Starting phenix.real_space_refine on Thu Mar 21 07:53:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vax_31869/03_2024/7vax_31869_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vax_31869/03_2024/7vax_31869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vax_31869/03_2024/7vax_31869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vax_31869/03_2024/7vax_31869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vax_31869/03_2024/7vax_31869_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vax_31869/03_2024/7vax_31869_updated.pdb" } resolution = 2.9 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 105 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 325": "OD1" <-> "OD2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 302": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29553 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.68, per 1000 atoms: 0.50 Number of scatterers: 29553 At special positions: 0 Unit cell: (148.23, 147.42, 174.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 8 15.00 Mg 2 11.99 O 5572 8.00 N 5131 7.00 C 18735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.80 Conformation dependent library (CDL) restraints added in 5.2 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 130 helices and 36 sheets defined 42.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.71 Creating SS restraints... Processing helix chain 'A' and resid 91 through 98 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 259 through 271 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 316 removed outlier: 3.901A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.181A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 394 through 400 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 471 removed outlier: 4.072A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 531 Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.675A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.146A pdb=" N ARG A 552 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.723A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.518A pdb=" N VAL B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 296 through 315 removed outlier: 4.443A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.624A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix removed outlier: 5.183A pdb=" N GLU B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 471 removed outlier: 4.477A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 493 removed outlier: 3.869A pdb=" N LEU B 482 " --> pdb=" O ASP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 544 through 553 removed outlier: 4.205A pdb=" N ARG B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR B 553 " --> pdb=" O GLY B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 577 Proline residue: B 560 - end of helix removed outlier: 4.027A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 259 through 271 Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 316 removed outlier: 3.789A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.728A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 394 through 400 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 471 removed outlier: 3.829A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 509 through 532 Processing helix chain 'C' and resid 536 through 541 removed outlier: 3.645A pdb=" N GLN C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 4.496A pdb=" N ARG C 552 " --> pdb=" O ILE C 548 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N TYR C 553 " --> pdb=" O GLY C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 575 Proline residue: C 560 - end of helix removed outlier: 3.923A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 213 through 216 Processing helix chain 'D' and resid 228 through 249 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.921A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.804A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'D' and resid 467 through 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 198 through 211 Processing helix chain 'E' and resid 214 through 216 No H-bonds generated for 'chain 'E' and resid 214 through 216' Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.545A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.628A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ARG E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 332 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 360 through 365 removed outlier: 4.357A pdb=" N ASN E 363 " --> pdb=" O ARG E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 398 removed outlier: 3.642A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 421 Processing helix chain 'E' and resid 432 through 443 removed outlier: 3.822A pdb=" N TRP E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.571A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 90' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 213 through 216 Processing helix chain 'F' and resid 229 through 249 removed outlier: 3.812A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.540A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N HIS F 249 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 285 through 297 removed outlier: 4.400A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLU F 296 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG F 297 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 346 removed outlier: 3.523A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.821A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 421 Processing helix chain 'F' and resid 432 through 445 removed outlier: 3.639A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 456 through 462 Processing helix chain 'F' and resid 467 through 470 No H-bonds generated for 'chain 'F' and resid 467 through 470' Processing helix chain 'G' and resid 8 through 70 Processing helix chain 'G' and resid 73 through 82 removed outlier: 3.564A pdb=" N GLY G 82 " --> pdb=" O GLY G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 206 removed outlier: 3.669A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 7 through 16 Processing helix chain 'H' and resid 28 through 37 Processing helix chain 'H' and resid 56 through 61 removed outlier: 4.340A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 82 No H-bonds generated for 'chain 'H' and resid 79 through 82' Processing helix chain 'H' and resid 86 through 98 Processing helix chain 'I' and resid 83 through 118 removed outlier: 3.613A pdb=" N GLU I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA I 110 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 92 Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 100 through 114 Processing helix chain 'J' and resid 125 through 138 Proline residue: J 129 - end of helix removed outlier: 4.727A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.612A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 105 removed outlier: 3.628A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'L' and resid 63 through 96 removed outlier: 3.556A pdb=" N ALA L 93 " --> pdb=" O GLU L 89 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Proline residue: L 95 - end of helix Processing helix chain 'L' and resid 98 through 114 Proline residue: L 101 - end of helix Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 3.582A pdb=" N GLU L 132 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 5.287A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 5 through 10 removed outlier: 6.561A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 76 Processing sheet with id= C, first strand: chain 'A' and resid 117 through 119 Processing sheet with id= D, first strand: chain 'A' and resid 223 through 227 removed outlier: 8.261A pdb=" N ALA A 224 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE A 380 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE A 226 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY A 382 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A 251 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 366 through 369 Processing sheet with id= F, first strand: chain 'A' and resid 134 through 139 removed outlier: 6.614A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.954A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.092A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 72 through 75 Processing sheet with id= J, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.648A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 223 through 227 removed outlier: 8.306A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 366 through 369 Processing sheet with id= M, first strand: chain 'B' and resid 157 through 160 removed outlier: 7.039A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.643A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= P, first strand: chain 'C' and resid 117 through 120 Processing sheet with id= Q, first strand: chain 'C' and resid 197 through 199 removed outlier: 4.410A pdb=" N LYS C 367 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C 249 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N MET C 323 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 251 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 223 through 227 removed outlier: 6.359A pdb=" N ILE C 380 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE C 226 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLY C 382 " --> pdb=" O ILE C 226 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.607A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.642A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 7 through 9 removed outlier: 6.989A pdb=" N ILE D 32 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TYR D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR D 13 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU D 22 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE D 11 " --> pdb=" O GLU D 22 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.586A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 91 through 93 removed outlier: 4.088A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= Y, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.627A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 81 through 84 Processing sheet with id= AA, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= AB, first strand: chain 'E' and resid 217 through 221 removed outlier: 8.692A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.499A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 81 through 84 Processing sheet with id= AE, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.877A pdb=" N PHE F 93 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU F 219 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AG, first strand: chain 'G' and resid 91 through 96 Processing sheet with id= AH, first strand: chain 'H' and resid 44 through 48 removed outlier: 5.894A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'J' and resid 141 through 144 removed outlier: 6.610A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA J 154 " --> pdb=" O VAL J 163 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 141 through 144 1220 hydrogen bonds defined for protein. 