Starting phenix.real_space_refine on Wed Feb 21 03:48:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7van_31853/02_2024/7van_31853_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7van_31853/02_2024/7van_31853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7van_31853/02_2024/7van_31853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7van_31853/02_2024/7van_31853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7van_31853/02_2024/7van_31853_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7van_31853/02_2024/7van_31853_updated.pdb" } resolution = 3.0 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= 0.009 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 9 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 525": "OE1" <-> "OE2" Residue "D GLU 265": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29558 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.07, per 1000 atoms: 0.51 Number of scatterers: 29558 At special positions: 0 Unit cell: (147.84, 139.92, 177.76, 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 103 16.00 P 9 15.00 Mg 2 11.99 O 5578 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=0, symmetry=0 Time building additional restraints: 11.39 Conformation dependent library (CDL) restraints added in 5.7 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 135 helices and 36 sheets defined 42.6% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.59 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 259 through 271 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 315 removed outlier: 3.512A 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: 4.328A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 364 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.769A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) 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: 3.911A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.734A 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 532 Processing helix chain 'A' and resid 536 through 541 removed outlier: 4.670A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 4.830A pdb=" N ARG A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.881A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.569A pdb=" N PHE B 269 " --> pdb=" O VAL B 265 " (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 315 removed outlier: 4.969A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 354 through 364 removed outlier: 4.256A 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 416 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 470 removed outlier: 3.689A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 478 through 493 Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 536 through 541 removed outlier: 4.277A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 550 Processing helix chain 'B' and resid 559 through 576 removed outlier: 3.567A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 259 through 271 removed outlier: 3.517A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) 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: 3.903A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.956A 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 401 removed outlier: 3.572A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 433 through 442 Proline residue: C 437 - end of helix Processing helix chain 'C' and resid 447 through 470 removed outlier: 4.119A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 509 through 531 Processing helix chain 'C' and resid 536 through 540 Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 559 through 577 removed outlier: 3.570A pdb=" N GLN C 571 " --> pdb=" O MET C 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 213 through 216 removed outlier: 3.585A pdb=" N ARG D 216 " --> pdb=" O ALA D 213 " (cutoff:3.500A) No H-bonds generated for '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 274 removed outlier: 3.504A pdb=" N ARG D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) 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: 4.471A pdb=" N ARG D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 removed outlier: 3.741A pdb=" N ILE D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) 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: 4.031A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.326A 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: 3.760A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'D' and resid 467 through 473 removed outlier: 3.712A pdb=" N TRP D 471 " --> pdb=" O GLU D 468 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY D 472 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.797A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 274 Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.622A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.866A 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 330 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 375 through 399 removed outlier: 3.963A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 403 No H-bonds generated for 'chain 'E' and resid 401 through 403' Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 445 removed outlier: 3.867A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 462 Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 229 through 249 removed outlier: 3.708A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.532A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.209A 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 287 through 297 removed outlier: 3.680A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 362 through 365 No H-bonds generated for 'chain 'F' and resid 362 through 365' Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.529A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 421 Processing helix chain 'F' and resid 432 through 445 removed outlier: 3.999A 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 'G' and resid 8 through 70 removed outlier: 3.811A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 123 through 208 removed outlier: 3.894A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 7 through 15 Processing helix chain 'H' and resid 26 through 38 removed outlier: 3.823A pdb=" N LEU H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 63 removed outlier: 5.878A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 82 removed outlier: 4.269A pdb=" N GLN H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 78 through 82' Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'I' and resid 82 through 118 removed outlier: 4.097A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 92 Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 100 through 114 Processing helix chain 'J' and resid 125 through 138 Proline residue: J 129 - end of helix removed outlier: 3.813A pdb=" N GLU J 132 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA J 133 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.797A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 3.847A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 96 removed outlier: 3.549A pdb=" N GLU L 92 " --> pdb=" O ARG L 88 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA L 93 " --> pdb=" O GLU L 89 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Proline residue: L 95 - end of helix Processing helix chain 'L' and resid 98 through 114 Proline residue: L 101 - end of helix Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 5.313A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 4.916A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 6.538A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 Processing sheet with id= C, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.931A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 249 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.705A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 197 through 199 removed outlier: 4.648A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 157 through 160 removed outlier: 7.119A 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: 6.519A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.754A 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: 8.579A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASP B 325 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 253 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 366 through 369 Processing sheet with id= L, first strand: chain 'B' and resid 134 through 140 removed outlier: 6.820A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.938A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 2 through 5 removed outlier: 4.290A pdb=" N ILE C 2 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.599A 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: 3.958A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 117 through 119 removed outlier: 3.511A 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: 3.579A pdb=" N ARG C 197 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 4.534A 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: 6.748A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.520A 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: 6.882A 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: 6.312A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.602A 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 removed outlier: 3.758A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.848A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N MET D 194 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.826A 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: 6.610A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU E 77 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.650A 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 91 through 93 removed outlier: 3.988A pdb=" N ARG E 91 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= AC, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.453A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.488A 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 91 through 94 removed outlier: 3.650A pdb=" N ARG F 91 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AG, first strand: chain 'G' and resid 91 through 96 Processing sheet with id= AH, first strand: chain 'H' and resid 19 through 22 removed outlier: 3.624A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.175A 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: 3.540A pdb=" N ALA J 120 " --> pdb=" O VAL J 155 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 141 through 144 1220 hydrogen bonds defined for protein. 