT: E 461 LYS cc_start: 0.5858 (tttt) cc_final: 0.4864 (mppt) REVERT: F 206 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7033 (mt0) REVERT: F 230 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6626 (mt-10) REVERT: F 406 GLU cc_start: 0.6235 (OUTLIER) cc_final: 0.5482 (mt-10) REVERT: F 409 ARG cc_start: 0.6863 (ttm110) cc_final: 0.6545 (ttm110) REVERT: F 437 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: F 461 LYS cc_start: 0.6913 (tttm) cc_final: 0.6581 (tttp) REVERT: G 19 ARG cc_start: 0.6763 (mtm-85) cc_final: 0.5897 (ttp-110) REVERT: G 23 LYS cc_start: 0.6549 (mttp) cc_final: 0.6299 (mtpp) REVERT: G 38 GLU cc_start: 0.6297 (tt0) cc_final: 0.6034 (tt0) REVERT: G 156 LYS cc_start: 0.6148 (tptp) cc_final: 0.5697 (tptp) REVERT: G 196 ARG cc_start: 0.6212 (mtp-110) cc_final: 0.5567 (tpp80) REVERT: H 1 MET cc_start: 0.3918 (OUTLIER) cc_final: 0.3369 (mmt) REVERT: J 121 LEU cc_start: 0.4285 (mp) cc_final: 0.3939 (mm) REVERT: J 164 GLU cc_start: 0.5142 (tt0) cc_final: 0.4616 (mp0) REVERT: J 186 LEU cc_start: 0.2869 (tt) cc_final: 0.2099 (mp) outliers start: 74 outliers final: 31 residues processed: 410 average time/residue: 1.8072 time to fit residues: 840.8213 Evaluate side-chains 402 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 355 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 416 ARG Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 140 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 204 optimal weight: 0.6980 chunk 303 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 359 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 219 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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: 0.7478 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30110 Z= 0.193 Angle : 0.542 8.751 40807 Z= 0.276 Chirality : 0.044 0.194 4576 Planarity : 0.005 0.066 5333 Dihedral : 6.309 99.308 4236 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.27 % Allowed : 14.79 % Favored : 82.94 % 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: 0.22 (0.14), residues: 3764 helix: 0.62 (0.13), residues: 1559 sheet: -0.32 (0.21), residues: 568 loop : 0.04 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 119 HIS 0.003 0.001 HIS C 185 PHE 0.015 0.001 PHE B 415 TYR 0.013 0.001 TYR C 562 ARG 0.012 0.000 ARG L 88 *********************** 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 431 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 361 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7936 (ttmt) cc_final: 0.7436 (tttm) REVERT: A 33 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6611 (mt-10) REVERT: A 124 LYS cc_start: 0.7260 (mtmm) cc_final: 0.6794 (mttm) REVERT: A 128 GLU cc_start: 0.5754 (mt-10) cc_final: 0.5478 (mt-10) REVERT: A 152 ASP cc_start: 0.6635 (OUTLIER) cc_final: 0.6284 (p0) REVERT: A 158 LYS cc_start: 0.7185 (ttmt) cc_final: 0.6552 (tttm) REVERT: A 197 ARG cc_start: 0.7863 (ptm-80) cc_final: 0.7032 (ptp90) REVERT: A 209 MET cc_start: 0.7477 (mtp) cc_final: 0.6954 (mtp) REVERT: A 248 ASP cc_start: 0.7465 (m-30) cc_final: 0.7081 (m-30) REVERT: A 342 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6233 (mt-10) REVERT: A 343 GLU cc_start: 0.6619 (mt-10) cc_final: 0.5814 (mm-30) REVERT: A 348 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7419 (mt-10) REVERT: A 393 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6589 (tm-30) REVERT: A 461 GLU cc_start: 0.7138 (tt0) cc_final: 0.6675 (pt0) REVERT: A 466 GLU cc_start: 0.6414 (mt-10) cc_final: 0.5372 (tp30) REVERT: A 485 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6393 (mm-30) REVERT: A 538 