3327 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.67 Time building geometry restraints manager: 12.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 10022 1.36 - 1.50: 7393 1.50 - 1.65: 12499 1.65 - 1.80: 119 1.80 - 1.95: 77 Bond restraints: 30110 Sorted by residual: bond pdb=" C4 ADP A 602 " pdb=" C5 ADP A 602 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C5 ADP A 602 " pdb=" C6 ADP A 602 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" O3B ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sigma weight residual 1.510 1.582 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" N GLU E 184 " pdb=" CA GLU E 184 " ideal model delta sigma weight residual 1.452 1.490 -0.037 1.25e-02 6.40e+03 8.89e+00 bond pdb=" N GLU E 182 " pdb=" CA GLU E 182 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.29e-02 6.01e+03 8.00e+00 ... (remaining 30105 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.79: 1065 106.79 - 113.59: 16319 113.59 - 120.40: 11414 120.40 - 127.20: 11695 127.20 - 134.01: 314 Bond angle restraints: 40807 Sorted by residual: angle pdb=" N ALA E 188 " pdb=" CA ALA E 188 " pdb=" C ALA E 188 " ideal model delta sigma weight residual 110.17 101.72 8.45 1.61e+00 3.86e-01 2.75e+01 angle pdb=" O1B ADP A 602 " pdb=" PB ADP A 602 " pdb=" O3B ADP A 602 " ideal model delta sigma weight residual 119.90 106.44 13.46 3.00e+00 1.11e-01 2.01e+01 angle pdb=" CA ALA E 188 " pdb=" C ALA E 188 " pdb=" O ALA E 188 " ideal model delta sigma weight residual 121.28 116.47 4.81 1.18e+00 7.18e-01 1.66e+01 angle pdb=" C ALA E 188 " pdb=" N VAL E 189 " pdb=" CA VAL E 189 " ideal model delta sigma weight residual 123.17 118.47 4.70 1.28e+00 6.10e-01 1.35e+01 angle pdb=" CA GLU E 182 " pdb=" C GLU E 182 " pdb=" O GLU E 182 " ideal model delta sigma weight residual 121.40 117.39 4.01 1.13e+00 7.83e-01 1.26e+01 ... (remaining 40802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.16: 17606 26.16 - 52.32: 650 52.32 - 78.49: 79 78.49 - 104.65: 19 104.65 - 130.81: 1 Dihedral angle restraints: 18355 sinusoidal: 7533 harmonic: 10822 Sorted by residual: dihedral pdb=" C5' ADP A 602 " pdb=" O5' ADP A 602 " pdb=" PA ADP A 602 " pdb=" O2A ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 70.81 -130.81 1 2.00e+01 2.50e-03 3.97e+01 dihedral pdb=" CA THR E 371 " pdb=" C THR E 371 " pdb=" N ARG E 372 " pdb=" CA ARG E 372 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ARG E 372 " pdb=" C ARG E 372 " pdb=" N GLU E 373 " pdb=" CA GLU E 373 " ideal model delta harmonic sigma weight residual -180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 18352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3677 0.051 - 0.102: 728 0.102 - 0.153: 162 0.153 - 0.204: 7 0.204 - 0.255: 2 Chirality restraints: 4576 Sorted by residual: chirality pdb=" CA GLU E 185 " pdb=" N GLU E 185 " pdb=" C GLU E 185 " pdb=" CB GLU E 185 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ALA E 188 " pdb=" N ALA E 188 " pdb=" C ALA E 188 " pdb=" CB ALA E 188 " both_signs ideal model delta sigma weight residual False 2.48 2.70 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE A 87 " pdb=" CA ILE A 87 " pdb=" CG1 ILE A 87 " pdb=" CG2 ILE A 87 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.61e-01 ... (remaining 4573 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 94 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO L 95 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 108 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO G 109 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO G 109 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 109 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO E 324 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.024 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 245 2.59 - 3.17: 24762 3.17 - 3.75: 47722 3.75 - 4.32: 66304 4.32 - 4.90: 110899 Nonbonded interactions: 249932 Sorted by model distance: nonbonded pdb=" OG SER A 235 " pdb="MG MG A 601 " model vdw 2.017 2.170 nonbonded pdb=" OG SER C 235 " pdb="MG MG C 601 " model vdw 2.027 2.170 nonbonded pdb="MG MG A 601 " pdb=" O3B ADP A 602 " model vdw 2.074 2.170 nonbonded pdb=" OH TYR F 263 " pdb=" OD2 ASP F 290 " model vdw 2.088 2.440 nonbonded pdb=" NH1 ARG A 258 " pdb="MG MG A 601 " model vdw 2.117 2.250 ... (remaining 249927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = chain 'B' selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 5.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.400 Check model and map are aligned: 0.430 Set scattering table: 0.280 Process input model: 76.820 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 30110 Z= 0.167 Angle : 0.509 13.456 40807 Z= 0.262 Chirality : 0.042 0.255 4576 Planarity : 0.004 0.047 5333 Dihedral : 13.522 130.812 11437 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.03 % Allowed : 0.39 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.14), residues: 3764 helix: 1.97 (0.14), residues: 1547 sheet: -0.16 (0.22), residues: 573 loop : 0.53 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 440 HIS 0.003 0.000 HIS C 418 PHE 0.014 0.001 PHE G 108 TYR 0.010 0.001 TYR D 13 ARG 0.005 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 593 time to evaluate : 3.299 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7308 (mm-30) REVERT: A 38 GLU cc_start: 0.7338 (tt0) cc_final: 0.7074 (tt0) REVERT: A 45 ASP cc_start: 0.7065 (t0) cc_final: 0.6769 (t70) REVERT: A 109 HIS cc_start: 0.7866 (m90) cc_final: 0.7388 (m170) REVERT: A 239 GLN cc_start: 0.7371 (mt0) cc_final: 0.7127 (mm-40) REVERT: A 248 ASP cc_start: 0.8470 (m-30) cc_final: 0.8263 (m-30) REVERT: A 262 MET cc_start: 0.8214 (mmp) cc_final: 0.7876 (mmp) REVERT: A 264 ASP cc_start: 0.7714 (t0) cc_final: 0.7162 (t0) REVERT: A 408 ARG cc_start: 0.8165 (ttt180) cc_final: 0.7877 (ttt90) REVERT: A 416 ARG cc_start: 0.7423 (mtp-110) cc_final: 0.7139 (mtp85) REVERT: A 466 GLU cc_start: 0.6731 (mp0) cc_final: 0.6517 (mp0) REVERT: A 491 ARG cc_start: 0.7096 (mtm-85) cc_final: 0.6794 (ttp-110) REVERT: A 524 LYS cc_start: 0.7114 (mmtt) cc_final: 0.6713 (ttmt) REVERT: A 541 GLN cc_start: 0.7271 (pt0) cc_final: 0.7018 (pt0) REVERT: A 550 ARG cc_start: 0.6670 (mmt180) cc_final: 0.6326 (mmm-85) REVERT: A 567 MET cc_start: 0.6870 (mmm) cc_final: 0.6442 (mmm) REVERT: B 19 MET cc_start: 0.8041 (ptm) cc_final: 0.7835 (ptm) REVERT: B 124 LYS cc_start: 0.7398 (ptpp) cc_final: 0.6829 (ptpt) REVERT: B 127 ASP cc_start: 0.7010 (m-30) cc_final: 0.6778 (m-30) REVERT: B 156 ARG cc_start: 0.7118 (mtp85) cc_final: 0.6899 (mtp-110) REVERT: B 166 TYR cc_start: 0.7838 (m-80) cc_final: 0.7265 (m-80) REVERT: B 200 ASP cc_start: 0.7014 (m-30) cc_final: 0.6501 (m-30) REVERT: B 220 MET cc_start: 0.6240 (tpp) cc_final: 0.5566 (mmm) REVERT: B 243 LYS cc_start: 0.7167 (tttm) cc_final: 0.5888 (mttm) REVERT: B 271 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7194 (tm-30) REVERT: B 342 GLU cc_start: 0.6727 (pt0) cc_final: 0.6454 (mt-10) REVERT: B 456 GLU cc_start: 0.6826 (tp30) cc_final: 0.6516 (tp30) REVERT: B 459 GLN cc_start: 0.7016 (tp40) cc_final: 0.6726 (tp40) REVERT: B 477 GLN cc_start: 0.5496 (pt0) cc_final: 0.4529 (tp40) REVERT: B 516 MET cc_start: 0.6877 (mtm) cc_final: 0.6675 (mtt) REVERT: B 563 PHE cc_start: 0.6919 (t80) cc_final: 0.6552 (t80) REVERT: C 1 MET cc_start: 0.6615 (mmt) cc_final: 0.6254 (pmm) REVERT: C 93 ARG cc_start: 0.7485 (mmm-85) cc_final: 0.6601 (mmm-85) REVERT: C 156 ARG cc_start: 0.6473 (ttt90) cc_final: 0.5834 (ttt180) REVERT: C 166 TYR cc_start: 0.8340 (m-80) cc_final: 0.7834 (m-80) REVERT: C 197 ARG cc_start: 0.7773 (ttp-110) cc_final: 0.7412 (ttt-90) REVERT: C 344 MET cc_start: 0.8208 (mmt) cc_final: 0.7955 (tpp) REVERT: C 374 GLU cc_start: 0.6371 (tp30) cc_final: 0.5929 (tp30) REVERT: C 433 SER cc_start: 0.8426 (p) cc_final: 0.8004 (m) REVERT: C 464 LEU cc_start: 0.7190 (mp) cc_final: 0.6866 (mp) REVERT: C 480 GLU cc_start: 0.5884 (mt-10) cc_final: 0.5674 (mm-30) REVERT: C 513 TYR cc_start: 0.8018 (t80) cc_final: 0.7691 (t80) REVERT: C 547 ARG cc_start: 0.6636 (mmm-85) cc_final: 0.6224 (ttm110) REVERT: D 52 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7625 (mm-30) REVERT: D 87 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7273 (mt-10) REVERT: D 98 LYS cc_start: 0.7483 (ttpp) cc_final: 0.6665 (mttm) REVERT: D 280 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7484 (mtm110) REVERT: D 401 GLU cc_start: 0.7321 (pt0) cc_final: 0.7010 (pt0) REVERT: D 420 ARG cc_start: 0.7544 (mmm160) cc_final: 0.6781 (mmt180) REVERT: D 434 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7170 (mt-10) REVERT: D 466 LYS cc_start: 0.7078 (mtmm) cc_final: 0.6690 (mmmm) REVERT: E 25 LYS cc_start: 0.7752 (ptpt) cc_final: 0.7475 (mtpt) REVERT: E 52 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7718 (mt-10) REVERT: E 77 GLU cc_start: 0.6644 (pt0) cc_final: 0.5990 (mt-10) REVERT: E 110 LYS cc_start: 0.7183 (tttt) cc_final: 0.6925 (tttm) REVERT: E 139 ASP cc_start: 0.7494 (m-30) cc_final: 0.7200 (m-30) REVERT: E 174 ARG cc_start: 0.6729 (mmm-85) cc_final: 0.6202 (ttm-80) REVERT: E 210 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7458 (ttt180) REVERT: E 216 ARG cc_start: 0.5801 (ttp80) cc_final: 0.5340 (ttp-110) REVERT: E 353 ASP cc_start: 0.7027 (t0) cc_final: 0.6794 (t0) REVERT: E 362 MET cc_start: 0.7983 (ttp) cc_final: 0.7686 (ttp) REVERT: E 368 LYS cc_start: 0.6420 (mmmt) cc_final: 0.5080 (mppt) REVERT: E 452 LYS cc_start: 0.6173 (ptpt) cc_final: 0.5935 (mptt) REVERT: F 6 LYS cc_start: 0.7621 (tppp) cc_final: 0.6553 (mttp) REVERT: F 78 ASP cc_start: 0.7114 (m-30) cc_final: 0.6909 (m-30) REVERT: F 98 LYS cc_start: 0.7715 (mptt) cc_final: 0.7306 (mmmt) REVERT: F 264 CYS cc_start: 0.8143 (m) cc_final: 0.7858 (m) REVERT: F 