3321 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.57 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: 1.22 - 1.34: 9958 1.34 - 1.46: 4411 1.46 - 1.57: 15542 1.57 - 1.69: 9 1.69 - 1.81: 194 Bond restraints: 30114 Sorted by residual: bond pdb=" O1 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.565 1.444 0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" O2 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.567 1.467 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O4 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.568 1.482 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" O3 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.569 1.485 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" O3B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.432 0.078 2.00e-02 2.50e+03 1.54e+01 ... (remaining 30109 not shown) Histogram of bond angle deviations from ideal: 92.65 - 102.11: 116 102.11 - 111.56: 14017 111.56 - 121.01: 18276 121.01 - 130.46: 8314 130.46 - 139.92: 90 Bond angle restraints: 40813 Sorted by residual: angle pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" O3B ADP A 601 " ideal model delta sigma weight residual 108.20 92.65 15.55 3.00e+00 1.11e-01 2.69e+01 angle pdb=" C THR E 371 " pdb=" CA THR E 371 " pdb=" CB THR E 371 " ideal model delta sigma weight residual 117.23 110.24 6.99 1.36e+00 5.41e-01 2.64e+01 angle pdb=" CA THR E 371 " pdb=" C THR E 371 " pdb=" N ARG E 372 " ideal model delta sigma weight residual 119.98 117.47 2.51 8.50e-01 1.38e+00 8.73e+00 angle pdb=" N GLY C 82 " pdb=" CA GLY C 82 " pdb=" C GLY C 82 " ideal model delta sigma weight residual 111.18 115.67 -4.49 1.54e+00 4.22e-01 8.50e+00 angle pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" N9 ADP A 601 " ideal model delta sigma weight residual 109.47 100.90 8.57 3.00e+00 1.11e-01 8.16e+00 ... (remaining 40808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.16: 17549 25.16 - 50.31: 733 50.31 - 75.47: 75 75.47 - 100.63: 24 100.63 - 125.78: 2 Dihedral angle restraints: 18383 sinusoidal: 7561 harmonic: 10822 Sorted by residual: dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual 300.00 174.22 125.78 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 -167.00 107.00 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" O2A ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PA ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 29.56 -89.56 1 2.00e+01 2.50e-03 2.38e+01 ... (remaining 18380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3425 0.048 - 0.095: 882 0.095 - 0.143: 256 0.143 - 0.191: 7 0.191 - 0.238: 2 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CB ILE C 83 " pdb=" CA ILE C 83 " pdb=" CG1 ILE C 83 " pdb=" CG2 ILE C 83 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C1' ADP A 601 " pdb=" C2' ADP A 601 " pdb=" N9 ADP A 601 " pdb=" O4' ADP A 601 " both_signs ideal model delta sigma weight residual False 2.48 2.69 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" C3' ADP A 601 " pdb=" O2' ADP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.33 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP A 601 " 0.023 2.00e-02 2.50e+03 1.06e-02 3.08e+00 pdb=" C2 ADP A 601 " -0.006 2.00e-02 2.50e+03 pdb=" C4 ADP A 601 " -0.001 2.00e-02 2.50e+03 pdb=" C5 ADP A 601 " 0.004 2.00e-02 2.50e+03 pdb=" C6 ADP A 601 " 0.012 2.00e-02 2.50e+03 pdb=" C8 ADP A 601 " -0.010 2.00e-02 2.50e+03 pdb=" N1 ADP A 601 " -0.004 2.00e-02 2.50e+03 pdb=" N3 ADP A 601 " -0.002 2.00e-02 2.50e+03 pdb=" N6 ADP A 601 " 0.004 2.00e-02 2.50e+03 pdb=" N7 ADP A 601 " -0.002 2.00e-02 2.50e+03 pdb=" N9 ADP A 601 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 323 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO D 324 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 324 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 324 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 393 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 394 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 394 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 394 " 0.021 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 90 2.51 - 3.11: 21287 3.11 - 3.70: 44173 3.70 - 4.30: 63968 4.30 - 4.90: 110129 Nonbonded interactions: 239647 Sorted by model distance: nonbonded pdb="MG MG A 602 " pdb=" O4 PO4 A 603 " model vdw 1.909 2.170 nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 1.966 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.969 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 2.062 2.170 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 2.077 2.440 ... (remaining 239642 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 7.970 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 79.600 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.240 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:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 30114 Z= 0.351 Angle : 0.585 15.546 40813 Z= 0.307 Chirality : 0.045 0.238 4572 Planarity : 0.004 0.043 5333 Dihedral : 13.652 125.781 11465 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.14), residues: 3764 helix: 1.95 (0.14), residues: 1544 sheet: 0.19 (0.23), residues: 561 loop : 0.18 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 175 HIS 0.004 0.001 HIS F 249 PHE 0.025 0.002 PHE G 40 TYR 0.010 0.001 TYR B 304 ARG 0.005 0.000 ARG A 401 *********************** 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 557 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 3.752 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5130 (mmt) cc_final: 0.4629 (mtp) REVERT: A 3 GLN cc_start: 0.7368 (mt0) cc_final: 0.6981 (tt0) REVERT: A 32 GLU cc_start: 0.6359 (mm-30) cc_final: 0.6019 (mt-10) REVERT: A 33 GLU cc_start: 0.7060 (tt0) cc_final: 0.6419 (mp0) REVERT: A 109 HIS cc_start: 0.6946 (m-70) cc_final: 0.6673 (m-70) REVERT: A 114 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6492 (mm-30) REVERT: A 122 MET cc_start: 0.6686 (mtp) cc_final: 0.6271 (mtt) REVERT: A 124 LYS cc_start: 0.6344 (mtmm) cc_final: 0.5902 (mttm) REVERT: A 128 GLU cc_start: 0.6170 (tp30) cc_final: 0.5435 (pt0) REVERT: A 137 THR cc_start: 0.8173 (m) cc_final: 0.7862 (p) REVERT: A 154 ARG cc_start: 0.6354 (mtp85) cc_final: 0.6035 (mtt90) REVERT: A 197 ARG cc_start: 0.7098 (ttp-110) cc_final: 0.6640 (ttp80) REVERT: A 209 MET cc_start: 0.6752 (mtp) cc_final: 0.6345 (mtp) REVERT: A 220 MET cc_start: 0.6962 (tpt) cc_final: 0.6579 (tpt) REVERT: A 276 LYS cc_start: 0.4794 (ptmt) cc_final: 0.4208 (ttpt) REVERT: A 277 THR cc_start: 0.7523 (m) cc_final: 0.7220 (p) REVERT: A 332 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6300 (mt-10) REVERT: A 410 ASP cc_start: 0.6068 (t0) cc_final: 0.5644 (t0) REVERT: A 441 GLU cc_start: 0.6485 (mm-30) cc_final: 0.6147 (mm-30) REVERT: A 469 GLN cc_start: 0.6122 (mt0) cc_final: 0.5615 (mm110) REVERT: A 476 LEU cc_start: 0.7559 (mt) cc_final: 0.7294 (mm) REVERT: A 491 ARG cc_start: 0.6049 (mmt180) cc_final: 0.5096 (mtm110) REVERT: A 493 ASP cc_start: 0.6889 (m-30) cc_final: 0.6450 (t70) REVERT: A 496 GLN cc_start: 0.7541 (tt0) cc_final: 0.7055 (tt0) REVERT: A 507 CYS cc_start: 0.7243 (t) cc_final: 0.6967 (p) REVERT: A 508 SER cc_start: 0.7993 (t) cc_final: 0.7406 (p) REVERT: A 524 LYS cc_start: 0.6643 (mtpp) cc_final: 0.6315 (ttpp) REVERT: A 527 GLU cc_start: 0.6276 (tt0) cc_final: 0.5542 (tp30) REVERT: A 546 GLU cc_start: 0.5654 (pp20) cc_final: 0.5407 (mm-30) REVERT: B 1 MET cc_start: 0.5883 (mtp) cc_final: 0.5642 (mtm) REVERT: B 2 ILE cc_start: 0.8134 (mm) cc_final: 0.7707 (mm) REVERT: B 33 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6420 (mt-10) REVERT: B 41 ARG cc_start: 0.7882 (ttp-110) cc_final: 0.7588 (ttp80) REVERT: B 53 GLU cc_start: 0.6557 (mp0) cc_final: 0.6331 (mp0) REVERT: B 79 MET cc_start: 0.8590 (mtm) cc_final: 0.8277 (mtm) REVERT: B 92 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6261 (mm-30) REVERT: B 106 VAL cc_start: 0.6982 (p) cc_final: 0.6610 (m) REVERT: B 114 GLU cc_start: 0.6633 (mm-30) cc_final: 0.6303 (mt-10) REVERT: B 137 THR cc_start: 0.8124 (p) cc_final: 0.7794 (t) REVERT: B 154 ARG cc_start: 0.6385 (mtp-110) cc_final: 0.5988 (mtp85) REVERT: B 156 ARG cc_start: 0.6717 (ttm170) cc_final: 0.6304 (mtp85) REVERT: B 159 GLU cc_start: 0.6200 (tm-30) cc_final: 0.5861 (tm-30) REVERT: B 180 GLU cc_start: 0.6369 (mt-10) cc_final: 0.6069 (pt0) REVERT: B 243 LYS cc_start: 0.5634 (mtmt) cc_final: 0.5231 (tttm) REVERT: B 273 THR cc_start: 0.7210 (p) cc_final: 0.6979 (t) REVERT: B 348 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7075 (mt-10) REVERT: B 408 ARG cc_start: 0.6641 (ttm170) cc_final: 0.6313 (tpp80) REVERT: B 516 MET cc_start: 0.4678 (mtm) cc_final: 0.4340 (mtp) REVERT: B 565 GLU cc_start: 0.5062 (mm-30) cc_final: 0.4712 (tp30) REVERT: C 122 MET cc_start: 0.7502 (mtm) cc_final: 0.7143 (mtp) REVERT: C 124 LYS cc_start: 0.7464 (mtmm) cc_final: 0.6509 (mptt) REVERT: C 128 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7075 (mm-30) REVERT: C 138 VAL cc_start: 0.7291 (t) cc_final: 0.7008 (m) REVERT: C 158 LYS cc_start: 0.7471 (ttpp) cc_final: 0.7183 (ttmm) REVERT: C 169 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6968 (tp30) REVERT: C 170 GLU cc_start: 0.6845 (tp30) cc_final: 0.6367 (mm-30) REVERT: C 182 LYS cc_start: 0.7134 (mtmt) cc_final: 0.6813 (mtmt) REVERT: C 197 ARG cc_start: 0.7169 (ttp-110) cc_final: 0.6605 (ttp-170) REVERT: C 209 MET cc_start: 0.7654 (mtp) cc_final: 0.7107 (mtp) REVERT: C 336 GLU cc_start: 0.5756 (tp30) cc_final: 0.5355 (tp30) REVERT: C 339 SER cc_start: 0.7848 (t) cc_final: 0.7496 (p) REVERT: C 347 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6860 (mt-10) REVERT: C 449 GLU cc_start: 0.6858 (mp0) cc_final: 0.6341 (mp0) REVERT: C 456 GLU cc_start: 0.6449 (mm-30) cc_final: 0.6060 (tm-30) REVERT: C 461 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6480 (tm-30) REVERT: C 480 GLU cc_start: 0.6653 (mp0) cc_final: 0.6180 (mp0) REVERT: C 488 ARG cc_start: 0.7101 (ttp-110) cc_final: 0.6745 (ttp-170) REVERT: C 527 GLU cc_start: 0.5858 (tt0) cc_final: 0.5495 (mm-30) REVERT: C 558 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6288 (tm-30) REVERT: C 565 GLU cc_start: 0.6133 (mm-30) cc_final: 0.5918 (mt-10) REVERT: D 6 LYS cc_start: 0.7155 (tttp) cc_final: 0.6837 (tppt) REVERT: D 34 ASP cc_start: 0.6552 (m-30) cc_final: 0.6324 (t0) REVERT: D 46 GLN cc_start: 0.8522 (tt0) cc_final: 0.8232 (tt0) REVERT: D 210 ARG cc_start: 0.7286 (ptt90) cc_final: 0.6970 (ptt90) REVERT: D 274 ARG cc_start: 0.7119 (mtt180) cc_final: 0.6833 (mtt180) REVERT: D 302 GLU cc_start: 0.7072 (tt0) cc_final: 0.6358 (tp30) REVERT: D 316 MET cc_start: 0.7433 (mtm) cc_final: 0.7143 (mtm) REVERT: D 342 GLU cc_start: 0.6531 (tt0) cc_final: 0.6298 (mp0) REVERT: D 373 GLU cc_start: 0.6728 (pm20) cc_final: 0.6477 (pm20) REVERT: D 380 ASP cc_start: 0.6896 (m-30) cc_final: 0.6638 (m-30) REVERT: D 410 ARG cc_start: 0.6401 (ttm170) cc_final: 0.5803 (ttt90) REVERT: D 413 GLN cc_start: 0.6231 (mt0) cc_final: 0.5904 (mm-40) REVERT: D 416 ASP cc_start: 0.6496 (m-30) cc_final: 0.5804 (t70) REVERT: D 420 ARG cc_start: 0.6960 (mtp180) cc_final: 0.6313 (mmt180) REVERT: D 452 LYS cc_start: 0.5851 (mmtp) cc_final: 0.5491 (mmmt) REVERT: D 456 LYS cc_start: 0.6084 (tppt) cc_final: 0.5633 (mmpt) REVERT: E 6 LYS cc_start: 0.6156 (tttt) cc_final: 0.5722 (ttpt) REVERT: E 25 LYS cc_start: 0.6837 (mtmt) cc_final: 0.6622 (mppt) REVERT: E 41 ARG cc_start: 0.6705 (ttt180) cc_final: 0.6474 (ttt-90) REVERT: E 49 GLU cc_start: 0.7456 (tt0) cc_final: 0.7211 (tt0) REVERT: E 88 MET cc_start: 0.7600 (mtp) cc_final: 0.7207 (mtp) REVERT: E 98 LYS cc_start: 0.6691 (mmmt) cc_final: 0.5443 (ttpp) REVERT: E 129 GLN cc_start: 0.7268 (mm110) cc_final: 0.7028 (mm-40) REVERT: E 194 MET cc_start: 0.8410 (mtm) cc_final: 0.8157 (mtm) REVERT: E 206 GLN cc_start: 0.6205 (pt0) cc_final: 0.5651 (mt0) REVERT: E 228 THR cc_start: 0.8514 (t) cc_final: 0.8175 (m) REVERT: E 260 MET cc_start: 0.6662 (mmm) cc_final: 0.6437 (mmm) REVERT: E 302 GLU cc_start: 0.7415 (tt0) cc_final: 0.7128 (tp30) REVERT: E 410 ARG cc_start: 0.6824 (tpp80) cc_final: 0.6485 (tpp80) REVERT: E 413 GLN cc_start: 0.6923 (mt0) cc_final: 0.6316 (mp-120) REVERT: E 420 ARG cc_start: 0.6917 (mtm110) cc_final: 0.6672 (mtp-110) REVERT: E 427 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7231 (mm110) REVERT: E 428 GLN cc_start: 0.6837 (tt0) cc_final: 0.6562 (mt0) REVERT: F 5 LYS cc_start: 0.5310 (ttpt) cc_final: 0.4785 (tttt) REVERT: F 8 TYR cc_start: 0.7118 (m-80) cc_final: 0.6856 (m-80) REVERT: F 23 ASN cc_start: 0.7416 (m110) cc_final: 0.7116 (t0) REVERT: F 26 ASP cc_start: 0.6473 (m-30) cc_final: 0.6216 (m-30) REVERT: F 52 GLU cc_start: 0.7238 (mt-10) cc_final: 0.7024 (mt-10) REVERT: F 53 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6854 (mt-10) REVERT: F 79 VAL cc_start: 0.6695 (t) cc_final: 0.6454 (p) REVERT: F 98 LYS cc_start: 0.7202 (mmtt) cc_final: 0.6398 (mmmt) REVERT: F 206 GLN cc_start: 0.6486 (mt0) cc_final: 0.5955 (tm-30) REVERT: F 280 ARG cc_start: 0.7190 (mtt180) cc_final: 0.6889 (mmt90) REVERT: F 305 LYS cc_start: 0.7527 (mmtm) cc_final: 0.7220 (mmmt) REVERT: F 316 MET cc_start: 0.8145 (mtm) cc_final: 0.7896 (mtm) REVERT: F 368 LYS cc_start: 0.7173 (ttpt) cc_final: 0.6914 (ttpp) REVERT: F 376 LYS cc_start: 0.6529 (tptm) cc_final: 0.6309 (mttt) REVERT: F 380 ASP cc_start: 0.6184 (m-30) cc_final: 0.5962 (m-30) REVERT: F 394 LYS cc_start: 0.6739 (mmtm) cc_final: 0.6437 (mttp) REVERT: F 398 ILE cc_start: 0.6746 (mt) cc_final: 0.6144 (tp) REVERT: F 452 LYS cc_start: 0.7314 (mmtp) cc_final: 0.6764 (mtpt) REVERT: F 456 LYS cc_start: 0.6181 (mttt) cc_final: 0.5942 (mmtp) REVERT: G 19 ARG cc_start: 0.5454 (mtm-85) cc_final: 0.5026 (ttp-110) REVERT: G 181 GLN cc_start: 0.6787 (mm-40) cc_final: 0.5627 (mt0) REVERT: G 196 ARG cc_start: 0.6235 (mtp-110) cc_final: 0.5829 (mtt180) REVERT: G 202 GLU cc_start: 0.5541 (mm-30) cc_final: 0.4823 (tm-30) REVERT: L 102 GLU cc_start: 0.3850 (tp30) cc_final: 0.3584 (tm-30) REVERT: L 167 LEU cc_start: 0.4400 (mt) cc_final: 0.4168 (tt) outliers start: 0 outliers