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.5701 (tm-30) REVERT: A 546 GLU cc_start: 0.6101 (mm-30) cc_final: 0.5488 (mt-10) REVERT: A 564 GLU cc_start: 0.5782 (mm-30) cc_final: 0.5489 (mm-30) REVERT: A 567 MET cc_start: 0.6540 (mmm) cc_final: 0.6318 (mmp) REVERT: B 114 GLU cc_start: 0.6624 (mp0) cc_final: 0.6349 (mp0) REVERT: B 128 GLU cc_start: 0.6270 (mm-30) cc_final: 0.5975 (mm-30) REVERT: B 156 ARG cc_start: 0.6606 (mtp180) cc_final: 0.6240 (ttt-90) REVERT: B 159 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6772 (pt0) REVERT: B 209 MET cc_start: 0.6621 (mtp) cc_final: 0.6237 (mtm) REVERT: B 271 GLU cc_start: 0.6672 (mm-30) cc_final: 0.6178 (mp0) REVERT: B 323 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7819 (mtp) REVERT: B 348 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6973 (tt0) REVERT: B 393 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6077 (pp20) REVERT: B 458 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6114 (mt) REVERT: B 460 ARG cc_start: 0.6500 (mtp85) cc_final: 0.5485 (mmm160) REVERT: B 477 GLN cc_start: 0.3715 (OUTLIER) cc_final: 0.3212 (mm110) REVERT: B 481 ARG cc_start: 0.6007 (mmm-85) cc_final: 0.5675 (mmm-85) REVERT: B 494 PHE cc_start: 0.7234 (t80) cc_final: 0.6997 (t80) REVERT: C 159 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6122 (mt-10) REVERT: C 294 MET cc_start: 0.7425 (mtt) cc_final: 0.7173 (mtp) REVERT: C 337 ILE cc_start: 0.7393 (mm) cc_final: 0.7101 (mp) REVERT: C 342 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6895 (mt-10) REVERT: C 344 MET cc_start: 0.7505 (ttp) cc_final: 0.7176 (tpp) REVERT: C 416 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7510 (ptm160) REVERT: C 441 GLU cc_start: 0.6857 (tt0) cc_final: 0.6407 (tp30) REVERT: C 485 GLU cc_start: 0.6394 (mm-30) cc_final: 0.6106 (mm-30) REVERT: C 546 GLU cc_start: 0.6232 (mm-30) cc_final: 0.5779 (mp0) REVERT: C 558 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6268 (mt-10) REVERT: D 7 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6714 (mm-30) REVERT: D 209 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: D 290 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.6956 (t70) REVERT: D 368 LYS cc_start: 0.7017 (ttpp) cc_final: 0.6537 (ptpt) REVERT: D 407 ASN cc_start: 0.6280 (p0) cc_final: 0.5165 (m110) REVERT: D 410 ARG cc_start: 0.6900 (mmm-85) cc_final: 0.6643 (mtp85) REVERT: D 428 GLN cc_start: 0.7521 (mt0) cc_final: 0.7202 (mt0) REVERT: D 452 LYS cc_start: 0.6784 (mttp) cc_final: 0.6446 (mtpt) REVERT: D 466 LYS cc_start: 0.5516 (ptpp) cc_final: 0.5249 (ptmt) REVERT: E 26 ASP cc_start: 0.6584 (m-30) cc_final: 0.6147 (t70) REVERT: E 128 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6535 (pt0) REVERT: E 130 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6341 (p90) REVERT: E 209 GLU cc_start: 0.6379 (mt-10) cc_final: 0.5623 (pt0) REVERT: E 236 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.5274 (mpt180) REVERT: E 243 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6030 (mt-10) REVERT: E 259 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6553 (t70) REVERT: E 265 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6167 (mm-30) REVERT: E 345 ARG cc_start: 0.6605 (mmt90) cc_final: 0.6231 (mmm-85) REVERT: E 446 LEU cc_start: 0.6031 (mm) cc_final: 0.5770 (mm) REVERT: E 461 LYS cc_start: 0.5744 (tttt) cc_final: 0.4787 (mppt) REVERT: F 206 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6990 (mt0) REVERT: F 406 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5788 (mm-30) REVERT: F 409 ARG cc_start: 0.6826 (ttm110) cc_final: 0.6576 (ttm110) REVERT: F 437 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: G 19 ARG cc_start: 0.6734 (mtm-85) cc_final: 0.5961 (ttp-110) REVERT: G 23 LYS cc_start: 0.6473 (mttp) cc_final: 0.6221 (mtpp) REVERT: G 38 GLU cc_start: 0.6265 (tt0) cc_final: 0.6007 (tt0) REVERT: G 156 LYS cc_start: 0.6109 (tptp) cc_final: 0.5661 (tptp) REVERT: G 196 ARG cc_start: 0.6192 (mtp-110) cc_final: 0.5574 (tpp80) REVERT: H 1 MET cc_start: 0.3695 (OUTLIER) cc_final: 0.2998 (mmm) REVERT: J 121 LEU cc_start: 0.4284 (mp) cc_final: 0.3940 (mm) REVERT: J 164 GLU cc_start: 0.5121 (tt0) cc_final: 0.4579 (mp0) REVERT: J 186 LEU cc_start: 0.2838 (tt) cc_final: 0.2142 (mp) REVERT: L 81 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.5385 (pt0) REVERT: L 88 ARG cc_start: 0.4306 (mtp-110) cc_final: 0.3893 (ptm160) REVERT: L 89 GLU cc_start: 0.3925 (pt0) cc_final: 0.3677 (pp20) outliers start: 70 outliers final: 28 residues processed: 413 average time/residue: 1.8008 time to fit residues: 845.9531 Evaluate side-chains 400 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 354 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 416 ARG Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 140 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 214 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 228 optimal weight: 0.4980 chunk 244 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 282 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 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: 0.7451 moved from start: 0.2233 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= 0.148 Angle : 0.500 8.649 40807 Z= 0.253 Chirality : 0.043 0.211 4576 Planarity : 0.004 0.050 5333 Dihedral : 5.966 100.074 4236 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.98 % Allowed : 15.44 % Favored : 82.58 % 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: 0.83 (0.14), residues: 1570 sheet: -0.27 (0.21), residues: 584 loop : 0.19 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 119 HIS 0.002 0.001 HIS E 323 PHE 0.014 0.001 PHE A 230 TYR 0.017 0.001 TYR D 13 ARG 0.011 0.000 ARG L 88 *********************** 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 433 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 372 time to evaluate : 3.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7963 (ttmt) cc_final: 0.7539 (tttm) REVERT: A 33 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6622 (mt-10) REVERT: A 124 LYS cc_start: 0.7260 (mtmm) cc_final: 0.6809 (mttm) REVERT: A 128 GLU cc_start: 0.5656 (mt-10) cc_final: 0.5444 (mt-10) REVERT: A 152 ASP cc_start: 0.6723 (OUTLIER) cc_final: 0.6395 (p0) REVERT: A 158 LYS cc_start: 0.7137 (ttmt) cc_final: 0.6531 (tttm) REVERT: A 197 ARG cc_start: 0.7882 (ptm-80) cc_final: 0.7054 (ptp90) REVERT: A 209 MET cc_start: 0.7430 (mtp) cc_final: 0.6920 (mtp) REVERT: A 239 GLN cc_start: 0.7417 (mt0) cc_final: 0.7066 (mp10) REVERT: A 248 ASP cc_start: 0.7428 (m-30) cc_final: 0.7041 (m-30) REVERT: A 257 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7048 (mm-30) REVERT: A 337 ILE cc_start: 0.7161 (mm) cc_final: 0.6959 (mm) REVERT: A 342 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6174 (mt-10) REVERT: A 343 GLU cc_start: 0.6556 (mt-10) cc_final: 0.5771 (mm-30) REVERT: A 348 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7429 (mt-10) REVERT: A 393 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6384 (pp20) REVERT: A 442 ASN cc_start: 0.7911 (m110) cc_final: 0.7700 (m-40) REVERT: A 450 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7427 (mp) REVERT: A 461 GLU cc_start: 0.7180 (tt0) cc_final: 0.6715 (pt0) REVERT: A 466 GLU cc_start: 0.6373 (mt-10) cc_final: 0.5345 (tp30) REVERT: A 546 GLU cc_start: 0.6053 (mm-30) cc_final: 