302 GLU cc_start: 0.7090 (tt0) cc_final: 0.6881 (mt-10) REVERT: F 373 GLU cc_start: 0.7807 (pm20) cc_final: 0.7500 (pt0) REVERT: F 394 LYS cc_start: 0.7398 (ttmt) cc_final: 0.7027 (mtpt) REVERT: G 17 GLN cc_start: 0.7089 (mm110) cc_final: 0.6855 (mm-40) REVERT: G 30 LYS cc_start: 0.7188 (mtpp) cc_final: 0.6908 (mtpp) REVERT: G 38 GLU cc_start: 0.7167 (tp30) cc_final: 0.6775 (tt0) REVERT: G 152 GLU cc_start: 0.6197 (mm-30) cc_final: 0.5856 (mt-10) REVERT: G 159 ARG cc_start: 0.6795 (mtm180) cc_final: 0.6356 (mtm-85) REVERT: G 181 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7093 (mt0) REVERT: G 187 GLU cc_start: 0.7449 (pp20) cc_final: 0.7226 (tm-30) REVERT: G 205 GLU cc_start: 0.3838 (tm-30) cc_final: 0.3285 (tt0) REVERT: H 38 GLU cc_start: 0.4660 (mm-30) cc_final: 0.4286 (mt-10) REVERT: H 90 MET cc_start: 0.7086 (tpp) cc_final: 0.6425 (ttm) REVERT: I 104 MET cc_start: 0.4136 (mtp) cc_final: 0.3934 (mpt) REVERT: J 66 LEU cc_start: 0.5784 (mt) cc_final: 0.5485 (mp) REVERT: J 78 GLU cc_start: 0.4292 (tt0) cc_final: 0.3928 (tt0) REVERT: J 79 VAL cc_start: 0.6331 (t) cc_final: 0.5741 (t) REVERT: L 105 ARG cc_start: 0.6160 (mtm-85) cc_final: 0.5939 (mtm-85) REVERT: L 126 GLU cc_start: 0.5250 (mp0) cc_final: 0.5012 (mp0) REVERT: L 181 LYS cc_start: 0.5799 (mttp) cc_final: 0.5456 (mmpt) outliers start: 1 outliers final: 0 residues processed: 594 average time/residue: 1.7484 time to fit residues: 1181.3550 Evaluate side-chains 379 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 7.9990 chunk 282 optimal weight: 0.0170 chunk 156 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 292 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 177 optimal weight: 9.9990 chunk 217 optimal weight: 8.9990 chunk 338 optimal weight: 0.0270 overall best weight: 2.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 202 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN C 571 GLN D 377 GLN D 437 GLN E 222 ASN E 364 ASN E 413 GLN ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 166 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30110 Z= 0.233 Angle : 0.547 7.680 40807 Z= 0.277 Chirality : 0.044 0.178 4576 Planarity : 0.005 0.046 5333 Dihedral : 5.327 106.253 4231 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.04 % Allowed : 9.18 % Favored : 88.78 % 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: 1.07 (0.14), residues: 3764 helix: 1.58 (0.14), residues: 1546 sheet: -0.26 (0.21), residues: 568 loop : 0.39 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 440 HIS 0.004 0.001 HIS E 375 PHE 0.013 0.001 PHE F 414 TYR 0.011 0.001 TYR B 513 ARG 0.014 0.000 ARG B 130 *********************** 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 449 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 386 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7378 (mm-30) REVERT: A 38 GLU cc_start: 0.7355 (tt0) cc_final: 0.7056 (tt0) REVERT: A 45 ASP cc_start: 0.7189 (t0) cc_final: 0.6530 (t70) REVERT: A 109 HIS cc_start: 0.7972 (m90) cc_final: 0.7537 (m170) REVERT: A 239 GLN cc_start: 0.7416 (mt0) cc_final: 0.7167 (mm-40) REVERT: A 248 ASP cc_start: 0.8514 (m-30) cc_final: 0.8301 (m-30) REVERT: A 262 MET cc_start: 0.8216 (mmp) cc_final: 0.7926 (mmp) REVERT: A 342 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7234 (mt-10) REVERT: A 400 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 408 ARG cc_start: 0.8075 (ttt180) cc_final: 0.7680 (ttt90) REVERT: A 491 ARG cc_start: 0.7208 (mtm-85) cc_final: 0.6875 (ttp-110) REVERT: A 524 LYS cc_start: 0.7130 (mmtt) cc_final: 0.6746 (ttmt) REVERT: A 541 GLN cc_start: 0.7301 (pt0) cc_final: 0.7019 (pt0) REVERT: A 550 ARG cc_start: 0.6679 (mmt180) cc_final: 0.5991 (mmm160) REVERT: A 567 MET cc_start: 0.6953 (mmm) cc_final: 0.6549 (mmm) REVERT: B 19 MET cc_start: 0.8006 (ptm) cc_final: 0.7793 (ptm) REVERT: B 32 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7089 (mt-10) REVERT: B 124 LYS cc_start: 0.7407 (ptpp) cc_final: 0.6873 (ptpt) REVERT: B 127 ASP cc_start: 0.6964 (m-30) cc_final: 0.6726 (m-30) REVERT: B 166 TYR cc_start: 0.7789 (m-80) cc_final: 0.7150 (m-80) REVERT: B 220 MET cc_start: 0.6306 (tpp) cc_final: 0.5663 (mmm) REVERT: B 271 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7202 (tm-30) REVERT: B 342 GLU cc_start: 0.6793 (pt0) cc_final: 0.6508 (mt-10) REVERT: B 397 GLN cc_start: 0.7196 (tp40) cc_final: 0.6820 (mp10) REVERT: B 456 GLU cc_start: 0.6897 (tp30) cc_final: 0.6583 (tp30) REVERT: B 459 GLN cc_start: 0.7019 (tp40) cc_final: 0.6719 (tp40) REVERT: B 563 PHE cc_start: 0.7037 (t80) cc_final: 0.6572 (t80) REVERT: C 1 MET cc_start: 0.6789 (mmt) cc_final: 0.6516 (mmp) REVERT: C 93 ARG cc_start: 0.7513 (mmm-85) cc_final: 0.6640 (mmm-85) REVERT: C 156 ARG cc_start: 0.6400 (ttt90) cc_final: 0.6065 (ttt180) REVERT: C 166 TYR cc_start: 0.8247 (m-80) cc_final: 0.7415 (m-80) REVERT: C 344 MET cc_start: 0.8337 (mmt) cc_final: 0.7940 (tpp) REVERT: C 348 GLU cc_start: 0.7924 (tt0) cc_final: 0.7611 (mm-30) REVERT: C 374 GLU cc_start: 0.6625 (tp30) cc_final: 0.6157 (tp30) REVERT: C 433 SER cc_start: 0.8443 (p) cc_final: 0.8032 (m) REVERT: C 464 LEU cc_start: 0.7171 (mp) cc_final: 0.6943 (mp) REVERT: C 547 ARG cc_start: 0.6757 (mmm-85) cc_final: 0.6303 (ttm110) REVERT: C 565 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7079 (mm-30) REVERT: D 52 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7782 (mt-10) REVERT: D 74 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.7816 (t) REVERT: D 98 LYS cc_start: 0.7559 (ttpp) cc_final: 0.6743 (mttm) REVERT: D 221 LEU cc_start: 0.8589 (mt) cc_final: 0.8386 (mm) REVERT: D 280 ARG cc_start: 0.7998 (mtp-110) cc_final: 0.7423 (mtm110) REVERT: D 401 GLU cc_start: 0.7377 (pt0) cc_final: 0.7049 (pt0) REVERT: D 420 ARG cc_start: 0.7656 (mmm160) cc_final: 0.6923 (mmt180) REVERT: D 434 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7274 (mt-10) REVERT: D 466 LYS cc_start: 0.7076 (mtmm) cc_final: 0.6665 (mmmm) REVERT: E 77 GLU cc_start: 0.6835 (pt0) cc_final: 0.5898 (mt-10) REVERT: E 96 ILE cc_start: 0.8077 (tp) cc_final: 0.7739 (tt) REVERT: E 110 LYS cc_start: 0.7034 (tttt) cc_final: 0.6703 (tttm) REVERT: E 174 ARG cc_start: 0.6701 (mmm-85) cc_final: 0.6208 (ttm-80) REVERT: E 210 ARG cc_start: 0.7797 (ttp80) cc_final: 0.7501 (ttt180) REVERT: E 216 ARG cc_start: 0.6117 (ttp80) cc_final: 0.5507 (ttp-110) REVERT: E 353 ASP cc_start: 0.7100 (t0) cc_final: 0.6759 (t0) REVERT: E 362 MET cc_start: 0.7915 (ttp) cc_final: 0.7590 (ttp) REVERT: E 368 LYS cc_start: 0.6366 (mmmt) cc_final: 0.5083 (mppt) REVERT: E 445 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6907 (tmm) REVERT: E 452 LYS cc_start: 0.6246 (ptpt) cc_final: 0.5626 (pmtt) REVERT: F 6 LYS cc_start: 0.7779 (tppp) cc_final: 0.6619 (mttp) REVERT: F 275 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: F 302 GLU cc_start: 0.7161 (tt0) cc_final: 0.6894 (mt-10) REVERT: F 373 GLU cc_start: 0.7866 (pm20) cc_final: 0.7528 (pt0) REVERT: F 394 LYS cc_start: 0.7426 (ttmt) cc_final: 0.7139 (mttm) REVERT: F 406 GLU cc_start: 0.6922 (tp30) cc_final: 0.6460 (tt0) REVERT: F 413 GLN cc_start: 0.7721 (mt0) cc_final: 0.6877 (mm110) REVERT: F 416 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7377 (t0) REVERT: F 420 ARG cc_start: 0.7698 (mmm160) cc_final: 0.6915 (mpp80) REVERT: G 17 GLN cc_start: 0.7212 (mm110) cc_final: 0.6994 (mm-40) REVERT: G 30 LYS cc_start: 0.7391 (mtpp) cc_final: 0.7134 (mtpp) REVERT: G 38 GLU cc_start: 0.7190 (tp30) cc_final: 0.6774 (tt0) REVERT: G 152 GLU cc_start: 0.6087 (mm-30) cc_final: 0.5808 (mt-10) REVERT: G 159 ARG cc_start: 0.6898 (mtm180) cc_final: 0.6479 (mtm-85) REVERT: G 181 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7048 (mt0) REVERT: G 187 GLU cc_start: 0.7373 (pp20) cc_final: 0.7153 (tm-30) REVERT: H 19 GLU cc_start: 0.3121 (OUTLIER) cc_final: 0.1737 (pp20) REVERT: H 38 GLU cc_start: 0.4648 (mm-30) cc_final: 0.4246 (mt-10) REVERT: H 90 MET cc_start: 0.7064 (tpp) cc_final: 0.6348 (mtp) REVERT: H 92 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6735 (tp30) REVERT: I 104 MET cc_start: 0.4035 (mtp) cc_final: 0.3808 (mpt) REVERT: J 66 LEU cc_start: 0.5749 (mt) cc_final: 0.5447 (mp) REVERT: J 79 VAL cc_start: 0.6178 (t) cc_final: 0.5544 (t) REVERT: J 82 GLU cc_start: 0.4826 (OUTLIER) cc_final: 0.4432 (mt-10) REVERT: L 126 GLU cc_start: 0.5376 (mp0) cc_final: 0.5062 (mp0) REVERT: L 181 LYS cc_start: 0.5870 (mttp) cc_final: 0.5472 (mmpt) outliers start: 63 outliers final: 19 residues processed: 422 average time/residue: 1.6257 time to fit residues: 788.7825 Evaluate side-chains 364 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 335 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 445 MET Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain L residue 166 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 281 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 339 optimal weight: 20.0000 chunk 366 optimal weight: 10.0000 chunk 302 optimal weight: 7.9990 chunk 336 optimal weight: 0.0030 chunk 115 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 overall best weight: 4.