final: 1 residues processed: 557 average time/residue: 1.8596 time to fit residues: 1169.7068 Evaluate side-chains 363 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 362 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 484 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 20.0000 chunk 282 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 292 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 338 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 316 GLN D 198 GLN D 323 HIS D 338 GLN E 364 ASN F 388 ASN F 437 GLN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30114 Z= 0.340 Angle : 0.661 9.674 40813 Z= 0.342 Chirality : 0.048 0.183 4572 Planarity : 0.006 0.065 5333 Dihedral : 6.879 120.476 4261 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.47 % Allowed : 8.60 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3764 helix: 1.11 (0.13), residues: 1571 sheet: 0.18 (0.22), residues: 565 loop : -0.14 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 175 HIS 0.012 0.002 HIS E 252 PHE 0.025 0.002 PHE A 230 TYR 0.020 0.002 TYR B 101 ARG 0.008 0.001 ARG A 408 *********************** 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 470 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 394 time to evaluate : 3.606 Fit side-chains REVERT: A 1 MET cc_start: 0.4845 (mmt) cc_final: 0.4549 (mtp) REVERT: A 3 GLN cc_start: 0.7293 (mt0) cc_final: 0.6888 (tt0) REVERT: A 32 GLU cc_start: 0.6593 (mm-30) cc_final: 0.6162 (mt-10) REVERT: A 33 GLU cc_start: 0.7006 (tt0) cc_final: 0.6298 (mp0) REVERT: A 109 HIS cc_start: 0.7168 (m-70) cc_final: 0.6834 (m-70) REVERT: A 114 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6663 (mm-30) REVERT: A 122 MET cc_start: 0.6768 (mtp) cc_final: 0.6294 (mtt) REVERT: A 124 LYS cc_start: 0.6302 (mtmm) cc_final: 0.5818 (mttp) REVERT: A 128 GLU cc_start: 0.6374 (tp30) cc_final: 0.5667 (pt0) REVERT: A 154 ARG cc_start: 0.6477 (mtp85) cc_final: 0.6069 (mtt90) REVERT: A 197 ARG cc_start: 0.6840 (ttp-110) cc_final: 0.6364 (ttp80) REVERT: A 220 MET cc_start: 0.6744 (tpt) cc_final: 0.6407 (tpt) REVERT: A 276 LYS cc_start: 0.4833 (ptmt) cc_final: 0.3954 (pptt) REVERT: A 277 THR cc_start: 0.7750 (m) cc_final: 0.7080 (p) REVERT: A 410 ASP cc_start: 0.6081 (t0) cc_final: 0.5585 (t0) REVERT: A 441 GLU cc_start: 0.6455 (mm-30) cc_final: 0.6032 (mm-30) REVERT: A 469 GLN cc_start: 0.5977 (mt0) cc_final: 0.5430 (mm110) REVERT: A 476 LEU cc_start: 0.7494 (mt) cc_final: 0.7292 (mm) REVERT: A 491 ARG cc_start: 0.6140 (mmt180) cc_final: 0.5146 (mtm110) REVERT: A 496 GLN cc_start: 0.7490 (tt0) cc_final: 0.7080 (tt0) REVERT: A 527 GLU cc_start: 0.6076 (tt0) cc_final: 0.5454 (tp30) REVERT: A 546 GLU cc_start: 0.5681 (pp20) cc_final: 0.5448 (mm-30) REVERT: B 2 ILE cc_start: 0.8089 (mm) cc_final: 0.7691 (mm) REVERT: B 29 LYS cc_start: 0.7471 (mtpt) cc_final: 0.7038 (mtmm) REVERT: B 53 GLU cc_start: 0.6711 (mp0) cc_final: 0.6480 (mt-10) REVERT: B 79 MET cc_start: 0.8580 (mtm) cc_final: 0.8252 (mtm) REVERT: B 92 GLU cc_start: 0.6710 (mm-30) cc_final: 0.6412 (mm-30) REVERT: B 104 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6095 (ptp-170) REVERT: B 106 VAL cc_start: 0.7085 (p) cc_final: 0.6677 (m) REVERT: B 114 GLU cc_start: 0.6559 (mm-30) cc_final: 0.6193 (mt-10) REVERT: B 137 THR cc_start: 0.8139 (p) cc_final: 0.7888 (t) REVERT: B 156 ARG cc_start: 0.6650 (ttm170) cc_final: 0.6178 (mtp85) REVERT: B 180 GLU cc_start: 0.6345 (mt-10) cc_final: 0.5974 (mm-30) REVERT: B 197 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6266 (ptp90) REVERT: B 243 LYS cc_start: 0.5612 (mtmt) cc_final: 0.5263 (ttmm) REVERT: B 261 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6409 (mt-10) REVERT: B 273 THR cc_start: 0.7137 (p) cc_final: 0.6894 (t) REVERT: B 408 ARG cc_start: 0.6597 (ttm170) cc_final: 0.6257 (tpp80) REVERT: B 516 MET cc_start: 0.4834 (mtm) cc_final: 0.4465 (mtp) REVERT: B 565 GLU cc_start: 0.4949 (mm-30) cc_final: 0.4491 (tp30) REVERT: C 112 ASP cc_start: 0.7158 (t0) cc_final: 0.6895 (t0) REVERT: C 122 MET cc_start: 0.7367 (mtm) cc_final: 0.6869 (mtp) REVERT: C 124 LYS cc_start: 0.7467 (mtmm) cc_final: 0.6394 (mptt) REVERT: C 128 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7031 (mm-30) REVERT: C 156 ARG cc_start: 0.6995 (ttm110) cc_final: 0.6490 (ttm110) REVERT: C 158 LYS cc_start: 0.7550 (ttpp) cc_final: 0.7150 (ttmm) REVERT: C 182 LYS cc_start: 0.7348 (mtmt) cc_final: 0.7109 (mtmt) REVERT: C 197 ARG cc_start: 0.7012 (ttp-110) cc_final: 0.6462 (ttp-170) REVERT: C 209 MET cc_start: 0.7714 (mtp) cc_final: 0.7370 (mtp) REVERT: C 282 MET cc_start: 0.8119 (tpt) cc_final: 0.7826 (tpt) REVERT: C 336 GLU cc_start: 0.5897 (tp30) cc_final: 0.5681 (tp30) REVERT: C 347 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6867 (mt-10) REVERT: C 441 GLU cc_start: 0.6702 (pt0) cc_final: 0.6402 (tt0) REVERT: C 450 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6688 (tp) REVERT: C 456 GLU cc_start: 0.6685 (mm-30) cc_final: 0.6150 (tm-30) REVERT: C 461 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6544 (tm-30) REVERT: C 480 GLU cc_start: 0.6831 (mp0) cc_final: 0.6114 (mp0) REVERT: C 488 ARG cc_start: 0.7101 (ttp-110) cc_final: 0.6839 (ttp-170) REVERT: C 527 GLU cc_start: 0.5714 (tt0) cc_final: 0.5418 (mm-30) REVERT: C 547 ARG cc_start: 0.7444 (ttm110) cc_final: 0.7234 (ttm110) REVERT: C 558 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6319 (tm-30) REVERT: D 6 LYS cc_start: 0.7049 (tttp) cc_final: 0.6815 (tppt) REVERT: D 46 GLN cc_start: 0.8485 (tt0) cc_final: 0.8154 (tt0) REVERT: D 49 GLU cc_start: 0.8109 (tt0) cc_final: 0.7722 (tt0) REVERT: D 162 GLU cc_start: 0.6746 (mp0) cc_final: 0.6474 (mm-30) REVERT: D 274 ARG cc_start: 0.6970 (mtt180) cc_final: 0.6608 (mtt180) REVERT: D 290 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6282 (t70) REVERT: D 302 GLU cc_start: 0.6905 (tt0) cc_final: 0.6318 (tp30) REVERT: D 342 GLU cc_start: 0.6916 (tt0) cc_final: 0.6394 (mp0) REVERT: D 373 GLU cc_start: 0.6541 (pm20) cc_final: 0.6143 (pm20) REVERT: D 380 ASP cc_start: 0.6840 (m-30) cc_final: 0.6510 (m-30) REVERT: D 410 ARG cc_start: 0.6455 (ttm170) cc_final: 0.5892 (ttt90) REVERT: D 413 GLN cc_start: 0.6222 (mt0) cc_final: 0.5860 (mm-40) REVERT: D 420 ARG cc_start: 0.6919 (mtp180) cc_final: 0.6484 (mmt180) REVERT: D 452 LYS cc_start: 0.5683 (mmtp) cc_final: 0.5415 (mmmt) REVERT: E 25 LYS cc_start: 0.6887 (mtmt) cc_final: 0.6622 (mppt) REVERT: E 62 GLU cc_start: 0.6727 (pm20) cc_final: 0.6414 (pm20) REVERT: E 98 LYS cc_start: 0.6677 (mmmt) cc_final: 0.5332 (ttpt) REVERT: E 129 GLN cc_start: 0.7266 (mm110) cc_final: 0.6984 (mm-40) REVERT: E 206 GLN cc_start: 0.6272 (pt0) cc_final: 0.5794 (mt0) REVERT: E 287 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7685 (ttp) REVERT: E 302 GLU cc_start: 0.7497 (tt0) cc_final: 0.6988 (tp30) REVERT: E 410 ARG cc_start: 0.6780 (tpp80) cc_final: 0.6352 (tpp80) REVERT: E 413 GLN cc_start: 0.6901 (mt0) cc_final: 0.6613 (mp10) REVERT: E 427 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7103 (mm110) REVERT: E 453 ARG cc_start: 0.6722 (mmt180) cc_final: 0.6290 (mmm160) REVERT: F 5 LYS cc_start: 0.5426 (ttpt) cc_final: 0.4854 (tttt) REVERT: F 23 ASN cc_start: 0.7409 (m110) cc_final: 0.7058 (t0) REVERT: F 52 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7030 (mt-10) REVERT: F 98 LYS cc_start: 0.7115 (mmtt) cc_final: 0.6715 (mmtt) REVERT: F 200 GLU cc_start: 0.7131 (mp0) cc_final: 0.6802 (mp0) REVERT: F 280 ARG cc_start: 0.7255 (mtt180) cc_final: 0.6866 (mmt90) REVERT: F 305 LYS cc_start: 0.7443 (mmtm) cc_final: 0.7194 (mmmt) REVERT: F 368 LYS cc_start: 0.7272 (ttpt) cc_final: 0.6988 (ttpp) REVERT: F 376 LYS cc_start: 0.6621 (tptm) cc_final: 0.6266 (mttt) REVERT: F 380 ASP cc_start: 0.6457 (m-30) cc_final: 0.6206 (m-30) REVERT: F 394 LYS cc_start: 0.6747 (mmtm) cc_final: 0.6518 (mttp) REVERT: F 398 ILE cc_start: 0.6698 (mt) cc_final: 0.6182 (tp) REVERT: F 456 LYS cc_start: 0.6212 (mttt) cc_final: 0.5997 (mmtp) REVERT: G 13 GLN cc_start: 0.6627 (OUTLIER) cc_final: 0.6046 (tt0) REVERT: G 17 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6210 (mp10) REVERT: G 19 ARG cc_start: 0.5403 (mtm-85) cc_final: 0.5109 (ttp-110) REVERT: G 196 ARG cc_start: 0.6198 (mtp-110) cc_final: 0.5928 (mtt-85) REVERT: G 202 GLU cc_start: 0.5773 (mm-30) cc_final: 0.4817 (tm-30) REVERT: L 85 ARG cc_start: 0.2061 (ttp80) cc_final: 0.1437 (ttp80) REVERT: L 162 GLN cc_start: 0.5294 (pt0) cc_final: 0.4783 (pt0) outliers start: 76 outliers final: 27 residues processed: 442 average time/residue: 1.8953 time to fit residues: 945.4986 Evaluate side-chains 377 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 342 time to evaluate : 3.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 chunk 230 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 339 optimal weight: 0.5980 chunk 366 optimal weight: 10.0000 chunk 302 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 overall best weight: 7.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN B 397 GLN B 465 GLN D 338 GLN E 58 GLN F 222 ASN F 388 ASN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 30114 Z= 0.447 Angle : 0.729 8.739 40813 Z= 0.378 Chirality : 0.051 0.200 4572 Planarity : 0.007 0.057 5333 Dihedral : 7.178 114.488 4259 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.05 % Allowed : 11.64 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 3764 helix: 0.49 (0.13), residues: 1562 sheet: 0.11 (0.23), residues: 536 loop : -0.57 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 175 HIS 0.008 0.002 HIS E 252 PHE 0.022 0.003 PHE C 574 TYR 0.021 0.003 TYR I 88 ARG 0.009 0.001 ARG C 335 *********************** 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 469 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 344 time to evaluate : 3.505 Fit side-chains REVERT: A 3 GLN cc_start: 0.7187 (mt0) cc_final: 0.6882 (tt0) REVERT: A 109 HIS cc_start: 0.7228 (m-70) cc_final: 0.6971 (m-70) REVERT: A 114 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6718 (mm-30) REVERT: A 122 MET cc_start: 0.6784 (mtp) cc_final: 0.6314 (mtt) REVERT: A 124 LYS cc_start: 0.6325 (mtmm) cc_final: 0.5804 (mttp) REVERT: A 128 GLU cc_start: 0.6263 (tp30) cc_final: 0.5673 (pt0) REVERT: A 137 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.6894 (p) REVERT: A 154 ARG cc_start: 0.6545 (mtp85) cc_final: 0.6074 (mtt90) REVERT: A 276 LYS cc_start: 0.5050 (ptmt) cc_final: 0.4176 (pptt) REVERT: A 277 THR cc_start: 0.7937 (m) cc_final: 0.7354 (p) REVERT: A 393 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6539 (tm-30) REVERT: A 410 ASP cc_start: 0.6121 (t0) cc_final: 0.5687 (t0) REVERT: A 441 GLU cc_start: 0.6476 (mm-30) cc_final: 0.5932 (mm-30) REVERT: A 469 GLN cc_start: 0.5848 (mt0) cc_final: 0.5330 (mm110) REVERT: A 491 ARG cc_start: 0.6254 (mmt180) cc_final: 0.5082 (mtp85) REVERT: A 492 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.5047 (mp0) REVERT: A 496 GLN cc_start: 0.7579 (tt0) cc_final: 0.7157 (tt0) REVERT: A 508 SER cc_start: 0.8024 (t) cc_final: 0.7480 (p) REVERT: A 516 MET cc_start: 0.7270 (mtm) cc_final: 0.6677 (mtp) REVERT: A 527 GLU cc_start: 0.5950 (tt0) cc_final: 0.5401 (tp30) REVERT: A 546 GLU cc_start: 0.5772 (pp20) cc_final: 0.5534 (mm-30) REVERT: B 1 MET cc_start: 0.6084 (mtm) cc_final: 0.5601 (mtp) REVERT: B 2 ILE cc_start: 0.8117 (mm) cc_final: 0.7783 (mm) REVERT: B 29 LYS cc_start: 0.7468 (mtpt) cc_final: 0.7014 (mtmm) REVERT: B 33 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6730 (tt0) REVERT: B 104 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.5662 (ptp-170) REVERT: B 114 GLU cc_start: 0.6401 (mm-30) cc_final: 0.6020 (mt-10) REVERT: B 137 THR cc_start: 0.8110 (p) cc_final: 0.7815 (t) REVERT: B 180 GLU cc_start: 0.6380 (mt-10) cc_final: 0.6004 (mm-30) REVERT: B 197 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.6138 (ptp90) REVERT: B 408 ARG cc_start: 0.6559 (ttm170) cc_final: 0.6276 (tpp80) REVERT: B 425 ASN cc_start: 0.5286 (m110) cc_final: 0.4909 (p0) REVERT: B 565 GLU cc_start: 0.5104 (mm-30) cc_final: 0.4601 (tp30) REVERT: C 112 ASP cc_start: 0.7082 (t0) cc_final: 0.6881 (t0) REVERT: C 122 MET cc_start: 0.7370 (mtm) cc_final: 0.6890 (mpp) REVERT: C 182 LYS cc_start: 0.7378 (mtmt) cc_final: 0.7126 (mtmt) REVERT: C 197 ARG cc_start: 0.7016 (ttp-110) cc_final: 0.6533 (ttp-170) REVERT: C 209 MET cc_start: 0.7783 (mtp) cc_final: 0.7367 (mtp) REVERT: C 336 GLU cc_start: 0.5981 (tp30) cc_final: 0.5741 (tp30) REVERT: C 347 GLU cc_start: 0.7222 (mt-10) cc_final: 0.7009 (mt-10) REVERT: C 441 GLU cc_start: 0.6674 (pt0) cc_final: 0.6375 (tt0) REVERT: C 456 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6196 (tm-30) REVERT: C 461 GLU cc_start: 0.6667 (tm-30) cc_final: 0.6392 (tm-30) REVERT: C 480 GLU cc_start: 0.6732 (mp0) cc_final: 0.6152 (mp0) REVERT: C 488 ARG cc_start: 0.7095 (ttp-110) cc_final: 0.6835 (ttp-170) REVERT: C 527 GLU cc_start: 0.5764 (tt0) cc_final: 0.5558 (mm-30) REVERT: C 547 ARG cc_start: 0.7548 (ttm110) cc_final: 0.7108 (ttm110) REVERT: C 558 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6297 (tm-30) REVERT: D 49 GLU cc_start: 0.8173 (tt0) cc_final: 0.7748 (tt0) REVERT: D 87 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: D 162 GLU cc_start: 0.6719 (mp0) cc_final: 0.6402 (mm-30) REVERT: D 207 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7315 (mm-30) REVERT: D 274 ARG cc_start: 0.6962 (mtt180) cc_final: 0.6544 (mtt180) REVERT: D 290 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6823 (t70) REVERT: D 302 GLU cc_start: 0.6927 (tt0) cc_final: 0.6457 (tp30) REVERT: D 314 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7485 (pt) REVERT: D 342 GLU cc_start: 0.6944 (tt0) cc_final: 0.6374 (mp0) REVERT: D 373 GLU cc_start: 0.6487 (pm20) cc_final: 0.6137 (pm20) REVERT: D 380 ASP cc_start: 0.6872 (m-30) cc_final: 0.6574 (m-30) REVERT: D 410 ARG cc_start: 0.6604 (ttm170) cc_final: 0.6037 (ttt90) REVERT: D 413 GLN cc_start: 0.6166 (mt0) cc_final: 0.5863 (mm-40) REVERT: D 420 ARG cc_start: 0.6966 (mtp180) cc_final: 0.6609 (mmt180) REVERT: D 453 ARG cc_start: 0.5139 (OUTLIER) cc_final: 0.4368 (mtt180) REVERT: D 465 GLN cc_start: 0.6044 (mm-40) cc_final: 0.5057 (pt0) REVERT: E 7 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6214 (mm-30) REVERT: E 25 LYS cc_start: 0.6919 (mtmt) cc_final: 0.6640 (mptm) REVERT: E 62 GLU cc_start: 0.6619 (pm20) cc_final: 0.6251 (pm20) REVERT: E 98 LYS cc_start: 0.6696 (mmmt) cc_final: 0.5389 (ttpt) REVERT: E 128 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6498 (pp20) REVERT: E 129 GLN cc_start: 0.7300 (mm110) cc_final: 0.6935 (mm-40) REVERT: E 206 GLN cc_start: 0.6260 (pt0) cc_final: 0.5723 (mt0) REVERT: E 287 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7659 (ttp) REVERT: E 302 GLU cc_start: 0.7471 (tt0) cc_final: 0.6957 (tp30) REVERT: E 334 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: E 405 THR cc_start: 0.5167 (OUTLIER) cc_final: 0.4627 (t) REVERT: E 410 ARG cc_start: 0.6811 (tpp80) cc_final: 0.6393 (tpp80) REVERT: E 413 GLN cc_start: 0.6910 (mt0) cc_final: 0.6576 (mp10) REVERT: E 453 ARG cc_start: 0.6520 (mmt180) cc_final: 0.6183 (mmm160) REVERT: F 5 LYS cc_start: 0.5609 (ttpt) cc_final: 0.5054 (tttt) REVERT: F 7 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7119 (mt-10) REVERT: F 23 ASN cc_start: 0.7476 (m110) cc_final: 0.7234 (t0) REVERT: F 52 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6965 (mt-10) REVERT: F 81 ARG cc_start: 0.7341 (mtt-85) cc_final: 0.7090 (mtt90) REVERT: F 98 LYS cc_start: 0.7158 (mmtt) cc_final: 0.6691 (mmmt) REVERT: F 200 GLU cc_start: 0.7334 (mp0) cc_final: 0.6914 (mp0) REVERT: F 206 GLN cc_start: 0.6660 (OUTLIER) cc_final: 0.6366 (mp10) REVERT: F 216 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7541 (mtm-85) REVERT: F 280 ARG cc_start: 0.7317 (mtt180) cc_final: 0.7065 (mmt90) REVERT: F 305 LYS cc_start: 0.7380 (mmtm) cc_final: 0.7153 (mmmt) REVERT: F 368 LYS cc_start: 0.7176 (ttpt) cc_final: 0.6877 (ttpp) REVERT: F 376 LYS cc_start: 0.6619 (tptm) cc_final: 0.6268 (mttt) REVERT: F 380 ASP cc_start: 0.6470 (m-30) cc_final: 0.6235 (m-30) REVERT: F 394 LYS cc_start: 0.6830 (mmtm) cc_final: 0.6537 (mttp) REVERT: F 398 ILE cc_start: 0.6525 (mt) cc_final: 0.6105 (tp) REVERT: F 456 LYS cc_start: 0.6524 (mttt) cc_final: 0.6148 (mmtp) REVERT: G 13 GLN cc_start: 0.6482 (OUTLIER) cc_final: 0.5839 (tt0) REVERT: G 17 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.6104 (mp10) REVERT: G 19 ARG cc_start: 0.5405 (mtm-85) cc_final: 0.5163 (ttp-110) REVERT: G 196 ARG cc_start: 0.6176 (mtp-110) cc_final: 0.5939 (mtt180) REVERT: G 202 GLU cc_start: 0.5662 (mm-30) cc_final: 0.4708 (tm-30) REVERT: I 115 LEU cc_start: 0.2678 (OUTLIER) cc_final: 0.2338 (mt) REVERT: J 158 GLU cc_start: 0.4116 (OUTLIER) cc_final: 0.3199 (tt0) REVERT: L 85 ARG cc_start: 0.2017 (ttp80) cc_final: 0.1546 (ttp-170) REVERT: L 162 GLN cc_start: 0.5581 (pt0) cc_final: 0.5148 (pt0) outliers start: 125 outliers final: 41 residues processed: 439 average time/residue: 1.8749 time to fit residues: 930.9810 Evaluate side-chains 372 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 311 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 364 ASN Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 158 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 80 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 8.9990 chunk 255 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 340 optimal weight: 2.9990 chunk 360 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 chunk 322 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN B 397 GLN D 338 GLN E 364 ASN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN J 143 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30114 Z= 0.230 Angle : 0.557 7.618 40813 Z= 0.288 Chirality : 0.044 0.176 4572 Planarity : 0.005 0.056 5333 Dihedral : 6.638 118.941 4259 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.44 % Allowed : 14.08 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3764 helix: 0.94 (0.13), residues: 1563 sheet: 0.23 (0.23), residues: 530 loop : -0.45 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 175 HIS 0.004 0.001 HIS E 252 PHE 0.020 0.002 PHE B 522 TYR 0.013 0.001 TYR C 562 ARG 0.007 0.000 ARG G 160 *********************** 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 437 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 331 time to evaluate : 3.589 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7230 (mt0) cc_final: 0.6946 (tt0) REVERT: A 109 HIS cc_start: 0.7223 (m-70) cc_final: 0.7003 (m-70) REVERT: A 114 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6736 (mm-30) REVERT: A 122 MET cc_start: 0.6742 (mtp) cc_final: 0.6236 (mtt) REVERT: A 124 LYS cc_start: 0.6200 (mtmm) cc_final: 0.5789 (mttp) REVERT: A 128 GLU cc_start: 0.6267 (tp30) cc_final: 0.5659 (pt0) REVERT: A 137 THR cc_start: 0.7561 (m) cc_final: 0.6525 (p) REVERT: A 154 ARG cc_start: 0.6642 (mtp85) cc_final: 0.6090 (mtt90) REVERT: A 220 MET cc_start: 0.6586 (tpt) cc_final: 0.6315 (tpt) REVERT: A 276 LYS cc_start: 0.5003 (ptmt) cc_final: 0.4169 (pptt) REVERT: A 277 THR cc_start: 0.7914 (m) cc_final: 0.7218 (p) REVERT: A 410 ASP cc_start: 0.6076 (t0) cc_final: 0.5620 (t0) REVERT: A 441 GLU cc_start: 0.6442 (mm-30) cc_final: 0.5850 (mm-30) REVERT: A 469 GLN cc_start: 0.5902 (mt0) cc_final: 0.5353 (mm110) REVERT: A 491 ARG cc_start: 0.6147 (mmt180) cc_final: 0.5115 (mtp85) REVERT: A 496 GLN cc_start: 0.7595 (tt0) cc_final: 0.7130 (tt0) REVERT: A 508 SER cc_start: 0.7982 (t) cc_final: 0.7413 (p) REVERT: A 527 GLU cc_start: 0.5954 (tt0) cc_final: 0.5436 (tp30) REVERT: A 546 GLU cc_start: 0.5702 (pp20) cc_final: 0.5370 (mm-30) REVERT: B 2 ILE cc_start: 0.8165 (mm) cc_final: 0.7810 (mm) REVERT: B 29 LYS cc_start: 0.7413 (mtpt) cc_final: 0.7000 (mttp) REVERT: B 33 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6584 (tt0) REVERT: B 114 GLU cc_start: 0.6411 (mm-30) cc_final: 0.6017 (mt-10) REVERT: B 137 THR cc_start: 0.8112 (p) cc_final: 0.7869 (t) REVERT: B 180 GLU cc_start: 0.6403 (mt-10) cc_final: 0.6005 (mm-30) REVERT: B 197 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6223 (ptp90) REVERT: B 276 LYS cc_start: 0.5909 (mttt) cc_final: 0.5029 (mtpm) REVERT: B 408 ARG cc_start: 0.6572 (ttm170) cc_final: 0.6258 (tpp80) REVERT: B 488 ARG cc_start: 0.4869 (ttp-110) cc_final: 0.4582 (ttm-80) REVERT: B 565 GLU cc_start: 0.5195 (mm-30) cc_final: 0.4687 (tp30) REVERT: C 29 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7910 (mmtm) REVERT: C 112 ASP cc_start: 0.7082 (t0) cc_final: 0.6870 (t0) REVERT: C 122 MET cc_start: 0.7382 (mtm) cc_final: 0.6878 (mpp) REVERT: C 138 VAL cc_start: 0.7496 (OUTLIER) cc_final: 0.7150 (p) REVERT: C 182 LYS cc_start: 0.7357 (mtmt) cc_final: 0.7155 (mtmt) REVERT: C 197 ARG cc_start: 0.6998 (ttp-110) cc_final: 0.6457 (ttp-170) REVERT: C 209 MET cc_start: 0.7708 (mtp) cc_final: 0.7374 (mtp) REVERT: C 282 MET cc_start: 0.8020 (tpt) cc_final: 0.7780 (tpt) REVERT: C 336 GLU cc_start: 0.5902 (tp30) cc_final: 0.5603 (tp30) REVERT: C 347 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6939 (mt-10) REVERT: C 441 GLU cc_start: 0.6527 (pt0) cc_final: 0.6298 (tt0) REVERT: C 456 GLU cc_start: 0.6682 (mm-30) cc_final: 0.6128 (tm-30) REVERT: C 461 GLU cc_start: 0.6626 (tm-30) cc_final: 0.6301 (tm-30) REVERT: C 480 GLU cc_start: 0.6792 (mp0) cc_final: 0.6156 (mp0) REVERT: C 488 ARG cc_start: 0.7014 (ttp-110) cc_final: 0.6800 (ttp-170) REVERT: C 527 GLU cc_start: 0.5758 (tt0) cc_final: 0.5531 (mm-30) REVERT: C 547 ARG cc_start: 0.7565 (ttm110) cc_final: 0.7319 (tpp-160) REVERT: C 558 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6301 (tm-30) REVERT: D 46 GLN cc_start: 0.8440 (tt0) cc_final: 0.7973 (tt0) REVERT: D 49 GLU cc_start: 0.8139 (tt0) cc_final: 0.7715 (tt0) REVERT: D 162 GLU cc_start: 0.6776 (mp0) cc_final: 0.6476 (mm-30) REVERT: D 207 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7247 (mm-30) REVERT: D 274 ARG cc_start: 0.6858 (mtt180) cc_final: 0.6411 (mtt180) REVERT: D 290 ASP cc_start: 0.6772 (OUTLIER) cc_final: 0.6469 (t70) REVERT: D 302 GLU cc_start: 0.6900 (tt0) cc_final: 0.6396 (tp30) REVERT: D 342 GLU cc_start: 0.6895 (tt0) cc_final: 0.6445 (mp0) REVERT: D 373 GLU cc_start: 0.6419 (pm20) cc_final: 0.6134 (pm20) REVERT: D 380 ASP cc_start: 0.6836 (m-30) cc_final: 0.6587 (m-30) REVERT: D 410 ARG cc_start: 0.6587 (ttm170) cc_final: 0.5898 (ttt90) REVERT: D 413 GLN cc_start: 0.6192 (mt0) cc_final: 0.5888 (mm-40) REVERT: D 420 ARG cc_start: 0.6839 (mtp180) cc_final: 0.6465 (mmt180) REVERT: D 453 ARG cc_start: 0.5150 (OUTLIER) cc_final: 0.4512 (mtt180) REVERT: D 465 GLN cc_start: 0.5989 (mm-40) cc_final: 0.5191 (pt0) REVERT: E 7 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6266 (mm-30) REVERT: E 25 LYS cc_start: 0.6808 (mtmt) cc_final: 0.6550 (mptm) REVERT: E 62 GLU cc_start: 0.6623 (pm20) cc_final: 0.6179 (pm20) REVERT: E 98 LYS cc_start: 0.6685 (mmmt) cc_final: 0.5370 (ttpt) REVERT: E 129 GLN cc_start: 0.7168 (mm110) cc_final: 0.6862 (mm-40) REVERT: E 206 GLN cc_start: 0.6307 (pt0) cc_final: 0.5667 (mt0) REVERT: E 287 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7756 (ttp) REVERT: E 302 GLU cc_start: 0.7423 (tt0) cc_final: 0.6875 (tp30) REVERT: E 334 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: E 405 THR cc_start: 0.4935 (OUTLIER) cc_final: 0.4508 (t) REVERT: E 410 ARG cc_start: 0.6702 (tpp80) cc_final: 0.6311 (tpp80) REVERT: E 413 GLN cc_start: 0.6924 (mt0) cc_final: 0.6570 (mp10) REVERT: E 453 ARG cc_start: 0.6487 (mmt180) cc_final: 0.6191 (mmm160) REVERT: F 5 LYS cc_start: 0.5600 (ttpt) cc_final: 0.5020 (tttt) REVERT: F 98 LYS cc_start: 0.7059 (mmtt) cc_final: 0.6574 (mmmt) REVERT: F 103 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7101 (mm) REVERT: F 194 MET cc_start: 0.8281 (mtm) cc_final: 0.8056 (mpp) REVERT: F 200 GLU cc_start: 0.7280 (mp0) cc_final: 0.7024 (mp0) REVERT: F 206 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6335 (mp10) REVERT: F 280 ARG cc_start: 0.7319 (mtt180) cc_final: 0.7045 (mmt90) REVERT: F 305 LYS cc_start: 0.7377 (mmtm) cc_final: 0.7175 (mmmt) REVERT: F 368 LYS cc_start: 0.7208 (ttpt) cc_final: 0.6907 (ttpp) REVERT: F 376 LYS cc_start: 0.6516 (tptm) cc_final: 0.6264 (mttt) REVERT: F 380 ASP cc_start: 0.6456 (m-30) cc_final: 0.6233 (m-30) REVERT: F 394 LYS cc_start: 0.6762 (mmtm) cc_final: 0.6518 (mttp) REVERT: F 398 ILE cc_start: 0.6645 (mt) cc_final: 0.6226 (tp) REVERT: F 456 LYS cc_start: 0.6557 (mttt) cc_final: 0.6188 (mmtp) REVERT: G 17 GLN cc_start: 0.6624 (OUTLIER) cc_final: 0.6032 (mp10) REVERT: G 19 ARG cc_start: 0.5269 (mtm-85) cc_final: 0.4984 (ttp-110) REVERT: G 181 GLN cc_start: 0.6736 (mm-40) cc_final: 0.5647 (mt0) REVERT: G 196 ARG cc_start: 0.6209 (mtp-110) cc_final: 0.5912 (mtt-85) REVERT: G 202 