0.5444 (mt-10) REVERT: A 564 GLU cc_start: 0.5743 (mm-30) cc_final: 0.5505 (mm-30) REVERT: B 114 GLU cc_start: 0.6626 (mp0) cc_final: 0.6337 (mp0) REVERT: B 128 GLU cc_start: 0.6224 (mm-30) cc_final: 0.5943 (mm-30) REVERT: B 156 ARG cc_start: 0.6582 (mtp180) cc_final: 0.6208 (ttt-90) REVERT: B 209 MET cc_start: 0.6602 (mtp) cc_final: 0.6121 (mtm) REVERT: B 220 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7384 (tpp) REVERT: B 271 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6183 (mp0) REVERT: B 323 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7805 (mtp) REVERT: B 348 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6993 (tt0) REVERT: B 393 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6074 (pp20) REVERT: B 458 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6121 (mt) REVERT: B 460 ARG cc_start: 0.6547 (mtp85) cc_final: 0.5489 (mmm160) REVERT: B 481 ARG cc_start: 0.6028 (mmm-85) cc_final: 0.5642 (mmm-85) REVERT: B 494 PHE cc_start: 0.7094 (t80) cc_final: 0.6868 (t80) REVERT: B 568 LYS cc_start: 0.4837 (mmpt) cc_final: 0.4496 (mmmt) REVERT: C 159 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6119 (mt-10) REVERT: C 294 MET cc_start: 0.7285 (mtt) cc_final: 0.7016 (mtp) REVERT: C 323 MET cc_start: 0.8356 (mmp) cc_final: 0.8029 (mmt) REVERT: C 337 ILE cc_start: 0.7418 (mm) cc_final: 0.7136 (mp) REVERT: C 342 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6865 (mt-10) REVERT: C 344 MET cc_start: 0.7445 (ttp) cc_final: 0.7160 (tpp) REVERT: C 416 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7455 (ptm160) REVERT: C 441 GLU cc_start: 0.6843 (tt0) cc_final: 0.6402 (tp30) REVERT: C 485 GLU cc_start: 0.6418 (mm-30) cc_final: 0.6179 (mm-30) REVERT: C 546 GLU cc_start: 0.6204 (mm-30) cc_final: 0.5225 (mt-10) REVERT: C 558 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6659 (mt-10) REVERT: D 7 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6745 (mm-30) REVERT: D 290 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6867 (t70) REVERT: D 316 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7575 (mtp) REVERT: D 368 LYS cc_start: 0.6982 (ttpp) cc_final: 0.6471 (ptpt) REVERT: D 407 ASN cc_start: 0.6166 (p0) cc_final: 0.5122 (m110) REVERT: D 410 ARG cc_start: 0.6901 (mmm-85) cc_final: 0.5802 (mtt90) REVERT: D 413 GLN cc_start: 0.6952 (mt0) cc_final: 0.6510 (pt0) REVERT: D 428 GLN cc_start: 0.7469 (mt0) cc_final: 0.7142 (mt0) REVERT: D 452 LYS cc_start: 0.6836 (mttp) cc_final: 0.6430 (mtpt) REVERT: D 466 LYS cc_start: 0.5663 (ptpp) cc_final: 0.5418 (ptmt) REVERT: E 26 ASP cc_start: 0.6495 (m-30) cc_final: 0.6079 (t70) REVERT: E 128 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6513 (pt0) REVERT: E 130 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6109 (p90) REVERT: E 209 GLU cc_start: 0.6374 (mt-10) cc_final: 0.5630 (pt0) REVERT: E 236 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.5256 (mpt180) REVERT: E 243 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6030 (mt-10) REVERT: E 265 GLU cc_start: 0.6356 (mt-10) cc_final: 0.6101 (mm-30) REVERT: E 345 ARG cc_start: 0.6528 (mmt90) cc_final: 0.6196 (mmm-85) REVERT: E 377 GLN cc_start: 0.5898 (mp10) cc_final: 0.5093 (mt0) REVERT: E 445 MET cc_start: 0.3753 (mmm) cc_final: 0.3153 (mtm) REVERT: E 446 LEU cc_start: 0.6177 (mm) cc_final: 0.5933 (mm) REVERT: E 461 LYS cc_start: 0.5727 (tttt) cc_final: 0.4769 (mppt) REVERT: F 206 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.6967 (mt0) REVERT: F 406 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5688 (mm-30) REVERT: F 409 ARG cc_start: 0.6751 (ttm110) cc_final: 0.6503 (ttm110) REVERT: G 19 ARG cc_start: 