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 GLN B 498 ASN C 425 ASN C 571 GLN D 448 GLN E 413 GLN ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 HIS G 166 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 30110 Z= 0.442 Angle : 0.658 9.253 40807 Z= 0.336 Chirality : 0.049 0.200 4576 Planarity : 0.006 0.051 5333 Dihedral : 5.781 87.735 4231 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.66 % Allowed : 12.13 % Favored : 85.21 % 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: 0.40 (0.14), residues: 3764 helix: 0.93 (0.13), residues: 1548 sheet: -0.39 (0.21), residues: 560 loop : 0.01 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 440 HIS 0.007 0.002 HIS E 252 PHE 0.029 0.002 PHE E 414 TYR 0.016 0.002 TYR C 562 ARG 0.008 0.001 ARG B 130 *********************** 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 428 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 346 time to evaluate : 3.435 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7488 (mm-30) REVERT: A 38 GLU cc_start: 0.7522 (tt0) cc_final: 0.7189 (tt0) REVERT: A 248 ASP cc_start: 0.8512 (m-30) cc_final: 0.8295 (m-30) REVERT: A 323 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7447 (mpp) REVERT: A 342 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7425 (mt-10) REVERT: A 408 ARG cc_start: 0.8040 (ttt180) cc_final: 0.7572 (ttt90) REVERT: A 469 GLN cc_start: 0.6789 (pp30) cc_final: 0.6554 (pt0) REVERT: A 470 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7076 (tm) REVERT: A 491 ARG cc_start: 0.7304 (mtm-85) cc_final: 0.7055 (ttp-110) REVERT: A 524 LYS cc_start: 0.7181 (mmtt) cc_final: 0.6776 (ttmt) REVERT: A 541 GLN cc_start: 0.7285 (pt0) cc_final: 0.7001 (pt0) REVERT: A 550 ARG cc_start: 0.6731 (mmt180) cc_final: 0.6028 (mmm160) REVERT: A 569 GLU cc_start: 0.7001 (tt0) cc_final: 0.6754 (tt0) REVERT: B 32 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: B 54 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6877 (t70) REVERT: B 124 LYS cc_start: 0.7255 (ptpp) cc_final: 0.6731 (ptpt) REVERT: B 127 ASP cc_start: 0.6973 (m-30) cc_final: 0.6722 (m-30) REVERT: B 166 TYR cc_start: 0.7832 (m-80) cc_final: 0.7154 (m-80) REVERT: B 220 MET cc_start: 0.6292 (tpp) cc_final: 0.5623 (mmm) REVERT: B 342 GLU cc_start: 0.6865 (pt0) cc_final: 0.6557 (mt-10) REVERT: B 417 ARG cc_start: 0.5408 (OUTLIER) cc_final: 0.4923 (tmt170) REVERT: B 456 GLU cc_start: 0.6697 (tp30) cc_final: 0.6432 (tp30) REVERT: B 459 GLN cc_start: 0.6989 (tp40) cc_final: 0.6726 (tp40) REVERT: B 481 ARG cc_start: 0.7124 (tmt-80) cc_final: 0.6482 (tmm-80) REVERT: B 485 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6312 (tp30) REVERT: B 563 PHE cc_start: 0.7016 (t80) cc_final: 0.6567 (t80) REVERT: C 1 MET cc_start: 0.6898 (mmt) cc_final: 0.6604 (mmp) REVERT: C 93 ARG cc_start: 0.7538 (mmm-85) cc_final: 0.6613 (mmm-85) REVERT: C 156 ARG cc_start: 0.6287 (ttt90) cc_final: 0.6014 (ttt180) REVERT: C 166 TYR cc_start: 0.8347 (m-80) cc_final: 0.7519 (m-80) REVERT: C 344 MET cc_start: 0.8253 (mmt) cc_final: 0.7891 (tpp) REVERT: C 348 GLU cc_start: 0.7965 (tt0) cc_final: 0.7730 (mm-30) REVERT: C 433 SER cc_start: 0.8521 (p) cc_final: 0.8145 (m) REVERT: C 547 ARG cc_start: 0.6861 (mmm-85) cc_final: 0.6349 (ttm110) REVERT: C 565 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: D 52 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7766 (mt-10) REVERT: D 185 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6923 (mt-10) REVERT: D 280 ARG cc_start: 0.7984 (mtp-110) cc_final: 0.7556 (mtm180) REVERT: D 401 GLU cc_start: 0.7466 (pt0) cc_final: 0.7134 (pt0) REVERT: D 420 ARG cc_start: 0.7713 (mmm160) cc_final: 0.7106 (mmt-90) REVERT: D 434 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7314 (mt-10) REVERT: D 469 GLU cc_start: 0.5359 (OUTLIER) cc_final: 0.5013 (pp20) REVERT: E 77 GLU cc_start: 0.6868 (pt0) cc_final: 0.5746 (mt-10) REVERT: E 88 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7630 (ttt) REVERT: E 96 ILE cc_start: 0.8330 (tp) cc_final: 0.7960 (tt) REVERT: E 110 LYS cc_start: 0.6993 (tttt) cc_final: 0.6719 (tttm) REVERT: E 139 ASP cc_start: 0.7541 (m-30) cc_final: 0.7052 (m-30) REVERT: E 216 ARG cc_start: 0.5999 (ttp80) cc_final: 0.5281 (ttp-110) REVERT: E 353 ASP cc_start: 0.7238 (t0) cc_final: 0.6908 (t0) REVERT: E 362 MET cc_start: 0.7849 (ttp) cc_final: 0.7597 (ttp) REVERT: E 368 LYS cc_start: 0.6458 (mmmt) cc_final: 0.4913 (mptm) REVERT: E 452 LYS cc_start: 0.6212 (ptpt) cc_final: 0.5378 (pttm) REVERT: E 461 LYS cc_start: 0.7034 (tmtt) cc_final: 0.6764 (tmtm) REVERT: F 6 LYS cc_start: 0.7780 (tppp) cc_final: 0.6774 (mttp) REVERT: F 275 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: F 302 GLU cc_start: 0.7190 (tt0) cc_final: 0.6898 (mt-10) REVERT: F 373 GLU cc_start: 0.7872 (pm20) cc_final: 0.7565 (pt0) REVERT: F 394 LYS cc_start: 0.7347 (ttmt) cc_final: 0.7063 (mttm) REVERT: F 406 GLU cc_start: 0.7010 (tp30) cc_final: 0.6435 (tt0) REVERT: F 416 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7508 (t0) REVERT: F 420 ARG cc_start: 0.7758 (mmm160) cc_final: 0.7197 (mtm110) REVERT: G 17 GLN cc_start: 0.7310 (mm110) cc_final: 0.7075 (mm-40) REVERT: G 38 GLU cc_start: 0.7241 (tp30) cc_final: 0.6940 (tt0) REVERT: G 152 GLU cc_start: 0.6110 (mm-30) cc_final: 0.5729 (mt-10) REVERT: G 159 ARG cc_start: 0.6932 (mtm180) cc_final: 0.6551 (ttp-170) REVERT: G 177 ARG cc_start: 0.7467 (ptm160) cc_final: 0.7214 (ptm160) REVERT: G 181 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7034 (mt0) REVERT: H 38 GLU cc_start: 0.4441 (mm-30) cc_final: 0.4103 (mt-10) REVERT: H 90 MET cc_start: 0.7113 (tpp) cc_final: 0.6473 (mtp) REVERT: I 104 MET cc_start: 0.4190 (mtp) cc_final: 0.3924 (mpt) REVERT: J 66 LEU cc_start: 0.5762 (mt) cc_final: 0.5421 (mp) REVERT: J 82 GLU cc_start: 0.4615 (OUTLIER) cc_final: 0.4188 (mt-10) REVERT: L 126 GLU cc_start: 0.5381 (mp0) cc_final: 0.5151 (mp0) REVERT: L 181 LYS cc_start: 0.5819 (mttp) cc_final: 0.5350 (mmpt) outliers start: 82 outliers final: 31 residues processed: 398 average time/residue: 1.6809 time to fit residues: 767.3582 Evaluate side-chains 360 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 317 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 417 ARG Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 469 GLU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 180 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 20.0000 chunk 255 optimal weight: 8.9990 chunk 176 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 227 optimal weight: 0.4980 chunk 340 optimal weight: 9.9990 chunk 360 optimal weight: 0.0980 chunk 177 optimal weight: 3.9990 chunk 322 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN B 425 ASN B 498 ASN C 425 ASN C 571 GLN ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30110 Z= 0.281 Angle : 0.565 8.479 40807 Z= 0.288 Chirality : 0.045 0.172 4576 Planarity : 0.005 0.052 5333 Dihedral : 5.512 78.065 4231 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.95 % Allowed : 13.30 % Favored : 83.75 % 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: 0.42 (0.14), residues: 3764 helix: 0.99 (0.13), residues: 1562 sheet: -0.48 (0.21), residues: 563 loop : 0.02 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 119 HIS 0.004 0.001 HIS F 249 PHE 0.015 0.002 PHE F 414 TYR 0.017 0.002 TYR B 513 ARG 0.008 0.000 ARG B 130 *********************** 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 427 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 336 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7512 (mm-30) REVERT: A 38 GLU cc_start: 0.7523 (tt0) cc_final: 0.7242 (tt0) REVERT: A 248 ASP cc_start: 0.8502 (m-30) cc_final: 0.8291 (m-30) REVERT: A 262 MET cc_start: 0.8358 (mmp) cc_final: 0.8103 (mmp) REVERT: A 323 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7419 (mpp) REVERT: A 342 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7309 (mt-10) REVERT: A 400 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8641 (mp) REVERT: A 408 ARG cc_start: 0.8039 (ttt180) cc_final: 0.7609 (ttt90) REVERT: A 469 GLN cc_start: 0.6731 (pp30) cc_final: 0.6502 (pt0) REVERT: A 470 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7107 (tm) REVERT: A 491 ARG cc_start: 0.7303 (mtm-85) cc_final: 0.7035 (ttp-110) REVERT: A 524 LYS cc_start: 0.7167 (mmtt) cc_final: 0.6775 (ttmt) REVERT: A 541 GLN cc_start: 0.7246 (pt0) cc_final: 0.6988 (pt0) REVERT: A 550 ARG cc_start: 0.6747 (mmt180) cc_final: 0.6055 (mmm160) REVERT: B 2 ILE cc_start: 0.8226 (mm) cc_final: 0.7996 (mm) REVERT: B 32 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7111 (mt-10) REVERT: B 54 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6822 (t70) REVERT: B 124 LYS cc_start: 0.7234 (ptpp) cc_final: 0.6748 (ptpt) REVERT: B 127 ASP cc_start: 0.6949 (m-30) cc_final: 0.6694 (m-30) REVERT: B 166 TYR cc_start: 0.7772 (m-80) cc_final: 0.7133 (m-80) REVERT: B 209 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6502 (mtt) REVERT: B 220 MET cc_start: 0.6217 (tpp) cc_final: 0.5499 (mmm) REVERT: B 342 GLU cc_start: 0.6838 (pt0) cc_final: 0.6515 (mt-10) REVERT: B 397 GLN cc_start: 0.7205 (tp40) cc_final: 0.6978 (mp10) REVERT: B 459 GLN cc_start: 0.7033 (tp40) cc_final: 0.6740 (tp40) REVERT: B 481 ARG cc_start: 0.7071 (tmt-80) cc_final: 0.6471 (tmm-80) REVERT: B 485 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6299 (tp30) REVERT: B 547 ARG cc_start: 0.4868 (OUTLIER) cc_final: 0.4331 (ttm170) REVERT: B 563 PHE cc_start: 0.7037 (t80) cc_final: 0.6618 (t80) REVERT: C 1 MET cc_start: 0.6884 (mmt) cc_final: 0.6642 (mmp) REVERT: C 93 ARG cc_start: 0.7540 (mmm-85) cc_final: 0.6656 (mmm-85) REVERT: C 344 MET cc_start: 0.8252 (mmt) cc_final: 0.7866 (tpp) REVERT: C 348 GLU cc_start: 0.7998 (tt0) cc_final: 0.7742 (mm-30) REVERT: C 433 SER cc_start: 0.8544 (p) cc_final: 0.8146 (m) REVERT: C 547 ARG cc_start: 0.6786 (mmm-85) cc_final: 0.6423 (ttm110) REVERT: C 565 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: D 52 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7742 (mt-10) REVERT: D 185 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6951 (mt-10) REVERT: D 268 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7599 (ttm170) REVERT: D 280 ARG cc_start: 0.8017 (mtp-110) cc_final: 0.7577 (mtm110) REVERT: D 401 GLU cc_start: 0.7441 (pt0) cc_final: 0.7106 (pt0) REVERT: D 434 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7303 (mt-10) REVERT: E 88 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7678 (ttt) REVERT: E 96 ILE cc_start: 0.8295 (tp) cc_final: 0.7909 (tt) REVERT: E 139 ASP cc_start: 0.7498 (m-30) cc_final: 0.7038 (m-30) REVERT: E 174 ARG cc_start: 0.6602 (mmm-85) cc_final: 0.5754 (ttt-90) REVERT: E 216 ARG cc_start: 0.6080 (ttp80) cc_final: 0.5359 (ttp-110) REVERT: E 353 ASP cc_start: 0.7265 (t0) cc_final: 0.6953 (t0) REVERT: E 362 MET cc_start: 0.7849 (ttp) cc_final: 0.7496 (ttp) REVERT: E 368 LYS cc_start: 0.6419 (mmmt) cc_final: 0.5059 (tppt) REVERT: E 452 LYS cc_start: 0.6090 (ptpt) cc_final: 0.5295 (pttm) REVERT: F 6 LYS cc_start: 0.7776 (tppp) cc_final: 0.6774 (mttp) REVERT: F 275 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: F 302 GLU cc_start: 0.7206 (tt0) cc_final: 0.6913 (mt-10) REVERT: F 373 GLU cc_start: 0.7811 (pm20) cc_final: 0.7561 (pt0) REVERT: F 394 LYS cc_start: 0.7421 (ttmt) cc_final: 0.7139 (mttm) REVERT: F 406 GLU cc_start: 0.6976 (tp30) cc_final: 0.6398 (tt0) REVERT: F 416 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7454 (t0) REVERT: F 420 ARG cc_start: 0.7689 (mmm160) cc_final: 0.7147 (mtm110) REVERT: G 9 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7061 (ttp) REVERT: G 17 GLN cc_start: 0.7273 (mm110) cc_final: 0.7019 (mm-40) REVERT: G 38 GLU cc_start: 0.7223 (tp30) cc_final: 0.6898 (tt0) REVERT: G 152 GLU cc_start: 0.5999 (mm-30) cc_final: 0.5717 (mt-10) REVERT: G 159 ARG cc_start: 0.6941 (mtm180) cc_final: 0.6549 (ttp-170) REVERT: G 177 ARG cc_start: 