GLU cc_start: 0.5701 (mm-30) cc_final: 0.4783 (tm-30) REVERT: I 115 LEU cc_start: 0.2227 (OUTLIER) cc_final: 0.1977 (mt) REVERT: L 80 LEU cc_start: 0.3099 (OUTLIER) cc_final: 0.2872 (tm) REVERT: L 85 ARG cc_start: 0.2251 (ttp80) cc_final: 0.1753 (ttp80) REVERT: L 162 GLN cc_start: 0.5535 (pt0) cc_final: 0.5134 (pt0) REVERT: L 164 GLU cc_start: 0.5462 (OUTLIER) cc_final: 0.5205 (tp30) outliers start: 106 outliers final: 43 residues processed: 411 average time/residue: 1.7955 time to fit residues: 843.5058 Evaluate side-chains 376 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 318 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 164 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 307 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 184 optimal weight: 0.5980 chunk 323 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 50 GLN B 316 GLN B 397 GLN E 364 ASN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30114 Z= 0.337 Angle : 0.639 7.907 40813 Z= 0.329 Chirality : 0.047 0.199 4572 Planarity : 0.006 0.055 5333 Dihedral : 6.852 117.449 4259 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.61 % Allowed : 14.82 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3764 helix: 0.72 (0.13), residues: 1567 sheet: 0.19 (0.23), residues: 545 loop : -0.59 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 175 HIS 0.005 0.001 HIS E 323 PHE 0.023 0.002 PHE B 522 TYR 0.015 0.002 TYR B 304 ARG 0.005 0.001 ARG L 84 *********************** 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 468 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 326 time to evaluate : 3.498 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7233 (mt0) cc_final: 0.6977 (tt0) REVERT: A 114 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6714 (mm-30) REVERT: A 122 MET cc_start: 0.6739 (mtp) cc_final: 0.6264 (mtt) REVERT: A 124 LYS cc_start: 0.6232 (mtmm) cc_final: 0.5819 (mttp) REVERT: A 128 GLU cc_start: 0.6192 (tp30) cc_final: 0.5683 (pt0) REVERT: A 154 ARG cc_start: 0.6558 (mtp85) cc_final: 0.5987 (mtt90) REVERT: A 276 LYS cc_start: 0.4952 (ptmt) cc_final: 0.4111 (pptt) REVERT: A 277 THR cc_start: 0.7902 (m) cc_final: 0.7308 (p) REVERT: A 357 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.4348 (mmt180) REVERT: A 410 ASP cc_start: 0.6111 (t0) cc_final: 0.5667 (t0) REVERT: A 441 GLU cc_start: 0.6526 (mm-30) cc_final: 0.5920 (mm-30) REVERT: A 469 GLN cc_start: 0.5816 (mt0) cc_final: 0.5285 (mm-40) REVERT: A 491 ARG cc_start: 0.6252 (mmt180) cc_final: 0.5184 (mtp85) REVERT: A 496 GLN cc_start: 0.7625 (tt0) cc_final: 0.7162 (tt0) REVERT: A 508 SER cc_start: 0.7996 (t) cc_final: 0.7449 (p) REVERT: A 527 GLU cc_start: 0.5933 (tt0) cc_final: 0.5350 (tp30) REVERT: A 546 GLU cc_start: 0.5615 (pp20) cc_final: 0.5350 (mm-30) REVERT: B 1 MET cc_start: 0.6203 (mtm) cc_final: 0.5778 (mtp) REVERT: B 2 ILE cc_start: 0.8198 (mm) cc_final: 0.7939 (mm) REVERT: B 29 LYS cc_start: 0.7422 (mtpt) cc_final: 0.7001 (mtmm) REVERT: B 33 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6651 (tt0) REVERT: B 104 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.5332 (ptp-170) REVERT: B 114 GLU cc_start: 0.6400 (mm-30) cc_final: 0.6008 (mt-10) REVERT: B 137 THR cc_start: 0.8112 (p) cc_final: 0.7851 (t) REVERT: B 180 GLU cc_start: 0.6330 (mt-10) cc_final: 0.6061 (pt0) REVERT: B 197 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6183 (ptp90) REVERT: B 276 LYS cc_start: 0.5848 (mttt) cc_final: 0.4962 (mtpm) REVERT: B 408 ARG cc_start: 0.6558 (ttm170) cc_final: 0.6261 (tpp80) REVERT: B 565 GLU cc_start: 0.5162 (mm-30) cc_final: 0.4627 (tp30) REVERT: C 29 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8008 (mmtm) REVERT: C 83 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8426 (tp) REVERT: C 112 ASP cc_start: 0.7087 (t0) cc_final: 0.6875 (t0) REVERT: C 122 MET cc_start: 0.7341 (mtm) cc_final: 0.6921 (mpp) REVERT: C 182 LYS cc_start: 0.7357 (mtmt) cc_final: 0.7143 (mtmt) REVERT: C 197 ARG cc_start: 0.7002 (ttp-110) cc_final: 0.6456 (ttp-170) REVERT: C 209 MET cc_start: 0.7784 (mtp) cc_final: 0.7463 (mtp) REVERT: C 336 GLU cc_start: 0.6025 (tp30) cc_final: 0.5709 (tp30) REVERT: C 347 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7043 (mt-10) REVERT: C 441 GLU cc_start: 0.6534 (pt0) cc_final: 0.6311 (tt0) REVERT: C 456 GLU cc_start: 0.6700 (mm-30) cc_final: 0.6158 (tm-30) REVERT: C 461 GLU cc_start: 0.6658 (tm-30) cc_final: 0.6374 (tm-30) REVERT: C 480 GLU cc_start: 0.6756 (mp0) cc_final: 0.6149 (mp0) REVERT: C 488 ARG cc_start: 0.7032 (ttp-110) cc_final: 0.6828 (ttp-170) REVERT: C 558 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6316 (tm-30) REVERT: D 46 GLN cc_start: 0.8459 (tt0) cc_final: 0.7964 (tt0) REVERT: D 49 GLU cc_start: 0.8156 (tt0) cc_final: 0.7735 (tt0) REVERT: D 87 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: D 162 GLU cc_start: 0.6624 (mp0) cc_final: 0.6301 (mm-30) REVERT: D 237 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7217 (mtt) REVERT: D 290 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6616 (t70) REVERT: D 302 GLU cc_start: 0.6852 (tt0) cc_final: 0.6405 (tp30) REVERT: D 314 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7442 (pt) REVERT: D 342 GLU cc_start: 0.6939 (tt0) cc_final: 0.6592 (mp0) REVERT: D 373 GLU cc_start: 0.6428 (pm20) cc_final: 0.6125 (pm20) REVERT: D 380 ASP cc_start: 0.6799 (m-30) cc_final: 0.6567 (m-30) REVERT: D 401 GLU cc_start: 0.5091 (OUTLIER) cc_final: 0.4735 (tm-30) REVERT: D 410 ARG cc_start: 0.6573 (ttm170) cc_final: 0.5974 (ttt90) REVERT: D 413 GLN cc_start: 0.6259 (mt0) cc_final: 0.5965 (mm-40) REVERT: D 420 ARG cc_start: 0.6821 (mtp180) cc_final: 0.6485 (mmt180) REVERT: D 453 ARG cc_start: 0.5116 (OUTLIER) cc_final: 0.4372 (mtt180) REVERT: D 465 GLN cc_start: 0.6003 (mm-40) cc_final: 0.5150 (pt0) REVERT: E 7 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6156 (mm-30) REVERT: E 25 LYS cc_start: 0.6798 (mtmt) cc_final: 0.6505 (mptm) REVERT: E 62 GLU cc_start: 0.6597 (pm20) cc_final: 0.6215 (pm20) REVERT: E 98 LYS cc_start: 0.6716 (mmmt) cc_final: 0.5426 (ttpt) REVERT: E 128 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6569 (pp20) REVERT: E 129 GLN cc_start: 0.7256 (mm110) cc_final: 0.6870 (mm-40) REVERT: E 206 GLN cc_start: 0.6332 (pt0) cc_final: 0.5685 (mt0) REVERT: E 287 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7669 (ttp) REVERT: E 302 GLU cc_start: 0.7480 (tt0) cc_final: 0.6927 (tp30) REVERT: E 334 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: E 405 THR cc_start: 0.5309 (OUTLIER) cc_final: 0.4867 (t) REVERT: E 410 ARG cc_start: 0.6711 (tpp80) cc_final: 0.6306 (tpp80) REVERT: E 413 GLN cc_start: 0.6895 (mt0) cc_final: 0.6533 (mp10) REVERT: E 453 ARG cc_start: 0.6468 (mmt180) cc_final: 0.6170 (mmm160) REVERT: F 5 LYS cc_start: 0.5480 (ttpt) cc_final: 0.4948 (tttt) REVERT: F 23 ASN cc_start: 0.7457 (m110) cc_final: 0.7146 (t0) REVERT: F 52 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7019 (mt-10) REVERT: F 98 LYS cc_start: 0.7133 (mmtt) cc_final: 0.6639 (mmmt) REVERT: F 103 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7132 (mm) REVERT: F 200 GLU cc_start: 0.7281 (mp0) cc_final: 0.6934 (mp0) REVERT: F 206 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.6356 (mp10) REVERT: F 280 ARG cc_start: 0.7336 (mtt180) cc_final: 0.7063 (mmt90) REVERT: F 305 LYS cc_start: 0.7382 (mmtm) cc_final: 0.7151 (mmmt) REVERT: F 368 LYS cc_start: 0.7141 (ttpt) cc_final: 0.6842 (ttpp) REVERT: F 376 LYS cc_start: 0.6589 (tptm) cc_final: 0.6308 (mttt) REVERT: F 380 ASP cc_start: 0.6447 (m-30) cc_final: 0.6233 (m-30) REVERT: F 394 LYS cc_start: 0.6843 (mmtm) cc_final: 0.6452 (mttp) REVERT: F 398 ILE cc_start: 0.6662 (mt) cc_final: 0.6230 (tp) REVERT: F 455 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.7164 (p) REVERT: F 456 LYS cc_start: 0.6677 (mttt) cc_final: 0.6265 (mmtp) REVERT: G 13 GLN cc_start: 0.6448 (OUTLIER) cc_final: 0.5667 (tt0) REVERT: G 17 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6104 (mp10) REVERT: G 19 ARG cc_start: 0.5337 (mtm-85) cc_final: 0.5100 (ttp-110) REVERT: G 181 GLN cc_start: 0.6769 (mm-40) cc_final: 0.5653 (mt0) REVERT: G 196 ARG cc_start: 0.6184 (mtp-110) cc_final: 0.5924 (mtt180) REVERT: H 104 LEU cc_start: 0.3648 (pp) cc_final: 0.3106 (mp) REVERT: I 115 LEU cc_start: 0.2339 (OUTLIER) cc_final: 0.2081 (mt) REVERT: L 85 ARG cc_start: 0.2112 (ttp80) cc_final: 0.1584 (ttp-170) REVERT: L 162 GLN cc_start: 0.5545 (pt0) cc_final: 0.5148 (pt0) REVERT: L 164 GLU cc_start: 0.5496 (OUTLIER) cc_final: 0.5225 (tp30) outliers start: 142 outliers final: 62 residues processed: 436 average time/residue: 1.7847 time to fit residues: 884.6048 Evaluate side-chains 399 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 313 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 164 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 9.9990 chunk 324 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 360 optimal weight: 9.9990 chunk 299 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 50 GLN B 316 GLN B 397 GLN ** D 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30114 Z= 0.335 Angle : 0.630 7.687 40813 Z= 0.326 Chirality : 0.047 0.205 4572 Planarity : 0.006 0.055 5333 Dihedral : 6.846 115.735 4259 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.51 % Allowed : 15.50 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3764 helix: 0.66 (0.13), residues: 1563 sheet: 0.16 (0.23), residues: 544 loop : -0.66 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 175 HIS 0.005 0.001 HIS E 323 PHE 0.027 0.002 PHE B 522 TYR 0.014 0.002 TYR H 21 ARG 0.006 0.001 ARG B 550 *********************** 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 456 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 317 time to evaluate : 3.661 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7277 (mt0) cc_final: 0.6966 (tt0) REVERT: A 114 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6714 (mm-30) REVERT: A 122 MET cc_start: 0.6780 (mtp) cc_final: 0.6308 (mtt) REVERT: A 124 LYS cc_start: 0.6199 (mtmm) cc_final: 0.5776 (mttp) REVERT: A 128 GLU cc_start: 0.6229 (tp30) cc_final: 0.5698 (pt0) REVERT: A 154 ARG cc_start: 0.6542 (mtp85) cc_final: 0.5975 (mtt90) REVERT: A 276 LYS cc_start: 0.5068 (ptmt) cc_final: 0.4165 (pptt) REVERT: A 277 THR cc_start: 0.7856 (m) cc_final: 0.7269 (p) REVERT: A 357 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.4346 (mmt180) REVERT: A 410 ASP cc_start: 0.5997 (t0) cc_final: 0.5575 (t0) REVERT: A 441 GLU cc_start: 0.6537 (mm-30) cc_final: 0.5891 (mm-30) REVERT: A 469 GLN cc_start: 0.5794 (mt0) cc_final: 0.5268 (mm-40) REVERT: A 491 ARG cc_start: 0.6228 (mmt180) cc_final: 0.5144 (mtp85) REVERT: A 496 GLN cc_start: 0.7609 (tt0) cc_final: 0.7168 (tt0) REVERT: A 508 SER cc_start: 0.7937 (t) cc_final: 0.7379 (p) REVERT: A 527 GLU cc_start: 0.5906 (tt0) cc_final: 0.5287 (tp30) REVERT: A 531 LYS cc_start: 0.4870 (mtpt) cc_final: 0.4542 (ttmt) REVERT: A 546 GLU cc_start: 0.5537 (pp20) cc_final: 0.5312 (mm-30) REVERT: B 1 MET cc_start: 0.6124 (mtm) cc_final: 0.5706 (mtp) REVERT: B 2 ILE cc_start: 0.8182 (mm) cc_final: 0.7942 (mm) REVERT: B 29 LYS cc_start: 0.7422 (mtpt) cc_final: 0.6988 (mtmm) REVERT: B 53 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: B 104 ARG cc_start: 0.6468 (OUTLIER) cc_final: 0.5104 (ptp-170) REVERT: B 114 GLU cc_start: 0.6412 (mm-30) cc_final: 0.5992 (mt-10) REVERT: B 137 THR cc_start: 0.8103 (p) cc_final: 0.7853 (t) REVERT: B 180 GLU cc_start: 0.6370 (mt-10) cc_final: 0.6075 (pt0) REVERT: B 197 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6163 (ptp90) REVERT: B 276 LYS cc_start: 0.5832 (mttt) cc_final: 0.4956 (mtpm) REVERT: B 408 ARG cc_start: 0.6492 (ttm170) cc_final: 0.6261 (tpp80) REVERT: B 565 GLU cc_start: 0.5183 (mm-30) cc_final: 0.4573 (tp30) REVERT: C 29 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7917 (mmtm) REVERT: C 83 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8403 (tp) REVERT: C 122 MET cc_start: 0.7394 (mtm) cc_final: 0.6989 (mpp) REVERT: C 182 LYS cc_start: 0.7364 (mtmt) cc_final: 0.7097 (mtmt) REVERT: C 197 ARG cc_start: 0.7014 (ttp-110) cc_final: 0.6452 (ttp-170) REVERT: C 209 MET cc_start: 0.7807 (mtp) cc_final: 0.7507 (mtp) REVERT: C 276 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6304 (ptmt) REVERT: C 336 GLU cc_start: 0.6054 (tp30) cc_final: 0.5701 (tp30) REVERT: C 