0.6738 (mtm-85) cc_final: 0.5973 (ttp-110) REVERT: G 23 LYS cc_start: 0.6519 (mttp) cc_final: 0.6266 (mtpp) REVERT: G 38 GLU cc_start: 0.6279 (tt0) cc_final: 0.6022 (tt0) REVERT: G 156 LYS cc_start: 0.6098 (tptp) cc_final: 0.5653 (tptp) REVERT: G 196 ARG cc_start: 0.6125 (mtp-110) cc_final: 0.5583 (tpp80) REVERT: H 1 MET cc_start: 0.3770 (OUTLIER) cc_final: 0.3040 (mmm) REVERT: J 121 LEU cc_start: 0.4323 (mp) cc_final: 0.3976 (mm) REVERT: J 164 GLU cc_start: 0.5208 (tt0) cc_final: 0.4609 (mp0) REVERT: J 186 LEU cc_start: 0.2891 (tt) cc_final: 0.2203 (mp) REVERT: L 81 GLU cc_start: 0.5723 (OUTLIER) cc_final: 0.5337 (pt0) REVERT: L 88 ARG cc_start: 0.4409 (mtp-110) cc_final: 0.4044 (ptm160) REVERT: L 89 GLU cc_start: 0.3947 (pt0) cc_final: 0.3726 (pp20) outliers start: 61 outliers final: 27 residues processed: 414 average time/residue: 1.7877 time to fit residues: 840.4526 Evaluate side-chains 394 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 352 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 416 ARG Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 140 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 5.9990 chunk 344 optimal weight: 10.0000 chunk 314 optimal weight: 10.0000 chunk 335 optimal weight: 9.9990 chunk 201 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 263 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 302 optimal weight: 7.9990 chunk 316 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 F 437 GLN G 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 30110 Z= 0.505 Angle : 0.758 10.385 40807 Z= 0.389 Chirality : 0.052 0.237 4576 Planarity : 0.007 0.067 5333 Dihedral : 6.871 103.768 4234 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 2.56 % Allowed : 15.12 % Favored : 82.32 % 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: 0.14 (0.13), residues: 1566 sheet: -0.45 (0.21), residues: 596 loop : -0.12 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 187 HIS 0.008 0.002 HIS F 249 PHE 0.019 0.003 PHE A 205 TYR 0.028 0.003 TYR C 562 ARG 0.009 0.001 ARG E 124 *********************** 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 430 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 351 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7479 (tttm) REVERT: A 33 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6591 (mt-10) REVERT: A 122 MET cc_start: 0.6971 (tpp) cc_final: 0.6704 (mpp) REVERT: A 124 LYS cc_start: 0.7170 (mtmm) cc_final: 0.6727 (mttm) REVERT: A 152 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6290 (p0) REVERT: A 158 LYS cc_start: 0.7225 (ttmt) cc_final: 0.6626 (tttm) REVERT: A 197 ARG cc_start: 0.7920 (ptm-80) cc_final: 0.7096 (ptp90) REVERT: A 209 MET cc_start: 0.7524 (mtp) cc_final: 0.7063 (mtp) REVERT: A 248 ASP cc_start: 0.7557 (m-30) cc_final: 0.7185 (m-30) REVERT: A 342 GLU cc_start: 0.6565 (mt-10) cc_final: 0.6212 (mt-10) REVERT: A 343 GLU cc_start: 0.6761 (mt-10) cc_final: 0.5918 (mm-30) REVERT: A 348 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 450 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7543 (mp) REVERT: A 461 GLU cc_start: 0.7228 (tt0) cc_final: 0.6778 (pt0) REVERT: A 466 GLU cc_start: 0.6393 (mt-10) cc_final: 0.5366 (tp30) REVERT: A 546 GLU cc_start: 0.6127 (mm-30) cc_final: 0.5474 (mt-10) REVERT: A 556 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: B 114 GLU cc_start: 0.6663 (mp0) cc_final: 0.6353 (mp0) REVERT: B 128 GLU cc_start: 0.6262 (mm-30) cc_final: 0.6033 (mm-30) REVERT: B 156 ARG cc_start: 0.6575 (mtp180) cc_final: 0.6199 (ttt-90) REVERT: B 209 MET cc_start: 0.6629 (mtp) cc_final: 0.6318 (mtm) REVERT: B 271 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6387 (mp0) REVERT: B 348 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7055 (tt0) REVERT: B 393 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6025 (pp20) REVERT: B 458 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6168 (mt) REVERT: B 460 ARG cc_start: 0.6357 (mtp85) cc_final: 0.5343 (mmm160) REVERT: B 477 GLN cc_start: 0.3837 (OUTLIER) cc_final: 0.3275 (mm110) REVERT: B 481 ARG cc_start: 0.6029 (mmm-85) cc_final: 0.5672 (mmm-85) REVERT: B 568 LYS cc_start: 0.5022 (mmpt) cc_final: 0.4652 (mmtt) REVERT: C 159 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6148 (mt-10) REVERT: C 342 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7024 (mt-10) REVERT: C 344 MET cc_start: 0.7597 (ttp) cc_final: 0.7243 (tpp) REVERT: C 416 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7516 (ptm160) REVERT: C 441 GLU cc_start: 0.6936 (tt0) cc_final: 0.6452 (tp30) REVERT: C 485 GLU cc_start: 0.6475 (mm-30) cc_final: 0.6200 (mm-30) REVERT: C 546 GLU cc_start: 0.6249 (mm-30) cc_final: 0.5769 (mp0) REVERT: C 558 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6459 (mt-10) REVERT: D 7 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6788 (mm-30) REVERT: D 368 LYS cc_start: 0.7011 (ttpp) cc_final: 0.6649 (ptpp) REVERT: D 380 ASP cc_start: 0.7105 (m-30) cc_final: 0.6901 (m-30) REVERT: D 407 ASN cc_start: 0.6516 (p0) cc_final: 0.5221 (m110) REVERT: D 410 ARG cc_start: 0.6952 (mmm-85) cc_final: 0.6667 (mtp85) REVERT: D 452 LYS cc_start: 0.6898 (mttp) cc_final: 0.6524 (mtpt) REVERT: D 466 LYS cc_start: 0.5516 (ptpp) cc_final: 0.5249 (ptmt) REVERT: E 26 ASP cc_start: 0.6626 (m-30) cc_final: 0.6192 (t70) REVERT: E 36 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7767 (ttpp) REVERT: E 128 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6539 (pt0) REVERT: E 130 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.6431 (p90) REVERT: E 209 GLU cc_start: 0.6433 (mt-10) cc_final: 0.5707 (pt0) REVERT: E 236 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.5724 (mtt180) REVERT: E 243 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6113 (mt-10) REVERT: E 265 GLU cc_start: 0.6567 (mt-10) cc_final: 0.6260 (mm-30) REVERT: E 345 ARG cc_start: 0.6649 (mmt90) cc_final: 0.6303 (mmm-85) REVERT: E 409 ARG cc_start: 0.4806 (mpp80) cc_final: 0.4178 (mmp80) REVERT: E 445 MET cc_start: 0.3700 (mmm) cc_final: 0.3154 (mtm) REVERT: E 461 LYS cc_start: 0.5829 (tttt) cc_final: 0.4772 (mppt) REVERT: F 11 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7917 (mm) REVERT: F 206 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7090 (mt0) REVERT: F 380 ASP cc_start: 0.7316 (m-30) cc_final: 0.6817 (m-30) REVERT: F 406 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5561 (mt-10) REVERT: F 409 ARG cc_start: 0.6899 (ttm110) cc_final: 0.6604 (ttm110) REVERT: G 19 ARG cc_start: 0.6742 (mtm-85) cc_final: 0.5853 (ttp-110) REVERT: G 23 LYS cc_start: 0.6730 (mttp) cc_final: 0.6474 (mtpp) REVERT: G 38 GLU cc_start: 0.6274 (tt0) cc_final: 0.6040 (tt0) REVERT: G 156 LYS cc_start: 0.6114 (tptp) cc_final: 0.5637 (tptp) REVERT: J 121 LEU cc_start: 0.4334 (mp) cc_final: 0.4007 (mm) REVERT: J 164 GLU cc_start: 0.5172 (tt0) cc_final: 0.4583 (mp0) REVERT: J 186 LEU cc_start: 0.2851 (tt) cc_final: 0.2015 (mp) REVERT: L 81 GLU cc_start: 0.5590 (OUTLIER) cc_final: 0.5213 (pt0) REVERT: L 176 ASP cc_start: 0.5148 (OUTLIER) cc_final: 0.4721 (t70) outliers start: 79 outliers final: 32 residues processed: 405 average time/residue: 1.8361 time to fit residues: 847.2571 Evaluate side-chains 384 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 337 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 