0.7234 (ptm160) cc_final: 0.6790 (ptp-170) REVERT: G 181 GLN cc_start: 0.7767 (mm-40) cc_final: 0.6993 (mt0) REVERT: H 8 GLU cc_start: 0.3723 (OUTLIER) cc_final: 0.3129 (mt-10) REVERT: H 19 GLU cc_start: 0.3262 (OUTLIER) cc_final: 0.2035 (pp20) REVERT: H 38 GLU cc_start: 0.4379 (mm-30) cc_final: 0.4074 (mt-10) REVERT: H 90 MET cc_start: 0.7073 (tpp) cc_final: 0.6434 (mtp) REVERT: I 104 MET cc_start: 0.4105 (mtp) cc_final: 0.3853 (mpt) REVERT: J 66 LEU cc_start: 0.5768 (mt) cc_final: 0.5420 (mp) REVERT: J 79 VAL cc_start: 0.5987 (t) cc_final: 0.5352 (t) REVERT: J 82 GLU cc_start: 0.4623 (OUTLIER) cc_final: 0.4114 (mt-10) REVERT: L 126 GLU cc_start: 0.5368 (mp0) cc_final: 0.5129 (mp0) REVERT: L 181 LYS cc_start: 0.5821 (mttp) cc_final: 0.5329 (mmpt) outliers start: 91 outliers final: 41 residues processed: 398 average time/residue: 1.6475 time to fit residues: 757.6883 Evaluate side-chains 373 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 315 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 113 GLU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 180 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 0.5980 chunk 204 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 307 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 323 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN B 202 ASN B 425 ASN B 498 ASN C 425 ASN C 571 GLN E 364 ASN ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 ASN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS L 162 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30110 Z= 0.287 Angle : 0.568 8.431 40807 Z= 0.290 Chirality : 0.045 0.236 4576 Planarity : 0.005 0.049 5333 Dihedral : 5.477 73.944 4231 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.34 % Allowed : 14.04 % Favored : 82.61 % 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: 0.40 (0.14), residues: 3764 helix: 0.97 (0.13), residues: 1571 sheet: -0.49 (0.21), residues: 563 loop : 0.00 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 119 HIS 0.004 0.001 HIS F 249 PHE 0.015 0.002 PHE F 414 TYR 0.017 0.002 TYR B 513 ARG 0.008 0.000 ARG E 111 *********************** 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 430 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 327 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7536 (mm-30) REVERT: A 38 GLU cc_start: 0.7501 (tt0) cc_final: 0.7216 (tt0) REVERT: A 248 ASP cc_start: 0.8496 (m-30) cc_final: 0.8293 (m-30) REVERT: A 262 MET cc_start: 0.8375 (mmp) cc_final: 0.8106 (mmp) REVERT: A 323 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7424 (mpp) REVERT: A 400 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8644 (mp) REVERT: A 408 ARG cc_start: 0.8040 (ttt180) cc_final: 0.7608 (ttt90) REVERT: A 461 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: A 469 GLN cc_start: 0.6765 (pp30) cc_final: 0.6475 (pt0) REVERT: A 470 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7145 (tm) REVERT: A 491 ARG cc_start: 0.7293 (mtm-85) cc_final: 0.7022 (ttp-110) REVERT: A 524 LYS cc_start: 0.7162 (mmtt) cc_final: 0.6774 (ttmt) REVERT: A 541 GLN cc_start: 0.7235 (pt0) cc_final: 0.6973 (pt0) REVERT: A 550 ARG cc_start: 0.6801 (mmt180) cc_final: 0.6082 (mmm160) REVERT: B 2 ILE cc_start: 0.8233 (mm) cc_final: 0.8015 (mm) REVERT: B 32 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: B 54 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6691 (t70) REVERT: B 104 ARG cc_start: 0.7637 (ptt180) cc_final: 0.7432 (ptt180) REVERT: B 124 LYS cc_start: 0.7217 (ptpp) cc_final: 0.6746 (ptpt) REVERT: B 127 ASP cc_start: 0.6970 (m-30) cc_final: 0.6678 (m-30) REVERT: B 133 MET cc_start: 0.7530 (ttm) cc_final: 0.7156 (ttt) REVERT: B 166 TYR cc_start: 0.7763 (m-80) cc_final: 0.7088 (m-80) REVERT: B 209 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6569 (mtt) REVERT: B 342 GLU cc_start: 0.6923 (pt0) cc_final: 0.6584 (mt-10) REVERT: B 397 GLN cc_start: 0.7220 (tp40) cc_final: 0.7008 (mp10) REVERT: B 459 GLN cc_start: 0.7042 (tp40) cc_final: 0.6746 (tp40) REVERT: B 461 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6514 (tt0) REVERT: B 481 ARG cc_start: 0.7097 (tmt-80) cc_final: 0.6448 (tmm-80) REVERT: B 485 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6390 (tp30) REVERT: B 491 ARG cc_start: 0.6447 (mtm-85) cc_final: 0.5291 (mtm-85) REVERT: B 547 ARG cc_start: 0.4732 (OUTLIER) cc_final: 0.4173 (ttm170) REVERT: B 563 PHE cc_start: 0.6957 (t80) cc_final: 0.6537 (t80) REVERT: C 1 MET cc_start: 0.6950 (mmt) cc_final: 0.6689 (mmp) REVERT: C 93 ARG cc_start: 0.7547 (mmm-85) cc_final: 0.6593 (mmm-85) REVERT: C 156 ARG cc_start: 0.6921 (ttp-110) cc_final: 0.6500 (ttt180) REVERT: C 344 MET cc_start: 0.8264 (mmt) cc_final: 0.7873 (tpp) REVERT: C 348 GLU cc_start: 0.7975 (tt0) cc_final: 0.7696 (mm-30) REVERT: C 433 SER cc_start: 0.8561 (p) cc_final: 0.8164 (m) REVERT: C 547 ARG cc_start: 0.6839 (mmm-85) cc_final: 0.6315 (ttm110) REVERT: C 565 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: D 52 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7730 (mt-10) REVERT: D 268 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7574 (ttm170) REVERT: D 280 ARG cc_start: 0.8007 (mtp-110) cc_final: 0.7550 (mtm110) REVERT: D 434 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7304 (mt-10) REVERT: E 52 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7856 (mt-10) REVERT: E 77 GLU cc_start: 0.6950 (pt0) cc_final: 0.5902 (mt-10) REVERT: E 88 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7722 (ttt) REVERT: E 96 ILE cc_start: 0.8310 (tp) cc_final: 0.7953 (tt) REVERT: E 139 ASP cc_start: 0.7472 (m-30) cc_final: 0.7028 (m-30) REVERT: E 174 ARG cc_start: 0.6669 (mmm-85) cc_final: 0.5875 (ttt-90) REVERT: E 216 ARG cc_start: 0.6008 (ttp80) cc_final: 0.5293 (ttp-110) REVERT: E 353 ASP cc_start: 0.7232 (t0) cc_final: 0.6968 (t0) REVERT: E 362 MET cc_start: 0.7850 (ttp) cc_final: 0.7485 (ttp) REVERT: E 368 LYS cc_start: 0.6328 (mmmt) cc_final: 0.5026 (tppt) REVERT: E 452 LYS cc_start: 0.6065 (ptpt) cc_final: 0.5570 (pmtt) REVERT: F 6 LYS cc_start: 0.7835 (tppp) cc_final: 0.6789 (mttp) REVERT: F 275 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: F 302 GLU cc_start: 0.7228 (tt0) cc_final: 0.6963 (mt-10) REVERT: F 373 GLU cc_start: 0.7773 (pm20) cc_final: 0.7529 (pt0) REVERT: F 394 LYS cc_start: 0.7501 (ttmt) cc_final: 0.7154 (mttm) REVERT: F 406 GLU cc_start: 0.7011 (tp30) cc_final: 0.6409 (tt0) REVERT: F 416 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7483 (t0) REVERT: F 420 ARG cc_start: 0.7685 (mmm160) cc_final: 0.7159 (mtt90) REVERT: G 9 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.6979 (ttp) REVERT: G 17 GLN cc_start: 0.7277 (mm110) cc_final: 0.7018 (mm-40) REVERT: G 38 GLU cc_start: 0.7195 (tp30) cc_final: 0.6695 (tt0) REVERT: G 152 GLU cc_start: 0.6119 (mm-30) cc_final: 0.5763 (mt-10) REVERT: G 159 ARG cc_start: 0.6881 (mtm180) cc_final: 0.6511 (ttp-170) REVERT: G 181 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7013 (mt0) REVERT: H 8 GLU cc_start: 0.3698 (OUTLIER) cc_final: 0.3118 (mt-10) REVERT: H 19 GLU cc_start: 0.3296 (OUTLIER) cc_final: 0.2037 (pp20) REVERT: H 38 GLU cc_start: 0.4382 (mm-30) cc_final: 0.4056 (mt-10) REVERT: H 56 GLU cc_start: 0.4385 (pp20) cc_final: 0.4141 (pm20) REVERT: H 90 MET cc_start: 0.7030 (tpp) cc_final: 0.6718 (mmm) REVERT: I 104 MET cc_start: 0.4111 (mtp) cc_final: 0.3851 (mpt) REVERT: J 66 LEU cc_start: 0.5776 (mt) cc_final: 0.5420 (mp) REVERT: J 79 VAL cc_start: 0.6048 (t) cc_final: 0.5473 (t) REVERT: J 82 GLU cc_start: 0.4550 (OUTLIER) cc_final: 0.4035 (mt-10) REVERT: L 126 GLU cc_start: 0.5311 (mp0) cc_final: 0.5102 (mp0) REVERT: L 181 LYS cc_start: 0.5823 (mttp) cc_final: 0.5328 (mmpt) outliers start: 103 outliers final: 49 residues processed: 397 average time/residue: 1.6541 time to fit residues: 756.5078 Evaluate side-chains 378 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 311 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 180 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 0.9980 chunk 324 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 360 optimal weight: 9.9990 chunk 299 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN B 425 ASN B 498 ASN C 425 ASN C 571 GLN ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS L 162 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30110 Z= 0.292 Angle : 0.570 9.048 40807 Z= 0.290 Chirality : 0.045 0.199 4576 Planarity : 0.005 0.050 5333 Dihedral : 5.468 75.169 4231 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.76 % Allowed : 14.34 % Favored : 81.90 % 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: 0.36 (0.14), residues: 3764 helix: 0.92 (0.13), residues: 1571 sheet: -0.50 (0.21), residues: 567 loop : 0.00 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 424 HIS 0.004 0.001 HIS F 249 PHE 0.016 0.002 PHE F 414 TYR 0.020 0.002 TYR B 513 ARG 0.009 0.000 ARG B 130 *********************** 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 446 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 330 time to evaluate : 3.