347 GLU cc_start: 0.7248 (mt-10) cc_final: 0.7000 (mt-10) REVERT: C 375 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6729 (pt0) REVERT: C 441 GLU cc_start: 0.6552 (pt0) cc_final: 0.6334 (tt0) REVERT: C 456 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6200 (tm-30) REVERT: C 461 GLU cc_start: 0.6602 (tm-30) cc_final: 0.6312 (tm-30) REVERT: C 480 GLU cc_start: 0.6707 (mp0) cc_final: 0.6108 (mp0) REVERT: C 558 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6308 (tm-30) REVERT: D 49 GLU cc_start: 0.8151 (tt0) cc_final: 0.7735 (tt0) REVERT: D 62 GLU cc_start: 0.6534 (tp30) cc_final: 0.5746 (pm20) REVERT: D 87 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: D 162 GLU cc_start: 0.6695 (mp0) cc_final: 0.6420 (mm-30) REVERT: D 237 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7222 (mtt) REVERT: D 290 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6645 (t70) REVERT: D 302 GLU cc_start: 0.6977 (tt0) cc_final: 0.6530 (tp30) REVERT: D 314 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7424 (pt) REVERT: D 342 GLU cc_start: 0.6951 (tt0) cc_final: 0.6596 (mp0) REVERT: D 373 GLU cc_start: 0.6387 (pm20) cc_final: 0.6167 (pm20) REVERT: D 380 ASP cc_start: 0.6801 (m-30) cc_final: 0.6580 (m-30) REVERT: D 401 GLU cc_start: 0.5133 (OUTLIER) cc_final: 0.4765 (tm-30) REVERT: D 410 ARG cc_start: 0.6600 (ttm170) cc_final: 0.5978 (ttt90) REVERT: D 413 GLN cc_start: 0.6232 (mt0) cc_final: 0.5965 (mm-40) REVERT: D 420 ARG cc_start: 0.6815 (mtp180) cc_final: 0.6483 (mmt180) REVERT: D 453 ARG cc_start: 0.5151 (OUTLIER) cc_final: 0.4512 (mtt180) REVERT: D 465 GLN cc_start: 0.6016 (mm-40) cc_final: 0.5055 (pt0) REVERT: E 7 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6199 (mm-30) REVERT: E 25 LYS cc_start: 0.6750 (mtmt) cc_final: 0.6448 (mptm) REVERT: E 62 GLU cc_start: 0.6597 (pm20) cc_final: 0.6201 (pm20) REVERT: E 98 LYS cc_start: 0.6747 (mmmt) cc_final: 0.5431 (ttpt) REVERT: E 128 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6510 (pp20) REVERT: E 129 GLN cc_start: 0.7251 (mm110) cc_final: 0.6846 (mm-40) REVERT: E 206 GLN cc_start: 0.6298 (pt0) cc_final: 0.5653 (mt0) REVERT: E 237 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.6714 (mtp) REVERT: E 287 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7770 (ttp) REVERT: E 302 GLU cc_start: 0.7471 (tt0) cc_final: 0.6930 (tp30) REVERT: E 334 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: E 405 THR cc_start: 0.5323 (OUTLIER) cc_final: 0.4955 (t) REVERT: E 410 ARG cc_start: 0.6721 (tpp80) cc_final: 0.6318 (tpp80) REVERT: E 413 GLN cc_start: 0.6896 (mt0) cc_final: 0.6536 (mp10) REVERT: E 453 ARG cc_start: 0.6419 (mmt180) cc_final: 0.6151 (mmm160) REVERT: E 470 ILE cc_start: 0.3604 (OUTLIER) cc_final: 0.2957 (tt) REVERT: F 5 LYS cc_start: 0.5392 (ttpt) cc_final: 0.4876 (tttt) REVERT: F 23 ASN cc_start: 0.7391 (m110) cc_final: 0.7104 (t0) REVERT: F 98 LYS cc_start: 0.7155 (mmtt) cc_final: 0.6525 (mmmt) REVERT: F 103 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7139 (mm) REVERT: F 200 GLU cc_start: 0.7296 (mp0) cc_final: 0.6960 (mp0) REVERT: F 206 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.6407 (mp10) REVERT: F 216 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7526 (mtm-85) REVERT: F 280 ARG cc_start: 0.7323 (mtt180) cc_final: 0.7086 (mmt90) REVERT: F 305 LYS cc_start: 0.7382 (mmtm) cc_final: 0.7143 (mmmt) REVERT: F 318 ASP cc_start: 0.6736 (t70) cc_final: 0.6377 (t0) REVERT: F 368 LYS cc_start: 0.7168 (ttpt) cc_final: 0.6870 (ttpp) REVERT: F 376 LYS cc_start: 0.6643 (tptm) cc_final: 0.6359 (mttt) REVERT: F 394 LYS cc_start: 0.6810 (mmtm) cc_final: 0.6409 (mttp) REVERT: F 398 ILE cc_start: 0.6643 (mt) cc_final: 0.6195 (tp) REVERT: F 455 SER cc_start: 0.7559 (OUTLIER) cc_final: 0.7174 (p) REVERT: G 13 GLN cc_start: 0.6394 (OUTLIER) cc_final: 0.5691 (tt0) REVERT: G 17 GLN cc_start: 0.6624 (OUTLIER) cc_final: 0.6073 (mp10) REVERT: G 19 ARG cc_start: 0.5329 (mtm-85) cc_final: 0.5028 (ttp-110) REVERT: G 181 GLN cc_start: 0.6761 (mm-40) cc_final: 0.5671 (mt0) REVERT: G 196 ARG cc_start: 0.6133 (mtp-110) cc_final: 0.5905 (mtt180) REVERT: H 104 LEU cc_start: 0.3706 (pp) cc_final: 0.3152 (mp) REVERT: I 115 LEU cc_start: 0.2323 (OUTLIER) cc_final: 0.2064 (mt) REVERT: L 85 ARG cc_start: 0.2084 (ttp80) cc_final: 0.1613 (ttp-170) REVERT: L 162 GLN cc_start: 0.5472 (pt0) cc_final: 0.5073 (pt0) REVERT: L 164 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5432 (tp30) outliers start: 139 outliers final: 70 residues processed: 425 average time/residue: 1.7163 time to fit residues: 833.5610 Evaluate side-chains 407 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 309 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 128 GLU 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 237 MET Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 164 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 303 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 359 optimal weight: 20.0000 chunk 224 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 316 GLN B 397 GLN D 338 GLN E 364 ASN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN H 84 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30114 Z= 0.211 Angle : 0.541 7.922 40813 Z= 0.280 Chirality : 0.044 0.186 4572 Planarity : 0.005 0.053 5333 Dihedral : 6.485 114.464 4259 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.05 % Allowed : 16.38 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.14), residues: 3764 helix: 0.94 (0.14), residues: 1565 sheet: 0.27 (0.23), residues: 540 loop : -0.55 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 175 HIS 0.023 0.001 HIS H 84 PHE 0.025 0.001 PHE B 522 TYR 0.013 0.001 TYR C 562 ARG 0.004 0.000 ARG B 550 *********************** 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 443 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 318 time to evaluate : 3.513 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7189 (mt0) cc_final: 0.6961 (tt0) REVERT: A 114 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6662 (mm-30) REVERT: A 122 MET cc_start: 0.6726 (mtp) cc_final: 0.6273 (mtt) REVERT: A 124 LYS cc_start: 0.6218 (mtmm) cc_final: 0.5822 (mttp) REVERT: A 128 GLU cc_start: 0.6203 (tp30) cc_final: 0.5697 (pt0) REVERT: A 154 ARG cc_start: 0.6547 (mtp85) cc_final: 0.5910 (mtt90) REVERT: A 220 MET cc_start: 0.6534 (tpt) cc_final: 0.6314 (tpt) REVERT: A 276 LYS cc_start: 0.5124 (ptmt) cc_final: 0.4179 (pptt) REVERT: A 277 THR cc_start: 0.7836 (m) cc_final: 0.7236 (p) REVERT: A 357 ARG cc_start: 0.6523 (OUTLIER) cc_final: 0.4215 (mmt180) REVERT: A 410 ASP cc_start: 0.6050 (t0) cc_final: 0.5604 (t0) REVERT: A 441 GLU cc_start: 0.6510 (mm-30) cc_final: 0.5872 (mm-30) REVERT: A 469 GLN cc_start: 0.5788 (mt0) cc_final: 0.5208 (mm-40) REVERT: A 491 ARG cc_start: 0.6203 (mmt180) cc_final: 0.5148 (mtp85) REVERT: A 496 GLN cc_start: 0.7609 (tt0) cc_final: 0.7185 (tt0) REVERT: A 508 SER cc_start: 0.7925 (t) cc_final: 0.7341 (p) REVERT: A 527 GLU cc_start: 0.5875 (tt0) cc_final: 0.5297 (tp30) REVERT: A 546 GLU cc_start: 0.5609 (pp20) cc_final: 0.5367 (mm-30) REVERT: B 1 MET cc_start: 0.6152 (mtm) cc_final: 0.5701 (mtp) REVERT: B 2 ILE cc_start: 0.8163 (mm) cc_final: 0.7918 (mm) REVERT: B 29 LYS cc_start: 0.7412 (mtpt) cc_final: 0.7003 (mttp) REVERT: B 53 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: B 104 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.5123 (ptp-170) REVERT: B 114 GLU cc_start: 0.6373 (mm-30) cc_final: 0.6002 (mt-10) REVERT: B 137 THR cc_start: 0.8096 (p) cc_final: 0.7870 (t) REVERT: B 180 GLU cc_start: 0.6377 (mt-10) cc_final: 0.6050 (pt0) REVERT: B 197 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6159 (ptp90) REVERT: B 408 ARG cc_start: 0.6548 (ttm170) cc_final: 0.6270 (tpp80) REVERT: B 565 GLU cc_start: 0.5187 (mm-30) cc_final: 0.4586 (tp30) REVERT: C 29 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7992 (mmtm) REVERT: C 83 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8424 (tp) REVERT: C 122 MET cc_start: 0.7395 (mtm) cc_final: 0.7054 (mpp) REVERT: C 138 VAL cc_start: 0.7399 (OUTLIER) cc_final: 0.7038 (p) REVERT: C 182 LYS cc_start: 0.7340 (mtmt) cc_final: 0.7077 (mtmt) REVERT: C 197 ARG cc_start: 0.7009 (ttp-110) cc_final: 0.6483 (ttp-170) REVERT: C 209 MET cc_start: 0.7706 (mtp) cc_final: 0.7433 (mtp) REVERT: C 276 LYS cc_start: 0.6613 (OUTLIER) cc_final: 0.6243 (ptmt) REVERT: C 336 GLU cc_start: 0.5995 (tp30) cc_final: 0.5646 (tp30) REVERT: C 347 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6997 (mt-10) REVERT: C 456 GLU cc_start: 0.6675 (mm-30) cc_final: 0.6221 (tm-30) REVERT: C 461 GLU cc_start: 0.6616 (tm-30) cc_final: 0.6277 (tm-30) REVERT: C 480 GLU cc_start: 0.6687 (mp0) cc_final: 0.6076 (mp0) REVERT: C 558 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6337 (tm-30) REVERT: D 46 GLN cc_start: 0.8492 (tt0) cc_final: 0.8006 (tt0) REVERT: D 49 GLU cc_start: 0.8134 (tt0) cc_final: 0.7729 (tt0) REVERT: D 62 GLU cc_start: 0.6543 (tp30) cc_final: 0.5748 (pm20) REVERT: D 162 GLU cc_start: 0.6643 (mp0) cc_final: 0.6351 (mm-30) REVERT: D 290 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6432 (t70) REVERT: D 302 GLU cc_start: 0.6909 (tt0) cc_final: 0.6441 (tp30) REVERT: D 342 GLU cc_start: 0.6924 (tt0) cc_final: 0.6365 (mp0) REVERT: D 373 GLU cc_start: 0.6355 (pm20) cc_final: 0.6101 (pm20) REVERT: D 380 ASP cc_start: 0.6729 (m-30) cc_final: 0.6524 (m-30) REVERT: D 401 GLU cc_start: 0.5099 (OUTLIER) cc_final: 0.4749 (tm-30) REVERT: D 410 ARG cc_start: 0.6588 (ttm170) cc_final: 0.5948 (ttt90) REVERT: D 413 GLN cc_start: 0.6200 (mt0) cc_final: 0.5958 (mm-40) REVERT: D 420 ARG cc_start: 0.6826 (mtp180) cc_final: 0.6489 (mmt180) REVERT: D 434 GLU cc_start: 0.5581 (mt-10) cc_final: 0.5183 (mt-10) REVERT: D 453 ARG cc_start: 0.5126 (OUTLIER) cc_final: 0.4365 (mtt180) REVERT: D 465 GLN cc_start: 0.6018 (mm-40) cc_final: 0.5086 (pt0) REVERT: E 7 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6199 (mm-30) REVERT: E 25 LYS cc_start: 0.6784 (mtmt) cc_final: 0.6484 (mptm) REVERT: E 62 GLU cc_start: 0.6683 (pm20) cc_final: 0.6284 (pm20) REVERT: E 78 ASP cc_start: 0.6979 (m-30) cc_final: 0.6762 (m-30) REVERT: E 98 LYS cc_start: 0.6756 (mmmt) cc_final: 0.5419 (ttpp) REVERT: E 128 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6499 (pp20) REVERT: E 129 GLN cc_start: 0.7196 (mm110) cc_final: 0.6856 (mm-40) REVERT: E 206 GLN cc_start: 0.6259 (pt0) cc_final: 0.5596 (mt0) REVERT: E 237 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.6745 (mtp) REVERT: E 287 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7734 (ttp) REVERT: E 302 GLU cc_start: 0.7461 (tt0) cc_final: 0.6916 (tp30) REVERT: E 334 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7172 (mt-10) REVERT: E 405 THR cc_start: 0.5168 (OUTLIER) cc_final: 0.4877 (t) REVERT: E 410 ARG cc_start: 0.6652 (tpp80) cc_final: 0.6423 (tpp80) REVERT: E 413 GLN cc_start: 0.6912 (mt0) cc_final: 0.6563 (mp10) REVERT: E 453 ARG cc_start: 0.6414 (mmt180) cc_final: 0.6147 (mmm160) REVERT: E 468 GLU cc_start: 0.3603 (OUTLIER) cc_final: 0.2867 (pp20) REVERT: E 470 ILE cc_start: 0.3690 (OUTLIER) cc_final: 0.3056 (tt) REVERT: F 5 LYS cc_start: 0.5423 (ttpt) cc_final: 0.4909 (tttt) REVERT: F 98 LYS cc_start: 0.7084 (mmtt) cc_final: 0.6450 (mmmt) REVERT: F 103 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7086 (mm) REVERT: F 206 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6397 (mp10) REVERT: F 280 ARG cc_start: 0.7352 (mtt180) cc_final: 0.7100 (mmt90) REVERT: F 305 LYS cc_start: 0.7383 (mmtm) cc_final: 0.7160 (mmmt) REVERT: F 368 LYS cc_start: 0.7113 (ttpt) cc_final: 0.6818 (ttpp) REVERT: F 394 LYS cc_start: 0.6766 (mmtm) cc_final: 0.6468 (mttp) REVERT: F 398 ILE cc_start: 0.6615 (mt) cc_final: 0.6193 (tp) REVERT: F 399 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6723 (pp) REVERT: G 13 GLN cc_start: 0.6362 (OUTLIER) cc_final: 0.5814 (tt0) REVERT: G 19 ARG cc_start: 0.5267 (mtm-85) cc_final: 0.4931 (ttp-110) REVERT: G 196 ARG cc_start: 0.6095 (mtp-110) cc_final: 0.5778 (mtt180) REVERT: H 104 LEU cc_start: 0.3648 (pp) cc_final: 0.3104 (mp) REVERT: I 115 LEU cc_start: 0.2096 (OUTLIER) cc_final: 0.1858 (mt) REVERT: L 85 ARG cc_start: 0.2081 (ttp80) cc_final: 0.1591 (ttp-170) REVERT: L 162 GLN cc_start: 0.5521 (pt0) cc_final: 0.5077 (pt0) REVERT: L 164 GLU cc_start: 0.5678 (OUTLIER) cc_final: 0.5382 (tp30) outliers start: 125 outliers final: 62 residues processed: 417 average time/residue: 1.6894 time to fit residues: 804.3568 Evaluate side-chains 393 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 306 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 164 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 282 optimal weight: 0.0470 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 397 GLN E 364 ASN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN H 84 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30114 Z= 0.286 Angle : 0.597 11.683 40813 Z= 0.306 Chirality : 0.046 0.207 4572 Planarity : 0.006 0.055 5333 Dihedral : 6.601 112.134 4259 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.09 % Allowed : 17.19 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3764 helix: 0.83 (0.13), residues: 1564 sheet: 0.17 (0.23), residues: 544 loop : -0.58 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 175 HIS 0.014 0.001 HIS H 84 PHE 0.027 0.002 PHE B 522 TYR 0.013 0.002 TYR F 463 ARG 0.006 0.001 ARG A 93 *********************** 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 434 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 308 time to evaluate : 3.872 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7201 (mt0) cc_final: 0.6977 (tt0) REVERT: A 114 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6631 (mm-30) REVERT: A 122 MET cc_start: 0.6789 (mtp) cc_final: 0.6338 (mtt) REVERT: A 124 LYS cc_start: 0.6214 (mtmm) cc_final: 0.5794 (mttp) REVERT: A 128 GLU cc_start: 0.6238 (tp30) cc_final: 0.5705 (pt0) REVERT: A 154 ARG cc_start: 0.6528 (mtp85) cc_final: 0.5928 (mtt90) REVERT: A 276 LYS cc_start: 0.5071 (OUTLIER) cc_final: 0.4180 (pptt) REVERT: A 277 THR cc_start: 0.7844 (m) cc_final: 0.7206 (p) REVERT: A 357 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.4346 (mmt180) REVERT: A 410 ASP cc_start: 0.6124 (t0) cc_final: 0.5666 (t0) REVERT: A 441 GLU cc_start: 0.6517 (mm-30) cc_final: 0.5893 (mm-30) REVERT: A 469 GLN cc_start: 0.5812 (mt0) cc_final: 0.5224 (mm-40) REVERT: A 491 ARG cc_start: 0.6173 (mmt180) cc_final: 0.4938 (mtp85) REVERT: A 492 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.4951 (mp0) REVERT: A 496 GLN cc_start: 0.7616 (tt0) cc_final: 0.7209 (tt0) REVERT: A 508 SER cc_start: 0.7912 (t) cc_final: 0.7320 (p) REVERT: A 527 GLU cc_start: 0.5909 (tt0) cc_final: 0.5291 (tp30) REVERT: A 531 LYS cc_start: 0.4969 (mtpt) cc_final: 0.4677 (ttmt) REVERT: B 1 MET cc_start: 0.6157 (mtm) cc_final: 0.5735 (mtp) REVERT: B 2 ILE cc_start: 0.8184 (mm) cc_final: 0.7969 (mm) REVERT: B 29 LYS cc_start: 0.7425 (mtpt) cc_final: 0.7031 (mttp) REVERT: B 53 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: B 104 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.5225 (ptp-170) REVERT: B 114 GLU cc_start: 0.6387 (mm-30) cc_final: 0.6018 (mt-10) REVERT: B 137 THR cc_start: 0.8105 (p) cc_final: 0.7862 (t) REVERT: B 180 GLU cc_start: 0.6379 (mt-10) cc_final: 0.6069 (pt0) REVERT: B 197 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6107 (ptp90) REVERT: B 408 ARG cc_start: 0.6541 (ttm170) cc_final: 0.6262 (tpp80) REVERT: B 565 GLU cc_start: 0.5143 (mm-30) cc_final: 0.4556 (tp30) REVERT: C 29 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7974 (mmtm) REVERT: C 83 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8410 (tp) REVERT: C 122 MET cc_start: 0.7407 (mtm) cc_final: 0.6999 (mpp) REVERT: C 182 LYS cc_start: 0.7361 (mtmt) cc_final: 0.7090 (mtmt) REVERT: C 197 ARG cc_start: 0.7011 (ttp-110) cc_final: 0.6477 (ttp-170) REVERT: C 209 MET cc_start: 0.7752 (mtp) cc_final: 0.7471 (mtp) REVERT: C 276 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.6165 (ptmt) REVERT: C 336 GLU cc_start: 0.6047 (tp30) cc_final: 0.5690 (tp30) REVERT: C 347 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7043 (mt-10) REVERT: C 456 GLU cc_start: 0.6670 (mm-30) cc_final: 0.6208 (tm-30) REVERT: C 461 GLU cc_start: 0.6589 (tm-30) cc_final: 0.6252 (tm-30) REVERT: C 480 GLU cc_start: 0.6712 (mp0) cc_final: 0.6020 (mp0) REVERT: C 558 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6325 (tm-30) REVERT: D 46 GLN cc_start: 0.8511 (tt0) cc_final: 0.8027 (tt0) REVERT: D 49 GLU cc_start: 0.8159 (tt0) cc_final: 0.7757 (tt0) REVERT: D 62 GLU cc_start: 0.6638 (tp30) cc_final: 0.5841 (pm20) REVERT: D 87 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: D 162 GLU cc_start: 0.6704 (mp0) cc_final: 0.6426 (mm-30) REVERT: D 237 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7220 (mtt) REVERT: D 290 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6549 (t70) REVERT: D 302 GLU cc_start: 0.6960 (tt0) cc_final: 0.6510 (tp30) REVERT: D 314 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7420 (pt) REVERT: D 342 GLU cc_start: 0.6931 (tt0) cc_final: 0.6571 (mp0) REVERT: D 373 GLU cc_start: 0.6355 (pm20) cc_final: 0.6095 (pm20) REVERT: D 380 ASP cc_start: 0.6788 (m-30) cc_final: 0.6565 (m-30) REVERT: D 401 GLU cc_start: 0.5169 (OUTLIER) cc_final: 0.4791 (tm-30) REVERT: D 410 ARG cc_start: 0.6596 (ttm170) cc_final: 0.5971 (ttt90) REVERT: D 413 GLN cc_start: 0.6147 (mt0) cc_final: 0.5914 (mm-40) REVERT: D 420 ARG cc_start: 0.6781 (mtp180) cc_final: 0.6426 (mmt180) REVERT: D 453 ARG cc_start: 0.5162 (OUTLIER) cc_final: 0.4382 (mtt180) REVERT: D 465 GLN cc_start: 0.5999 (mm-40) cc_final: 0.5067 (pt0) REVERT: E 7 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6171 (mm-30) REVERT: E 25 LYS cc_start: 0.6795 (mtmt) cc_final: 0.6485 (mptm) REVERT: E 62 GLU cc_start: 0.6613 (pm20) cc_final: 0.6201 (pm20) REVERT: E 98 LYS cc_start: 0.6782 (mmmt) cc_final: 0.5426 (ttpp) REVERT: E 128 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6536 (pp20) REVERT: E 129 GLN cc_start: 0.7210 (mm110) cc_final: 0.6857 (mm-40) REVERT: E 206 GLN cc_start: 0.6268 (pt0) cc_final: 0.5656 (mt0) REVERT: E 237 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.6713 (mtp) REVERT: E 287 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7760 (ttp) REVERT: E 302 GLU cc_start: 0.7501 (tt0) cc_final: 0.6960 (tp30) REVERT: E 334 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: E 405 THR cc_start: 0.5439 (OUTLIER) cc_final: 0.5114 (t) REVERT: E 413 GLN cc_start: 0.6905 (mt0) cc_final: 0.6550 (mp10) REVERT: E 453 ARG cc_start: 0.6412 (mmt180) cc_final: 0.6164 (mmm160) REVERT: E 468 GLU cc_start: 0.3620 (OUTLIER) cc_final: 0.2891 (pp20) REVERT: E 470 ILE cc_start: 0.3620 (OUTLIER) cc_final: 0.2965 (tt) REVERT: F 5 LYS cc_start: 0.5339 (ttpt) cc_final: 0.4863 (tttt) REVERT: F 81 ARG cc_start: 0.7213 (mtt-85) cc_final: 0.6907 (mtt180) REVERT: F 98 LYS cc_start: 0.7144 (mmtt) cc_final: 0.6529 (mmmt) REVERT: F 103 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7106 (mm) REVERT: F 206 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6393 (mp10) REVERT: F 280 ARG cc_start: 0.7358 (mtt180) cc_final: 0.7121 (mmt90) REVERT: F 305 LYS cc_start: 0.7377 (mmtm) cc_final: 0.7135 (mmmt) REVERT: F 368 LYS cc_start: 0.7094 (ttpt) cc_final: 0.6819 (ttpp) REVERT: F 394 LYS cc_start: 0.6832 (mmtm) cc_final: 0.6536 (mttp) REVERT: F 398 ILE cc_start: 0.6598 (mt) cc_final: 0.6181 (tp) REVERT: F 399 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6768 (pp) REVERT: F 413 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6743 (mp10) REVERT: F 455 SER cc_start: 0.7614 (OUTLIER) cc_final: 0.7234 (p) REVERT: G 13 GLN cc_start: 0.6425 (OUTLIER) cc_final: 0.5841 (tt0) REVERT: G 19 ARG cc_start: 0.5343 (mtm-85) cc_final: 0.5003 (ttp-110) REVERT: G 196 ARG cc_start: 0.6067 (mtp-110) cc_final: 0.5788 (mtt180) REVERT: H 104 LEU cc_start: 0.3624 (pp) cc_final: 0.3092 (mp) REVERT: I 115 LEU cc_start: 0.2134 (OUTLIER) cc_final: 0.1897 (mt) REVERT: J 92 GLU cc_start: 0.2934 (pt0) cc_final: 0.1841 (mt-10) REVERT: L 85 ARG cc_start: 0.2381 (ttp80) cc_final: 0.1852 (ttp-170) REVERT: L 86 ARG cc_start: 0.2111 (ttp80) cc_final: 0.1595 (tpt170) REVERT: L 162 GLN cc_start: 0.5507 (pt0) cc_final: 0.5069 (pt0) REVERT: L 164 GLU cc_start: 0.5617 (OUTLIER) cc_final: 0.5323 (tp30) outliers start: 126 outliers final: 70 residues processed: 407 average time/residue: 1.7469 time to fit residues: 816.4064 Evaluate side-chains 401 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 300 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 164 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 7.9990 chunk 344 optimal weight: 8.9990 chunk 314 optimal weight: 20.0000 chunk 335 optimal weight: 30.0000 chunk 201 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 263 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 316 optimal weight: 5.9990 chunk 333 optimal weight: 40.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 397 GLN E 364 ASN G 180 GLN H 84 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 30114 Z= 0.377 Angle : 0.661 9.668 40813 Z= 0.340 Chirality : 0.048 0.223 4572 Planarity : 0.006 0.053 5333 Dihedral : 6.868 110.431 4259 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.12 % Allowed : 17.29 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3764 helix: 0.63 (0.13), residues: 1557 sheet: 0.06 (0.23), residues: 544 loop : -0.69 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 175 HIS 0.015 0.002 HIS H 84 PHE 0.028 0.002 PHE B 522 TYR 0.015 0.002 TYR F 203 ARG 0.005 0.001 ARG E 297 *********************** 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 432 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 305 time to evaluate : 3.712 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7278 (mt0) cc_final: 0.7010 (tt0) REVERT: A 114 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6680 (mm-30) REVERT: A 122 MET cc_start: 0.6742 (mtp) cc_final: 0.6278 (mtt) REVERT: A 124 LYS cc_start: 0.6170 (mtmm) cc_final: 0.5798 (mttp) REVERT: A 128 GLU cc_start: 0.6307 (tp30) cc_final: 0.5763 (pt0) REVERT: A 154 ARG cc_start: 0.6412 (mtp85) cc_final: 0.5917 (mtm-85) REVERT: A 276 LYS cc_start: 0.5105 (OUTLIER) cc_final: 0.4183 (pptt) REVERT: A 277 THR cc_start: 0.7870 (m) cc_final: 0.7271 (p) REVERT: A 357 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.4355 (mmt180) REVERT: A 410 ASP cc_start: 0.6139 (t0) cc_final: 0.5685 (t0) REVERT: A 441 GLU cc_start: 0.6524 (mm-30) cc_final: 0.5882 (mm-30) REVERT: A 469 GLN cc_start: 0.5810 (mt0) cc_final: 0.5240 (mm-40) REVERT: A 491 ARG cc_start: 0.6188 (mmt180) cc_final: 0.4925 (mtp85) REVERT: A 492 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.4987 (mp0) REVERT: A 496 GLN cc_start: 0.7631 (tt0) cc_final: 0.7308 (tt0) REVERT: A 508 SER cc_start: 0.7911 (t) cc_final: 0.7322 (p) REVERT: A 516 MET cc_start: 0.7252 (mtm) cc_final: 0.6789 (mtp) REVERT: A 531 LYS cc_start: 0.5106 (mtpt) cc_final: 0.4788 (ttmt) REVERT: B 2 ILE cc_start: 0.8125 (mm) cc_final: 0.7914 (mm) REVERT: B 29 LYS cc_start: 0.7462 (mtpt) cc_final: 0.7065 (mttp) REVERT: B 53 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7130 (mt-10) REVERT: B 104 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.5333 (ptp-170) REVERT: B 114 GLU cc_start: 0.6397 (mm-30) cc_final: 0.5983 (mt-10) REVERT: B 137 THR cc_start: 0.8125 (p) cc_final: 0.7854 (t) REVERT: B 180 GLU cc_start: 0.6398 (mt-10) cc_final: 0.6053 (pt0) REVERT: B 197 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6126 (ptp90) REVERT: B 276 LYS cc_start: 0.5850 (mttt) cc_final: 0.4975 (mtpm) REVERT: B 375 GLU cc_start: 0.7384 (tt0) cc_final: 0.6940 (tt0) REVERT: B 408 ARG cc_start: 0.6527 (ttm170) cc_final: 0.6253 (tpp80) REVERT: B 565 GLU cc_start: 0.5260 (mm-30) cc_final: 0.4617 (tp30) REVERT: C 83 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8368 (tp) REVERT: C 122 MET cc_start: 0.7457 (mtm) cc_final: 0.6974 (mpp) REVERT: C 182 LYS cc_start: 0.7361 (mtmt) cc_final: 0.7155 (mtmt) REVERT: C 197 ARG cc_start: 0.7018 (ttp-110) cc_final: 0.6471 (ttp-170) REVERT: C 209 MET cc_start: 0.7788 (mtp) cc_final: 0.7492 (mtp) REVERT: C 276 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6222 (ptmt) REVERT: C 336 GLU cc_start: 0.6033 (tp30) cc_final: 0.5764 (tp30) REVERT: C 347 GLU cc_start: 0.7259 (mt-10) cc_final: 0.7015 (mt-10) REVERT: C 375 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6726 (pt0) REVERT: C 456 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6219 (tm-30) REVERT: C 461 GLU cc_start: 0.6605 (tm-30) cc_final: 0.6315 (tm-30) REVERT: C 480 GLU cc_start: 0.6838 (mp0) cc_final: 0.6153 (mp0) REVERT: C 558 