416 ARG Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 176 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 1.9990 chunk 354 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 371 optimal weight: 20.0000 chunk 342 optimal weight: 5.9990 chunk 295 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 181 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN D 170 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30110 Z= 0.181 Angle : 0.548 9.028 40807 Z= 0.280 Chirality : 0.044 0.228 4576 Planarity : 0.005 0.052 5333 Dihedral : 6.331 99.177 4234 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.43 % Allowed : 16.32 % Favored : 82.26 % 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: 0.62 (0.13), residues: 1566 sheet: -0.38 (0.21), residues: 570 loop : -0.01 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 119 HIS 0.003 0.001 HIS F 249 PHE 0.015 0.001 PHE B 415 TYR 0.017 0.001 TYR F 203 ARG 0.009 0.000 ARG L 88 ********************** 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 391 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 347 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7492 (tttm) REVERT: A 33 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6544 (mt-10) REVERT: A 124 LYS cc_start: 0.7207 (mtmm) cc_final: 0.6762 (mttm) REVERT: A 152 ASP cc_start: 0.6601 (OUTLIER) cc_final: 0.6264 (p0) REVERT: A 158 LYS cc_start: 0.7265 (ttmt) cc_final: 0.6637 (tttm) REVERT: A 197 ARG cc_start: 0.7895 (ptm-80) cc_final: 0.7041 (ptp90) REVERT: A 209 MET cc_start: 0.7483 (mtp) cc_final: 0.6938 (mtp) REVERT: A 248 ASP cc_start: 0.7436 (m-30) cc_final: 0.7054 (m-30) REVERT: A 342 GLU cc_start: 0.6607 (mt-10) cc_final: 0.6194 (mt-10) REVERT: A 343 GLU cc_start: 0.6631 (mt-10) cc_final: 0.5818 (mm-30) REVERT: A 348 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7512 (mt-10) REVERT: A 393 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6533 (tm-30) REVERT: A 450 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7402 (mp) REVERT: A 461 GLU cc_start: 0.7125 (tt0) cc_final: 0.6669 (pt0) REVERT: A 466 GLU cc_start: 0.6365 (mt-10) cc_final: 0.5353 (tp30) REVERT: A 491 ARG cc_start: 0.6825 (mtm110) cc_final: 0.6599 (mtm110) REVERT: A 546 GLU cc_start: 0.6119 (mm-30) cc_final: 0.5498 (mt-10) REVERT: A 564 GLU cc_start: 0.5750 (mm-30) cc_final: 0.5461 (mm-30) REVERT: B 114 GLU cc_start: 0.6619 (mp0) cc_final: 0.6322 (mp0) REVERT: B 128 GLU cc_start: 0.6278 (mm-30) cc_final: 0.5974 (mm-30) REVERT: B 156 ARG cc_start: 0.6579 (mtp180) cc_final: 0.6127 (ttt180) REVERT: B 209 MET cc_start: 0.6578 (mtp) cc_final: 0.6228 (mtm) REVERT: B 271 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6199 (mp0) REVERT: B 323 MET cc_start: 0.8110 (mtp) cc_final: 0.7761 (mtp) REVERT: B 348 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6971 (tt0) REVERT: B 393 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.5949 (pp20) REVERT: B 458 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6112 (mt) REVERT: B 460 ARG cc_start: 0.6437 (mtp85) cc_final: 0.5464 (mmm160) REVERT: B 481 ARG cc_start: 0.6003 (mmm-85) cc_final: 0.5719 (mmm-85) REVERT: B 494 PHE cc_start: 0.7166 (t80) cc_final: 0.6958 (t80) REVERT: C 159 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6112 (mt-10) REVERT: C 337 ILE cc_start: 0.7495 (mm) cc_final: 0.7201 (mp) REVERT: C 342 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6941 (mt-10) REVERT: C 344 MET cc_start: 0.7482 (ttp) cc_final: 0.7141 (tpp) REVERT: C 416 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7519 (ptm160) REVERT: C 441 GLU cc_start: 0.6884 (tt0) cc_final: 0.6409 (tp30) REVERT: C 485 GLU cc_start: 