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7530 (mm-30) REVERT: A 38 GLU cc_start: 0.7503 (tt0) cc_final: 0.7191 (tt0) REVERT: A 262 MET cc_start: 0.8376 (mmp) cc_final: 0.8085 (mmp) REVERT: A 268 GLU cc_start: 0.7057 (pt0) cc_final: 0.6856 (pt0) REVERT: A 323 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7441 (mpp) REVERT: A 344 MET cc_start: 0.8090 (mmm) cc_final: 0.7590 (ttm) REVERT: A 400 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8639 (mp) REVERT: A 408 ARG cc_start: 0.8038 (ttt180) cc_final: 0.7606 (ttt90) REVERT: A 469 GLN cc_start: 0.6775 (pp30) cc_final: 0.6440 (pt0) REVERT: A 470 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7247 (tm) REVERT: A 491 ARG cc_start: 0.7295 (mtm-85) cc_final: 0.7021 (ttp-110) REVERT: A 524 LYS cc_start: 0.7132 (mmtt) cc_final: 0.6754 (ttmt) REVERT: A 541 GLN cc_start: 0.7238 (pt0) cc_final: 0.6980 (pt0) REVERT: A 550 ARG cc_start: 0.6796 (mmt180) cc_final: 0.6062 (mmm160) REVERT: B 2 ILE cc_start: 0.8232 (mm) cc_final: 0.8025 (mm) REVERT: B 32 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7113 (mt-10) REVERT: B 54 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6702 (t70) REVERT: B 124 LYS cc_start: 0.7251 (ptpp) cc_final: 0.6761 (ptpt) REVERT: B 127 ASP cc_start: 0.6968 (m-30) cc_final: 0.6704 (m-30) REVERT: B 133 MET cc_start: 0.7485 (ttm) cc_final: 0.7126 (ttt) REVERT: B 166 TYR cc_start: 0.7765 (m-80) cc_final: 0.7101 (m-80) REVERT: B 200 ASP cc_start: 0.7281 (m-30) cc_final: 0.7043 (m-30) REVERT: B 209 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6772 (mtp) REVERT: B 342 GLU cc_start: 0.6945 (pt0) cc_final: 0.6587 (mt-10) REVERT: B 397 GLN cc_start: 0.7181 (tp40) cc_final: 0.6965 (mp10) REVERT: B 417 ARG cc_start: 0.5837 (tmm160) cc_final: 0.5516 (tmm160) REVERT: B 459 GLN cc_start: 0.7054 (tp40) cc_final: 0.6754 (tp40) REVERT: B 461 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6564 (tt0) REVERT: B 481 ARG cc_start: 0.7090 (tmt-80) cc_final: 0.6448 (tmm-80) REVERT: B 485 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6383 (tp30) REVERT: B 502 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6343 (pp20) REVERT: B 547 ARG cc_start: 0.4628 (OUTLIER) cc_final: 0.4128 (ttm-80) REVERT: B 558 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.5720 (pm20) REVERT: B 563 PHE cc_start: 0.6908 (t80) cc_final: 0.6420 (t80) REVERT: C 1 MET cc_start: 0.7037 (mmt) cc_final: 0.6709 (mmp) REVERT: C 93 ARG cc_start: 0.7534 (mmm-85) cc_final: 0.6577 (mmm-85) REVERT: C 156 ARG cc_start: 0.6940 (ttp-110) cc_final: 0.6503 (ttt180) REVERT: C 268 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6818 (mt-10) REVERT: C 344 MET cc_start: 0.8261 (mmt) cc_final: 0.7848 (tpp) REVERT: C 348 GLU cc_start: 0.7974 (tt0) cc_final: 0.7704 (mm-30) REVERT: C 374 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6702 (pt0) REVERT: C 433 SER cc_start: 0.8566 (p) cc_final: 0.8170 (m) REVERT: C 547 ARG cc_start: 0.6854 (mmm-85) cc_final: 0.6348 (ttm110) REVERT: D 52 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7726 (mt-10) REVERT: D 268 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7560 (ttm170) REVERT: D 280 ARG cc_start: 0.7998 (mtp-110) cc_final: 0.7530 (mtm110) REVERT: D 401 GLU cc_start: 0.7555 (pt0) cc_final: 0.7278 (pt0) REVERT: D 434 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7306 (mt-10) REVERT: E 52 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7855 (mt-10) REVERT: E 77 GLU cc_start: 0.7007 (pt0) cc_final: 0.5911 (mt-10) REVERT: E 88 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7786 (ttm) REVERT: E 96 ILE cc_start: 0.8325 (tp) cc_final: 0.7939 (tt) REVERT: E 139 ASP cc_start: 0.7459 (m-30) cc_final: 0.7006 (m-30) REVERT: E 174 ARG cc_start: 0.6743 (mmm-85) cc_final: 0.6130 (ttt-90) REVERT: E 216 ARG cc_start: 0.6072 (ttp80) cc_final: 0.5344 (ttp-110) REVERT: E 313 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8010 (mp) REVERT: E 353 ASP cc_start: 0.7327 (t0) cc_final: 0.7072 (t0) REVERT: E 362 MET cc_start: 0.7836 (ttp) cc_final: 0.7546 (ttp) REVERT: E 368 LYS cc_start: 0.6402 (mmmt) cc_final: 0.5015 (tppt) REVERT: E 450 GLU cc_start: 0.5142 (mt-10) cc_final: 0.4400 (mm-30) REVERT: E 452 LYS cc_start: 0.6065 (ptpt) cc_final: 0.5585 (pmtt) REVERT: F 6 LYS cc_start: 0.7849 (tppp) cc_final: 0.6793 (mttp) REVERT: F 275 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: F 302 GLU cc_start: 0.7211 (tt0) cc_final: 0.6924 (mt-10) REVERT: F 373 GLU cc_start: 0.7772 (pm20) cc_final: 0.7546 (pt0) REVERT: F 394 LYS cc_start: 0.7479 (ttmt) cc_final: 0.7110 (mttm) REVERT: F 406 GLU cc_start: 0.7052 (tp30) cc_final: 0.6425 (tt0) REVERT: F 416 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7463 (t0) REVERT: F 420 ARG cc_start: 0.7695 (mmm160) cc_final: 0.7155 (mtt90) REVERT: G 9 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7017 (ttp) REVERT: G 17 GLN cc_start: 0.7296 (mm110) cc_final: 0.7025 (mm-40) REVERT: G 38 GLU cc_start: 0.7274 (tp30) cc_final: 0.6783 (tt0) REVERT: G 152 GLU cc_start: 0.6086 (mm-30) cc_final: 0.5794 (mt-10) REVERT: G 159 ARG cc_start: 0.6852 (mtm180) cc_final: 0.6470 (ttp-170) REVERT: G 181 GLN cc_start: 0.7772 (mm-40) cc_final: 0.6992 (mt0) REVERT: H 19 GLU cc_start: 0.3298 (OUTLIER) cc_final: 0.2047 (pp20) REVERT: H 38 GLU cc_start: 0.4338 (mm-30) cc_final: 0.4080 (mt-10) REVERT: H 63 MET cc_start: 0.5061 (OUTLIER) cc_final: 0.4704 (ptp) REVERT: H 90 MET cc_start: 0.7039 (tpp) cc_final: 0.6676 (mmm) REVERT: I 104 MET cc_start: 0.4099 (mtp) cc_final: 0.3844 (mpt) REVERT: J 79 VAL cc_start: 0.6036 (t) cc_final: 0.5483 (t) REVERT: J 82 GLU cc_start: 0.4141 (OUTLIER) cc_final: 0.3808 (mt-10) REVERT: L 126 GLU cc_start: 0.5306 (mp0) cc_final: 0.5060 (mp0) REVERT: L 181 LYS cc_start: 0.5826 (mttp) cc_final: 0.5327 (mmpt) outliers start: 116 outliers final: 55 residues processed: 417 average time/residue: 1.6415 time to fit residues: 791.0662 Evaluate side-chains 379 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 305 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 180 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 204 optimal weight: 0.9990 chunk 303 optimal weight: 8.9990 chunk 201 optimal weight: 0.7980 chunk 359 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN B 425 ASN B 469 GLN B 498 ASN C 425 ASN C 571 GLN ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS L 162 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30110 Z= 0.229 Angle : 0.541 8.353 40807 Z= 0.275 Chirality : 0.044 0.199 4576 Planarity : 0.005 0.049 5333 Dihedral : 5.327 74.967 4231 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.41 % Allowed : 15.34 % Favored : 81.25 % 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: 0.48 (0.14), residues: 3764 helix: 1.05 (0.13), residues: 1569 sheet: -0.48 (0.21), residues: 562 loop : 0.06 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 424 HIS 0.004 0.001 HIS D 249 PHE 0.015 0.001 PHE F 414 TYR 0.018 0.001 TYR B 513 ARG 0.009 0.000 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 326 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7527 (mm-30) REVERT: A 38 GLU cc_start: 0.7448 (tt0) cc_final: 0.7131 (tt0) REVERT: A 344 MET cc_start: 0.8070 (mmm) cc_final: 0.7633 (ttm) REVERT: A 408 ARG cc_start: 0.8027 (ttt180) cc_final: 0.7682 (ttt90) REVERT: A 461 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: A 469 GLN cc_start: 0.6706 (pp30) cc_final: 0.6381 (pt0) REVERT: A 470 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7235 (tm) REVERT: A 491 ARG cc_start: 0.7296 (mtm-85) cc_final: 0.7026 (ttp-110) REVERT: A 524 LYS cc_start: 0.7112 (mmtt) cc_final: 0.6762 (ttmt) REVERT: A 541 GLN cc_start: 0.7249 (pt0) cc_final: 0.6979 (pt0) REVERT: A 550 ARG cc_start: 0.6767 (mmt180) cc_final: 0.6057 (mmm160) REVERT: B 2 ILE cc_start: 0.8210 (mm) cc_final: 0.8001 (mm) REVERT: B 32 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7089 (mt-10) REVERT: B 54 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6787 (t70) REVERT: B 124 LYS cc_start: 0.7273 (ptpp) cc_final: 0.6829 (ptpt) REVERT: B 127 ASP cc_start: 0.6958 (m-30) cc_final: 0.6723 (m-30) REVERT: B 133 MET cc_start: 0.7426 (ttm) cc_final: 0.7180 (ttt) REVERT: B 166 TYR cc_start: 0.7729 (m-80) cc_final: 0.7086 (m-80) REVERT: B 200 ASP cc_start: 0.7248 (m-30) cc_final: 0.7010 (m-30) REVERT: B 209 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6811 (mtp) REVERT: B 342 GLU cc_start: 0.6911 (pt0) cc_final: 0.6560 (mt-10) REVERT: B 417 ARG cc_start: 0.5787 (tmm160) cc_final: 0.5499 (tmm160) REVERT: B 459 GLN cc_start: 0.7040 (tp40) cc_final: 0.6739 (tp40) REVERT: B 461 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6539 (tt0) REVERT: B 477 GLN cc_start: 0.5528 (OUTLIER) cc_final: 0.5183 (pt0) REVERT: B 481 ARG cc_start: 0.7128 (tmt-80) cc_final: 0.6461 (tmm-80) REVERT: B 485 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6400 (tp30) REVERT: B 491 ARG cc_start: 0.6310 (mtm-85) cc_final: 0.5715 (mtm-85) REVERT: B 502 GLU cc_start: 0.6783 (tm-30) cc_final: 0.6375 (pp20) REVERT: B 547 ARG cc_start: 0.4828 (OUTLIER) cc_final: 0.4283 (ttm170) REVERT: B 563 PHE cc_start: 0.6863 (t80) cc_final: 0.6377 (t80) REVERT: C 1 MET cc_start: 0.7008 (mmt) cc_final: 0.6678 (mmp) REVERT: C 93 ARG cc_start: 0.7550 (mmm-85) cc_final: 0.6600 (mmm-85) REVERT: C 156 ARG cc_start: 0.6919 (ttp-110) cc_final: 0.6459 (ttt180) REVERT: C 176 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6896 (tm-30) REVERT: C 268 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6810 (mt-10) REVERT: C 344 MET cc_start: 0.8251 (mmt) cc_final: 0.7847 (tpp) REVERT: C 348 GLU cc_start: 0.7985 (tt0) cc_final: 0.7700 (mm-30) REVERT: C 374 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6710 (pt0) REVERT: C 433 SER cc_start: 0.8554 (p) cc_final: 0.8153 (m) REVERT: C 547 ARG cc_start: 0.6861 (mmm-85) cc_final: 0.6325 (ttm110) REVERT: C 565 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6947 (mm-30) REVERT: D 49 GLU cc_start: 0.8080 (tt0) cc_final: 0.7783 (tt0) REVERT: D 268 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7571 (ttm170) REVERT: D 280 ARG cc_start: 0.7999 (mtp-110) cc_final: 0.7544 (mtm110) REVERT: D 401 GLU cc_start: 0.7520 (pt0) cc_final: 0.7256 (pt0) REVERT: E 52 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7839 (mt-10) REVERT: E 77 GLU cc_start: 0.7096 (pt0) cc_final: 0.5900 (mt-10) REVERT: E 88 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7792 (ttm) REVERT: E 96 ILE cc_start: 0.8239 (tp) cc_final: 0.7871 (tt) REVERT: E 139 ASP cc_start: 0.7411 (m-30) cc_final: 0.6949 (m-30) REVERT: E 216 ARG cc_start: 0.6047 (ttp80) cc_final: 0.5327 (ttp-110) REVERT: E 353 ASP cc_start: 0.7306 (t0) cc_final: 0.7094 (t0) REVERT: E 362 MET cc_start: 0.7822 (ttp) cc_final: 0.7520 (ttp) REVERT: E 368 LYS cc_start: 0.6350 (mmmt) cc_final: 0.4997 (tppt) REVERT: E 450 GLU cc_start: 0.5155 (mt-10) cc_final: 0.4536 (mm-30) REVERT: E 452 LYS cc_start: 0.6070 (ptpt) cc_final: 0.5562 (tttt) REVERT: F 6 LYS cc_start: 0.7833 (tppp) cc_final: 0.6757 (mttp) REVERT: F 258 THR cc_start: 0.7300 (OUTLIER) cc_final: 0.6846 (m) REVERT: F 264 CYS cc_start: 0.8229 (m) cc_final: 0.7858 (m) REVERT: F 275 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: F 302 GLU cc_start: 0.7232 (tt0) cc_final: 0.6950 (mt-10) REVERT: F 373 GLU cc_start: 0.7762 (pm20) cc_final: 0.7528 (pt0) REVERT: F 394 LYS cc_start: 0.7426 (ttmt) cc_final: 0.7131 (mttm) REVERT: F 406 GLU cc_start: 0.7053 (tp30) cc_final: 0.6409 (tt0) REVERT: F 420 ARG cc_start: 0.7694 (mmm160) cc_final: 0.7187 (mtm110) REVERT: G 9 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7030 (ttp) REVERT: G 17 GLN cc_start: 0.7280 (mm110) cc_final: 0.7007 (mm-40) REVERT: G 38 GLU cc_start: 0.7263 (tp30) cc_final: 0.6975 (tt0) REVERT: G 152 GLU cc_start: 0.6067 (mm-30) cc_final: 0.5805 (mt-10) REVERT: G 159 ARG cc_start: 0.6917 (mtm180) cc_final: 0.6531 (ttp-170) REVERT: G 181 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7014 (mt0) REVERT: H 19 GLU cc_start: 0.3385 (OUTLIER) cc_final: 0.2164 (pp20) REVERT: H 38 GLU cc_start: 0.4412 (mm-30) cc_final: 0.4162 (mt-10) REVERT: H 63 MET cc_start: 0.5027 (OUTLIER) cc_final: 0.4638 (ptp) REVERT: H 90 MET cc_start: 0.7010 (tpp) cc_final: 0.6693 (mmm) REVERT: I 84 LEU cc_start: 0.3967 (OUTLIER) cc_final: 0.3733 (mm) REVERT: I 104 MET cc_start: 0.4040 (mtp) cc_final: 0.3789 (mpt) REVERT: J 79 VAL cc_start: 0.6125 (t) cc_final: 0.5615 (t) REVERT: J 82 GLU cc_start: 0.4210 (OUTLIER) cc_final: 0.3984 (mt-10) REVERT: L 126 GLU cc_start: 0.5289 (mp0) cc_final: 0.5042 (mp0) REVERT: L 181 LYS cc_start: 0.5813 (mttp) cc_final: 0.5309 (mmpt) outliers start: 105 outliers final: 53 residues processed: 402 average time/residue: 1.6469 time to fit residues: 773.5771 Evaluate side-chains 379 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 306 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 179 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 214 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 33 optimal weight: 0.0870 chunk 282 optimal weight: 8.