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6292 (tm-30) REVERT: D 46 GLN cc_start: 0.8510 (tt0) cc_final: 0.8013 (tt0) REVERT: D 49 GLU cc_start: 0.8155 (tt0) cc_final: 0.7734 (tt0) REVERT: D 162 GLU cc_start: 0.6718 (mp0) cc_final: 0.6446 (mm-30) REVERT: D 237 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7207 (mtt) REVERT: D 290 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6762 (t70) REVERT: D 302 GLU cc_start: 0.6967 (tt0) cc_final: 0.6530 (tp30) REVERT: D 314 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7460 (pt) REVERT: D 342 GLU cc_start: 0.6900 (tt0) cc_final: 0.6521 (mp0) REVERT: D 373 GLU cc_start: 0.6394 (pm20) cc_final: 0.6124 (pm20) REVERT: D 380 ASP cc_start: 0.6845 (m-30) cc_final: 0.6615 (m-30) REVERT: D 401 GLU cc_start: 0.5267 (OUTLIER) cc_final: 0.4807 (tm-30) REVERT: D 410 ARG cc_start: 0.6611 (ttm170) cc_final: 0.5979 (ttt90) REVERT: D 413 GLN cc_start: 0.6166 (mt0) cc_final: 0.5951 (mm-40) REVERT: D 420 ARG cc_start: 0.6816 (mtp180) cc_final: 0.6481 (mmt180) REVERT: D 453 ARG cc_start: 0.5182 (OUTLIER) cc_final: 0.4433 (mtt180) REVERT: D 465 GLN cc_start: 0.6019 (mm-40) cc_final: 0.5158 (pt0) REVERT: E 7 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6140 (mm-30) REVERT: E 25 LYS cc_start: 0.6774 (mtmt) cc_final: 0.6458 (mptm) REVERT: E 62 GLU cc_start: 0.6570 (pm20) cc_final: 0.6110 (pm20) REVERT: E 98 LYS cc_start: 0.6844 (mmmt) cc_final: 0.5501 (ttpt) REVERT: E 128 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6522 (pp20) REVERT: E 129 GLN cc_start: 0.7257 (mm110) cc_final: 0.6843 (mm-40) REVERT: E 206 GLN cc_start: 0.6288 (pt0) cc_final: 0.5654 (mt0) REVERT: E 237 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.6759 (mtp) REVERT: E 287 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7673 (ttp) REVERT: E 302 GLU cc_start: 0.7503 (tt0) cc_final: 0.6958 (tp30) REVERT: E 334 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: E 405 THR cc_start: 0.5796 (OUTLIER) cc_final: 0.5375 (t) REVERT: E 413 GLN cc_start: 0.6965 (mt0) cc_final: 0.6602 (mp10) REVERT: E 453 ARG cc_start: 0.6412 (mmt180) cc_final: 0.6166 (mmm160) REVERT: E 468 GLU cc_start: 0.3609 (OUTLIER) cc_final: 0.2891 (pp20) REVERT: E 470 ILE cc_start: 0.3676 (OUTLIER) cc_final: 0.3012 (tt) REVERT: F 5 LYS cc_start: 0.5373 (ttpt) cc_final: 0.4920 (tttt) REVERT: F 23 ASN cc_start: 0.7422 (m110) cc_final: 0.7112 (t0) REVERT: F 98 LYS cc_start: 0.7219 (mmtt) cc_final: 0.6604 (mmmt) REVERT: F 103 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7138 (mm) REVERT: F 130 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7365 (t80) REVERT: F 206 GLN cc_start: 0.6747 (OUTLIER) cc_final: 0.6407 (mp10) REVERT: F 216 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7525 (mtm-85) REVERT: F 305 LYS cc_start: 0.7380 (mmtm) cc_final: 0.7141 (mmmt) REVERT: F 368 LYS cc_start: 0.7099 (ttpt) cc_final: 0.6819 (ttpp) REVERT: F 394 LYS cc_start: 0.6957 (mmtm) cc_final: 0.6544 (mttp) REVERT: F 398 ILE cc_start: 0.6610 (mt) cc_final: 0.6155 (tp) REVERT: F 448 GLN cc_start: 0.7349 (tt0) cc_final: 0.7036 (mt0) REVERT: F 455 SER cc_start: 0.7582 (OUTLIER) cc_final: 0.7250 (p) REVERT: G 13 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.5809 (tt0) REVERT: G 19 ARG cc_start: 0.5288 (mtm-85) cc_final: 0.5020 (ttp-110) REVERT: G 196 ARG cc_start: 0.6057 (mtp-110) cc_final: 0.5812 (mtt180) REVERT: I 115 LEU cc_start: 0.2301 (OUTLIER) cc_final: 0.2033 (mt) REVERT: J 92 GLU cc_start: 0.3050 (pt0) cc_final: 0.1944 (mt-10) REVERT: L 85 ARG cc_start: 0.2478 (ttp80) cc_final: 0.1898 (ttp-170) REVERT: L 86 ARG cc_start: 0.2057 (ttp80) cc_final: 0.1552 (tpt170) REVERT: L 162 GLN cc_start: 0.5564 (pt0) cc_final: 0.5140 (pt0) REVERT: L 164 GLU cc_start: 0.5682 (OUTLIER) cc_final: 0.5372 (tp30) outliers start: 127 outliers final: 76 residues processed: 403 average time/residue: 1.7385 time to fit residues: 805.5411 Evaluate side-chains 409 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 304 time to evaluate : 3.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 164 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 0.0980 chunk 354 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 246 optimal weight: 0.9990 chunk 371 optimal weight: 10.0000 chunk 342 optimal weight: 20.0000 chunk 295 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 228 optimal weight: 0.0870 chunk 181 optimal weight: 7.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 50 GLN E 364 ASN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 407 ASN F 413 GLN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN G 181 GLN H 84 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30114 Z= 0.147 Angle : 0.499 10.615 40813 Z= 0.258 Chirality : 0.042 0.202 4572 Planarity : 0.005 0.051 5333 Dihedral : 6.107 109.514 4259 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.30 % Allowed : 19.27 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3764 helix: 1.21 (0.14), residues: 1544 sheet: 0.27 (0.22), residues: 561 loop : -0.40 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 424 HIS 0.032 0.001 HIS H 84 PHE 0.020 0.001 PHE B 522 TYR 0.012 0.001 TYR F 463 ARG 0.005 0.000 ARG A 93 ********************** 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 393 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 322 time to evaluate : 3.297 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6627 (mm-30) REVERT: A 122 MET cc_start: 0.6666 (mtp) cc_final: 0.6189 (mtt) REVERT: A 124 LYS cc_start: 0.6214 (mtmm) cc_final: 0.5835 (mttp) REVERT: A 128 GLU cc_start: 0.6303 (tp30) cc_final: 0.5731 (pt0) REVERT: A 154 ARG cc_start: 0.6511 (mtp85) cc_final: 0.5864 (mtt90) REVERT: A 276 LYS cc_start: 0.5107 (ptmt) cc_final: 0.4184 (pptt) REVERT: A 277 THR cc_start: 0.7789 (m) cc_final: 0.7047 (p) REVERT: A 357 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.4199 (mmt180) REVERT: A 410 ASP cc_start: 0.6076 (t0) cc_final: 0.5619 (t0) REVERT: A 441 GLU cc_start: 0.6537 (mm-30) cc_final: 0.5893 (mm-30) REVERT: A 469 GLN cc_start: 0.5752 (mt0) cc_final: 0.5336 (mm-40) REVERT: A 476 LEU cc_start: 0.7128 (mm) cc_final: 0.6920 (mt) REVERT: A 496 GLN cc_start: 0.7635 (tt0) cc_final: 0.7218 (tt0) REVERT: A 508 SER cc_start: 0.7842 (t) cc_final: 0.7267 (p) REVERT: A 516 MET cc_start: 0.7121 (mtm) cc_final: 0.6778 (mtp) REVERT: A 527 GLU cc_start: 0.5807 (tt0) cc_final: 0.5247 (tp30) REVERT: A 531 LYS cc_start: 0.4877 (mtpt) cc_final: 0.4581 (ttmt) REVERT: B 1 MET cc_start: 0.6211 (mtm) cc_final: 0.5808 (mtp) REVERT: B 2 ILE cc_start: 0.8197 (mm) cc_final: 0.7948 (mm) REVERT: B 29 LYS cc_start: 0.7420 (mtpt) cc_final: 0.7019 (mttp) REVERT: B 53 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6935 (mt-10) REVERT: B 104 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.5298 (ptp-170) REVERT: B 114 GLU cc_start: 0.6240 (mm-30) cc_final: 0.5820 (mt-10) REVERT: B 137 THR cc_start: 0.8098 (p) cc_final: 0.7897 (t) REVERT: B 156 ARG cc_start: 0.6563 (ttp80) cc_final: 0.6167 (ttp80) REVERT: B 180 GLU cc_start: 0.6417 (mt-10) cc_final: 0.5999 (pt0) REVERT: B 197 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.6234 (ptt180) REVERT: B 408 ARG cc_start: 0.6526 (ttm170) cc_final: 0.6114 (tpp80) REVERT: B 565 GLU cc_start: 0.5310 (mm-30) cc_final: 0.4675 (tp30) REVERT: C 29 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7977 (mmtp) REVERT: C 122 MET cc_start: 0.7437 (mtm) cc_final: 0.6987 (mpp) REVERT: C 197 ARG cc_start: 0.7083 (ttp-110) cc_final: 0.6491 (ttp-170) REVERT: C 336 GLU cc_start: 0.5940 (tp30) cc_final: 0.5602 (tp30) REVERT: C 347 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6992 (mt-10) REVERT: C 456 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6304 (tm-30) REVERT: C 461 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6321 (tm-30) REVERT: C 480 GLU cc_start: 0.6734 (mp0) cc_final: 0.6131 (mp0) REVERT: C 536 ILE cc_start: 0.6424 (OUTLIER) cc_final: 0.5930 (pt) REVERT: C 558 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6362 (tm-30) REVERT: D 46 GLN cc_start: 0.8502 (tt0) cc_final: 0.8055 (tt0) REVERT: D 49 GLU cc_start: 0.8114 (tt0) cc_final: 0.7708 (tt0) REVERT: D 87 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: D 162 GLU cc_start: 0.6764 (mp0) cc_final: 0.6454 (mm-30) REVERT: D 290 ASP cc_start: 0.6628 (OUTLIER) cc_final: 0.6343 (t70) REVERT: D 302 GLU cc_start: 0.6994 (tt0) cc_final: 0.6463 (tp30) REVERT: D 314 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7350 (pt) REVERT: D 342 GLU cc_start: 0.6918 (tt0) cc_final: 0.6393 (mp0) REVERT: D 410 ARG cc_start: 0.6540 (ttm170) cc_final: 0.5815 (ttt90) REVERT: D 420 ARG cc_start: 0.6723 (mtp180) cc_final: 0.6435 (mmt180) REVERT: D 434 GLU cc_start: 0.5513 (mt-10) cc_final: 0.5149 (mt-10) REVERT: D 453 ARG cc_start: 0.5287 (OUTLIER) cc_final: 0.4478 (mtt180) REVERT: D 465 GLN cc_start: 0.5967 (mm-40) cc_final: 0.5154 (pt0) REVERT: E 25 LYS cc_start: 0.6782 (mtmt) cc_final: 0.6467 (mppt) REVERT: E 62 GLU cc_start: 0.6721 (pm20) cc_final: 0.6204 (pm20) REVERT: E 98 LYS cc_start: 0.6819 (mmmt) cc_final: 0.5417 (ttpp) REVERT: E 129 GLN cc_start: 0.7144 (mm110) cc_final: 0.6827 (mm-40) REVERT: E 206 GLN cc_start: 0.6268 (pt0) cc_final: 0.5642 (mt0) REVERT: E 237 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.6703 (mtp) REVERT: E 287 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7716 (ttp) REVERT: E 302 GLU cc_start: 0.7448 (tt0) cc_final: 0.6921 (tp30) REVERT: E 334 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: E 413 GLN cc_start: 0.6919 (mt0) cc_final: 0.6613 (mp10) REVERT: E 453 ARG cc_start: 0.6452 (mmt180) cc_final: 0.6148 (mmm160) REVERT: E 470 ILE cc_start: 0.3722 (OUTLIER) cc_final: 0.3080 (tt) REVERT: F 5 LYS cc_start: 0.5370 (ttpt) cc_final: 0.4920 (tttt) REVERT: F 98 LYS cc_start: 0.7008 (mmtt) cc_final: 0.6288 (mmmt) REVERT: F 103 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7105 (mm) REVERT: F 194 MET cc_start: 0.8260 (mtm) cc_final: 0.7764 (mpp) REVERT: F 305 LYS cc_start: 0.7407 (mmtm) cc_final: 0.7179 (mmmt) REVERT: F 368 LYS cc_start: 0.7022 (ttpt) cc_final: 0.6786 (ttpp) REVERT: F 394 LYS cc_start: 0.6702 (mmtm) cc_final: 0.6410 (mttp) REVERT: F 398 ILE cc_start: 0.6776 (mt) cc_final: 0.6288 (tp) REVERT: F 399 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6561 (pp) REVERT: F 455 SER cc_start: 0.7437 (OUTLIER) cc_final: 0.7164 (p) REVERT: G 19 ARG cc_start: 0.5310 (mtm-85) cc_final: 0.4927 (ttp-110) REVERT: G 196 ARG cc_start: 0.6093 (mtp-110) cc_final: 0.5851 (mtt-85) REVERT: J 89 GLU cc_start: 0.3773 (tm-30) cc_final: 0.3112 (pp20) REVERT: J 92 GLU cc_start: 0.3105 (pt0) cc_final: 0.1926 (mt-10) REVERT: L 85 ARG cc_start: 0.2474 (ttp80) cc_final: 0.1895 (ttp-170) REVERT: L 86 ARG cc_start: 0.2173 (ttp80) cc_final: 0.1628 (tpt170) REVERT: L 162 GLN cc_start: 0.5396 (pt0) cc_final: 0.4936 (pt0) REVERT: L 164 GLU cc_start: 0.5493 (OUTLIER) cc_final: 0.5196 (tp30) outliers start: 71 outliers final: 33 residues processed: 377 average time/residue: 1.7381 time to fit residues: 746.7213 Evaluate side-chains 355 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 304 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 164 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 7.9990 chunk 315 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 296 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 304 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 81 ASN D 338 GLN E 364 ASN F 262 ASN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.154886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.118082 restraints weight = 36528.757| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.66 r_work: 0.3082 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 30114 Z= 0.210 Angle : 0.640 59.200 40813 Z= 0.355 Chirality : 0.043 0.467 4572 Planarity : 0.005 0.051 5333 Dihedral : 6.116 109.334 4259 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.08 % Allowed : 19.95 % Favored : 77.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3764 helix: 1.20 (0.14), residues: 1544 sheet: 0.28 (0.22), residues: 561 loop : -0.39 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 100 HIS 0.017 0.001 HIS H 84 PHE 0.012 0.001 PHE C 230 TYR 0.012 0.001 TYR F 463 ARG 0.005 0.000 ARG A 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12521.91 seconds wall clock time: 221 minutes 41.59 seconds (13301.59 seconds total)