0.6354 (mm-30) cc_final: 0.6104 (mm-30) REVERT: C 546 GLU cc_start: 0.6147 (mm-30) cc_final: 0.5689 (mp0) REVERT: C 558 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6446 (pt0) REVERT: D 7 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6682 (mm-30) REVERT: D 407 ASN cc_start: 0.6284 (p0) cc_final: 0.5133 (m110) REVERT: D 452 LYS cc_start: 0.6857 (mttp) cc_final: 0.6506 (mtpt) REVERT: D 466 LYS cc_start: 0.5513 (ptpp) cc_final: 0.5281 (ptmt) REVERT: E 26 ASP cc_start: 0.6568 (m-30) cc_final: 0.6131 (t70) REVERT: E 128 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6513 (pt0) REVERT: E 130 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6321 (p90) REVERT: E 209 GLU cc_start: 0.6382 (mt-10) cc_final: 0.5621 (pt0) REVERT: E 236 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.5283 (mpt180) REVERT: E 243 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6033 (mt-10) REVERT: E 265 GLU cc_start: 0.6449 (mt-10) cc_final: 0.6198 (mm-30) REVERT: E 345 ARG cc_start: 0.6569 (mmt90) cc_final: 0.6274 (mmm-85) REVERT: E 461 LYS cc_start: 0.5717 (tttt) cc_final: 0.4799 (mppt) REVERT: F 34 ASP cc_start: 0.7441 (m-30) cc_final: 0.6907 (m-30) REVERT: F 206 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7048 (mt0) REVERT: F 406 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5683 (mm-30) REVERT: F 409 ARG cc_start: 0.6842 (ttm110) cc_final: 0.6601 (ttm110) REVERT: G 19 ARG cc_start: 0.6731 (mtm-85) cc_final: 0.5967 (ttp-110) REVERT: G 23 LYS cc_start: 0.6617 (mttp) cc_final: 0.6348 (mtpp) REVERT: G 38 GLU cc_start: 0.6263 (tt0) cc_final: 0.6000 (tt0) REVERT: G 156 LYS cc_start: 0.6125 (tptp) cc_final: 0.5672 (tptp) REVERT: G 196 ARG cc_start: 0.6204 (mtp-110) cc_final: 0.5737 (tpp80) REVERT: J 121 LEU cc_start: 0.4270 (mp) cc_final: 0.3933 (mm) REVERT: J 164 GLU cc_start: 0.5214 (tt0) cc_final: 0.4625 (mp0) REVERT: J 186 LEU cc_start: 0.2845 (tt) cc_final: 0.2110 (mp) REVERT: L 81 GLU cc_start: 0.5792 (OUTLIER) cc_final: 0.5401 (pt0) REVERT: L 88 ARG cc_start: 0.4321 (mtp-110) cc_final: 0.4006 (ptm160) REVERT: L 89 GLU cc_start: 0.3860 (pt0) cc_final: 0.3573 (pp20) outliers start: 44 outliers final: 24 residues processed: 381 average time/residue: 1.8603 time to fit residues: 813.8919 Evaluate side-chains 381 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 347 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 416 ARG Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 6.9990 chunk 315 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 296 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 304 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 54 optimal weight: 0.6980 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN E 166 GLN ** E 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.154811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121175 restraints weight = 36496.413| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.59 r_work: 0.3243 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 30110 Z= 0.336 Angle : 0.646 9.042 40807 Z= 0.330 Chirality : 0.048 0.233 4576 Planarity : 0.006 0.063 5333 Dihedral : 6.605 101.126 4234 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.62 % Allowed : 16.25 % Favored : 82.13 % 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: 0.37 (0.13), residues: 1565 sheet: -0.47 (0.21), residues: 588 loop : -0.08 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 187 HIS 0.005 0.001 HIS F 249 PHE 0.018 0.002 PHE C 559 TYR 0.022 0.002 TYR C 562 ARG 0.008 0.001 ARG G 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12775.79 seconds wall clock time: 224 minutes 43.81 seconds (13483.81 seconds total)