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN B 425 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN C 425 ASN C 571 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30110 Z= 0.264 Angle : 0.560 8.689 40807 Z= 0.285 Chirality : 0.044 0.202 4576 Planarity : 0.005 0.049 5333 Dihedral : 5.364 75.216 4231 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.02 % Allowed : 16.12 % Favored : 80.86 % 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: 0.43 (0.14), residues: 3764 helix: 1.00 (0.13), residues: 1570 sheet: -0.53 (0.21), residues: 571 loop : 0.04 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 424 HIS 0.004 0.001 HIS F 249 PHE 0.015 0.002 PHE F 414 TYR 0.022 0.002 TYR E 462 ARG 0.009 0.000 ARG B 130 *********************** 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 410 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 317 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7542 (mm-30) REVERT: A 38 GLU cc_start: 0.7474 (tt0) cc_final: 0.7151 (tt0) REVERT: A 268 GLU cc_start: 0.7053 (pt0) cc_final: 0.6729 (pt0) REVERT: A 323 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7452 (mpp) REVERT: A 344 MET cc_start: 0.8026 (mmm) cc_final: 0.7688 (ttm) REVERT: A 408 ARG cc_start: 0.8025 (ttt180) cc_final: 0.7587 (ttt90) REVERT: A 469 GLN cc_start: 0.6677 (pp30) cc_final: 0.6351 (pt0) REVERT: A 470 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7239 (tm) REVERT: A 491 ARG cc_start: 0.7292 (mtm-85) cc_final: 0.7021 (ttp-110) REVERT: A 524 LYS cc_start: 0.7115 (mmtt) cc_final: 0.6761 (ttmt) REVERT: A 541 GLN cc_start: 0.7210 (pt0) cc_final: 0.6949 (pt0) REVERT: A 550 ARG cc_start: 0.6765 (mmt180) cc_final: 0.6062 (mmm160) REVERT: B 32 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: B 54 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6824 (t70) REVERT: B 124 LYS cc_start: 0.7242 (ptpp) cc_final: 0.6762 (ptpt) REVERT: B 127 ASP cc_start: 0.6962 (m-30) cc_final: 0.6727 (m-30) REVERT: B 133 MET cc_start: 0.7421 (ttm) cc_final: 0.7192 (ttt) REVERT: B 166 TYR cc_start: 0.7781 (m-80) cc_final: 0.7077 (m-80) REVERT: B 200 ASP cc_start: 0.7316 (m-30) cc_final: 0.7076 (m-30) REVERT: B 342 GLU cc_start: 0.6944 (pt0) cc_final: 0.6574 (mt-10) REVERT: B 397 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6993 (mp10) REVERT: B 417 ARG cc_start: 0.5829 (tmm160) cc_final: 0.5528 (tmm160) REVERT: B 459 GLN cc_start: 0.7073 (tp40) cc_final: 0.6773 (tp40) REVERT: B 461 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6527 (tt0) REVERT: B 481 ARG cc_start: 0.7124 (tmt-80) cc_final: 0.6410 (tmm-80) REVERT: B 485 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6378 (tp30) REVERT: B 491 ARG cc_start: 0.6373 (mtm-85) cc_final: 0.5554 (mtm-85) REVERT: B 502 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6422 (pp20) REVERT: B 547 ARG cc_start: 0.4785 (OUTLIER) cc_final: 0.4223 (ttm170) REVERT: B 558 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6021 (pm20) REVERT: B 563 PHE cc_start: 0.6893 (t80) cc_final: 0.6401 (t80) REVERT: C 1 MET cc_start: 0.7051 (mmt) cc_final: 0.6728 (mmp) REVERT: C 56 SER cc_start: 0.8347 (m) cc_final: 0.7951 (p) REVERT: C 93 ARG cc_start: 0.7551 (mmm-85) cc_final: 0.6589 (mmm-85) REVERT: C 176 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: C 344 MET cc_start: 0.8265 (mmt) cc_final: 0.7842 (tpp) REVERT: C 348 GLU cc_start: 0.7982 (tt0) cc_final: 0.7699 (mm-30) REVERT: C 374 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6719 (pt0) REVERT: C 433 SER cc_start: 0.8565 (p) cc_final: 0.8168 (m) REVERT: C 547 ARG cc_start: 0.6875 (mmm-85) cc_final: 0.6347 (ttm110) REVERT: C 565 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7010 (mm-30) REVERT: D 268 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7520 (ttm170) REVERT: D 280 ARG cc_start: 0.8022 (mtp-110) cc_final: 0.7565 (mtm110) REVERT: D 401 GLU cc_start: 0.7523 (pt0) cc_final: 0.7259 (pt0) REVERT: E 52 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7837 (mt-10) REVERT: E 77 GLU cc_start: 0.7128 (pt0) cc_final: 0.5922 (mt-10) REVERT: E 88 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7787 (ttm) REVERT: E 96 ILE cc_start: 0.8259 (tp) cc_final: 0.7886 (tt) REVERT: E 139 ASP cc_start: 0.7410 (m-30) cc_final: 0.6966 (m-30) REVERT: E 216 ARG cc_start: 0.6032 (ttp80) cc_final: 0.5315 (ttp-110) REVERT: E 362 MET cc_start: 0.7814 (ttp) cc_final: 0.7510 (ttp) REVERT: E 368 LYS cc_start: 0.6354 (mmmt) cc_final: 0.5006 (mppt) REVERT: E 413 GLN cc_start: 0.5640 (mt0) cc_final: 0.5365 (mt0) REVERT: E 450 GLU cc_start: 0.5279 (mt-10) cc_final: 0.4523 (mm-30) REVERT: E 452 LYS cc_start: 0.6017 (ptpt) cc_final: 0.5544 (tttt) REVERT: F 6 LYS cc_start: 0.7885 (tppp) cc_final: 0.6819 (mttp) REVERT: F 258 THR cc_start: 0.7380 (OUTLIER) cc_final: 0.6902 (m) REVERT: F 275 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: F 302 GLU cc_start: 0.7231 (tt0) cc_final: 0.6945 (mt-10) REVERT: F 394 LYS cc_start: 0.7450 (ttmt) cc_final: 0.7160 (mttm) REVERT: F 406 GLU cc_start: 0.7027 (tp30) cc_final: 0.6378 (tt0) REVERT: F 416 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7401 (t0) REVERT: F 420 ARG cc_start: 0.7656 (mmm160) cc_final: 0.7175 (mtm110) REVERT: G 9 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7005 (ttp) REVERT: G 17 GLN cc_start: 0.7286 (mm110) cc_final: 0.7010 (mm-40) REVERT: G 38 GLU cc_start: 0.7191 (tp30) cc_final: 0.6712 (tt0) REVERT: G 152 GLU cc_start: 0.6051 (mm-30) cc_final: 0.5801 (mt-10) REVERT: G 159 ARG cc_start: 0.6882 (mtm180) cc_final: 0.6493 (ttp-170) REVERT: G 181 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7025 (mt0) REVERT: H 63 MET cc_start: 0.5052 (OUTLIER) cc_final: 0.4630 (ptp) REVERT: H 90 MET cc_start: 0.7007 (tpp) cc_final: 0.6760 (mmm) REVERT: I 84 LEU cc_start: 0.3961 (OUTLIER) cc_final: 0.3726 (mm) REVERT: I 104 MET cc_start: 0.4038 (mtp) cc_final: 0.3804 (mpt) REVERT: J 79 VAL cc_start: 0.6173 (t) cc_final: 0.5688 (t) REVERT: J 82 GLU cc_start: 0.4085 (OUTLIER) cc_final: 0.3883 (mt-10) REVERT: L 126 GLU cc_start: 0.5274 (mp0) cc_final: 0.5042 (mp0) REVERT: L 181 LYS cc_start: 0.5819 (mttp) cc_final: 0.5313 (mmpt) outliers start: 93 outliers final: 58 residues processed: 386 average time/residue: 1.6251 time to fit residues: 725.1867 Evaluate side-chains 384 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 306 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 179 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 5.9990 chunk 344 optimal weight: 4.9990 chunk 314 optimal weight: 8.9990 chunk 335 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 302 optimal weight: 4.9990 chunk 316 optimal weight: 20.0000 chunk 333 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN B 425 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN C 425 ASN C 571 GLN E 142 ASN F 437 GLN F 465 GLN G 166 GLN G 175 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 30110 Z= 0.386 Angle : 0.630 9.054 40807 Z= 0.321 Chirality : 0.047 0.220 4576 Planarity : 0.005 0.050 5333 Dihedral : 5.658 75.907 4231 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.28 % Allowed : 16.22 % Favored : 80.51 % 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: 0.21 (0.14), residues: 3764 helix: 0.78 (0.13), residues: 1560 sheet: -0.64 (0.21), residues: 582 loop : -0.02 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 440 HIS 0.005 0.001 HIS F 249 PHE 0.016 0.002 PHE F 414 TYR 0.023 0.002 TYR B 513 ARG 0.011 0.001 ARG A 156 *********************** 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 399 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 298 time to evaluate : 3.370 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7521 (mm-30) REVERT: A 38 GLU cc_start: 0.7582 (tt0) cc_final: 0.7219 (tt0) REVERT: A 268 GLU cc_start: 0.7060 (pt0) cc_final: 0.6698 (pt0) REVERT: A 323 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7452 (mpp) REVERT: A 344 MET cc_start: 0.8003 (mmm) cc_final: 0.7755 (ttm) REVERT: A 408 ARG cc_start: 0.8034 (ttt180) cc_final: 0.7585 (ttt90) REVERT: A 469 GLN cc_start: 0.6740 (pp30) cc_final: 0.6385 (pt0) REVERT: A 470 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7208 (tm) REVERT: A 491 ARG cc_start: 0.7249 (mtm-85) cc_final: 0.7000 (ttp-110) REVERT: A 524 LYS cc_start: 0.7133 (mmtt) cc_final: 0.6754 (ttmt) REVERT: A 541 GLN cc_start: 0.7206 (pt0) cc_final: 0.6946 (pt0) REVERT: A 550 ARG cc_start: 0.6737 (mmt180) cc_final: 0.6064 (mmm160) REVERT: B 32 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: B 54 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6811 (t70) REVERT: B 166 TYR cc_start: 0.7845 (m-80) cc_final: 0.7151 (m-80) REVERT: B 200 ASP cc_start: 0.7356 (m-30) cc_final: 0.7097 (m-30) REVERT: B 342 GLU cc_start: 0.7043 (pt0) cc_final: 0.6585 (mt-10) REVERT: B 459 GLN cc_start: 0.7049 (tp40) cc_final: 0.6745 (tp40) REVERT: B 461 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6552 (tt0) REVERT: B 477 GLN cc_start: 0.5314 (OUTLIER) cc_final: 0.4988 (tt0) REVERT: B 485 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6723 (tp30) REVERT: B 502 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6408 (pp20) REVERT: B 547 ARG cc_start: 0.4838 (OUTLIER) cc_final: 0.4315 (ttm170) REVERT: B 558 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.5994 (pm20) REVERT: B 563 PHE cc_start: 0.6956 (t80) cc_final: 0.6519 (t80) REVERT: C 1 MET cc_start: 0.7151 (mmt) cc_final: 0.6799 (mmp) REVERT: C 93 ARG cc_start: 0.7529 (mmm-85) cc_final: 0.6568 (mmm-85) REVERT: C 176 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: C 344 MET cc_start: 0.8233 (mmt) cc_final: 0.7821 (tpp) REVERT: C 348 GLU cc_start: 0.7972 (tt0) cc_final: 0.7720 (mm-30) REVERT: C 433 SER cc_start: 0.8625 (p) cc_final: 0.8224 (m) REVERT: C 547 ARG cc_start: 0.6886 (mmm-85) cc_final: 0.6326 (ttm110) REVERT: C 565 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7090 (mm-30) REVERT: D 268 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7508 (ttm170) REVERT: D 280 ARG cc_start: 0.8039 (mtp-110) cc_final: 0.7548 (mtm110) REVERT: D 314 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8300 (pt) REVERT: E 52 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7860 (mt-10) REVERT: E 77 GLU cc_start: 0.7165 (pt0) cc_final: 0.5977 (mt-10) REVERT: E 88 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7766 (ttm) REVERT: E 96 ILE cc_start: 0.8369 (tp) cc_final: 0.8018 (tt) REVERT: E 139 ASP cc_start: 0.7509 (m-30) cc_final: 0.7027 (m-30) REVERT: E 216 ARG cc_start: 0.6018 (ttp80) cc_final: 0.5270 (ttp-110) REVERT: E 362 MET cc_start: 0.7833 (ttp) cc_final: 0.7547 (ttp) REVERT: E 368 LYS cc_start: 0.6386 (mmmt) cc_final: 0.4844 (mptm) REVERT: E 413 GLN cc_start: 0.5667 (mt0) cc_final: 0.5368 (mt0) REVERT: E 450 GLU cc_start: 0.5213 (mt-10) cc_final: 0.4489 (mm-30) REVERT: E 452 LYS cc_start: 0.6038 (ptpt) cc_final: 0.5526 (tttp) REVERT: F 6 LYS cc_start: 0.7964 (tppp) cc_final: 0.6931 (mttp) REVERT: F 275 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: F 302 GLU cc_start: 0.7179 (tt0) cc_final: 0.6936 (mt-10) REVERT: F 394 LYS cc_start: 0.7471 (ttmt) cc_final: 0.7168 (mttp) REVERT: F 406 GLU cc_start: 0.7023 (tp30) cc_final: 0.6390 (tt0) REVERT: F 416 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7384 (t0) REVERT: F 420 ARG cc_start: 0.7651 (mmm160) cc_final: 0.7176 (mtt90) REVERT: G 9 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7022 (ttt) REVERT: G 17 GLN cc_start: 0.7290 (mm110) cc_final: 0.7014 (mm-40) REVERT: G 38 GLU cc_start: 0.7222 (tp30) cc_final: 0.6899 (tt0) REVERT: G 152 GLU cc_start: 0.6160 (mm-30) cc_final: 0.5880 (mt-10) REVERT: G 159 ARG cc_start: 0.6857 (mtm180) cc_final: 0.6470 (ttp-170) REVERT: G 181 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7039 (mt0) REVERT: H 90 MET cc_start: 0.7054 (tpp) cc_final: 0.6713 (mmm) REVERT: I 84 LEU cc_start: 0.4013 (OUTLIER) cc_final: 0.3775 (mm) REVERT: I 104 MET cc_start: 0.4070 (mtp) cc_final: 0.3818 (mpt) REVERT: L 126 GLU cc_start: 0.5261 (mp0) cc_final: 0.5034 (mp0) REVERT: L 181 LYS cc_start: 0.5839 (mttp) cc_final: 0.5332 (mmpt) outliers start: 101 outliers final: 64 residues processed: 369 average time/residue: 1.6611 time to fit residues: 706.9072 Evaluate side-chains 372 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 291 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 180 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 1.9990 chunk 354 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 371 optimal weight: 3.9990 chunk 342 optimal weight: 1.9990 chunk 295 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 228 optimal weight: 0.4980 chunk 181 optimal weight: 0.0470 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN B 425 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN C 571 GLN D 166 GLN D 170 GLN F 437 GLN F 465 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30110 Z= 0.159 Angle : 0.517 8.351 40807 Z= 0.263 Chirality : 0.042 0.170 4576 Planarity : 0.004 0.052 5333 Dihedral : 5.154 73.538 4231 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.11 % Allowed : 17.71 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3764 helix: 1.16 (0.14), residues: 1569 sheet: -0.52 (0.21), residues: 572 loop : 0.07 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 119 HIS 0.002 0.001 HIS E 375 PHE 0.015 0.001 PHE F 414 TYR 0.018 0.001 TYR B 513 ARG 0.013 0.000 ARG A 156 ********************** 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: 65 poor density : 328 time to evaluate : 3.448 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7335 (tt0) cc_final: 0.7066 (tt0) REVERT: A 268 GLU cc_start: 0.7004 (pt0) cc_final: 0.6763 (pt0) REVERT: A 300 GLU cc_start: 0.7482 (tt0) cc_final: 0.7263 (tt0) REVERT: A 323 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7413 (mpp) REVERT: A 344 MET cc_start: 0.7997 (mmm) cc_final: 0.7662 (ttm) REVERT: A 408 ARG cc_start: 0.8011 (ttt180) cc_final: 0.7660 (ttt90) REVERT: A 461 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: A 469 GLN cc_start: 0.6743 (pp30) cc_final: 0.6449 (pt0) REVERT: A 491 ARG cc_start: 0.7255 (mtm-85) cc_final: 0.6968 (ttp-110) REVERT: A 524 LYS cc_start: 0.7085 (mmtt) cc_final: 0.6740 (ttmt) REVERT: A 541 GLN cc_start: 0.7211 (pt0) cc_final: 0.6937 (pt0) REVERT: A 550 ARG cc_start: 0.6768 (mmt180) cc_final: 0.6076 (mmm160) REVERT: B 32 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6979 (mt-10) REVERT: B 54 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6806 (t70) REVERT: B 166 TYR cc_start: 0.7783 (m-80) cc_final: 0.7069 (m-80) REVERT: B 200 ASP cc_start: 0.7198 (m-30) cc_final: 0.6978 (m-30) REVERT: B 342 GLU cc_start: 0.6884 (pt0) cc_final: 0.6424 (mt-10) REVERT: B 417 ARG cc_start: 0.5959 (tmm160) cc_final: 0.5744 (tmm160) REVERT: B 459 GLN cc_start: 0.7087 (tp40) cc_final: 0.6759 (tp40) REVERT: B 481 ARG cc_start: 0.7101 (tmt-80) cc_final: 0.6430 (tmm-80) REVERT: B 485 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6403 (tp30) REVERT: B 502 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6430 (pp20) REVERT: B 558 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5746 (mt-10) REVERT: B 563 PHE cc_start: 0.6858 (t80) cc_final: 0.6330 (t80) REVERT: C 1 MET cc_start: 0.7125 (mmt) cc_final: 0.6771 (mmp) REVERT: C 93 ARG cc_start: 0.7537 (mmm-85) cc_final: 0.6599 (mmm-85) REVERT: C 176 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: C 344 MET cc_start: 0.8248 (mmt) cc_final: 0.7833 (tpp) REVERT: C 348 GLU cc_start: 0.7987 (tt0) cc_final: 0.7698 (mm-30) REVERT: C 374 GLU cc_start: 0.7133 (pt0) cc_final: 0.6800 (pt0) REVERT: C 433 SER cc_start: 0.8568 (p) cc_final: 0.8151 (m) REVERT: C 481 ARG cc_start: 0.7073 (tpt-90) cc_final: 0.6793 (ttt180) REVERT: C 547 ARG cc_start: 0.6866 (mmm-85) cc_final: 0.6498 (ttm110) REVERT: C 565 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6987 (mm-30) REVERT: D 268 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7584 (ttm170) REVERT: D 280 ARG cc_start: 0.8013 (mtp-110) cc_final: 0.7560 (mtm110) REVERT: D 287 MET cc_start: 0.8690 (ttp) cc_final: 0.8388 (ttp) REVERT: D 401 GLU cc_start: 0.7496 (pt0) cc_final: 0.7257 (pt0) REVERT: E 52 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7820 (mt-10) REVERT: E 88 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7822 (ttm) REVERT: E 96 ILE cc_start: 0.8169 (tp) cc_final: 0.7802 (tt) REVERT: E 139 ASP cc_start: 0.7366 (m-30) cc_final: 0.6928 (m-30) REVERT: E 216 ARG cc_start: 0.5846 (ttp80) cc_final: 0.5240 (ttp-110) REVERT: E 362 MET cc_start: 0.7855 (ttp) cc_final: 0.7544 (ttp) REVERT: E 368 LYS cc_start: 0.6366 (mmmt) cc_final: 0.4936 (mppt) REVERT: E 413 GLN cc_start: 0.5631 (mt0) cc_final: 0.5357 (mt0) REVERT: E 442 LEU cc_start: 0.5708 (mt) cc_final: 0.5351 (mm) REVERT: E 450 GLU cc_start: 0.5317 (mt-10) cc_final: 0.4575 (mm-30) REVERT: E 452 LYS cc_start: 0.5955 (ptpt) cc_final: 0.5434 (tttp) REVERT: F 6 LYS cc_start: 0.7777 (tppp) cc_final: 0.6779 (mttp) REVERT: F 258 THR cc_start: 0.7087 (OUTLIER) cc_final: 0.6846 (m) REVERT: F 264 CYS cc_start: 0.8201 (m) cc_final: 0.7798 (m) REVERT: F 302 GLU cc_start: 0.7166 (tt0) cc_final: 0.6894 (mt-10) REVERT: F 394 LYS cc_start: 0.7467 (ttmt) cc_final: 0.6951 (mtmt) REVERT: F 406 GLU cc_start: 0.6959 (tp30) cc_final: 0.6342 (tt0) REVERT: F 420 ARG cc_start: 0.7640 (mmm160) cc_final: 0.7206 (mtm110) REVERT: G 9 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6785 (ttt) REVERT: G 17 GLN cc_start: 0.7255 (mm110) cc_final: 0.6980 (mm-40) REVERT: G 38 GLU cc_start: 0.7183 (tp30) cc_final: 0.6875 (tt0) REVERT: G 152 GLU cc_start: 0.6005 (mm-30) cc_final: 0.5701 (mt-10) REVERT: G 159 ARG cc_start: 0.6879 (mtm180) cc_final: 0.6464 (ttp-170) REVERT: G 181 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7016 (mt0) REVERT: G 205 GLU cc_start: 0.3917 (tm-30) cc_final: 0.3177 (tt0) REVERT: H 19 GLU cc_start: 0.3575 (OUTLIER) cc_final: 0.3342 (pp20) REVERT: H 63 MET cc_start: 0.5150 (OUTLIER) cc_final: 0.4720 (ptp) REVERT: H 90 MET cc_start: 0.6999 (tpp) cc_final: 0.6792 (mmm) REVERT: H 92 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6765 (tp30) REVERT: J 79 VAL cc_start: 0.6101 (t) cc_final: 0.5807 (t) REVERT: J 82 GLU cc_start: 0.4157 (mt-10) cc_final: 0.3882 (mp0) REVERT: L 181 LYS cc_start: 0.5830 (mttp) cc_final: 0.5333 (mmpt) outliers start: 65 outliers final: 31 residues processed: 376 average time/residue: 1.5905 time to fit residues: 691.2236 Evaluate side-chains 351 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 306 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 166 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 9.9990 chunk 315 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 272 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 296 optimal weight: 0.9990 chunk 124 optimal weight: 0.0870 chunk 304 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN B 425 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN C 425 ASN C 571 GLN D 166 GLN G 22 GLN ** L 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112501 restraints weight = 39350.915| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.88 r_work: 0.3200 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30110 Z= 0.150 Angle : 0.509 8.151 40807 Z= 0.257 Chirality : 0.042 0.161 4576 Planarity : 0.004 0.054 5333 Dihedral : 4.952 71.704 4231 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.62 % Allowed : 18.68 % Favored : 79.70 % 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: 0.70 (0.14), residues: 3764 helix: 1.30 (0.14), residues: 1565 sheet: -0.50 (0.21), residues: 581 loop : 0.16 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 424 HIS 0.002 0.000 HIS F 249 PHE 0.014 0.001 PHE F 414 TYR 0.017 0.001 TYR B 513 ARG 0.013 0.000 ARG A 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11698.51 seconds wall clock time: 206 minutes 10.40 seconds (12370.40 seconds total)