Starting phenix.real_space_refine on Thu Feb 22 13:05:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dav_27277/02_2024/8dav_27277_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dav_27277/02_2024/8dav_27277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dav_27277/02_2024/8dav_27277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dav_27277/02_2024/8dav_27277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dav_27277/02_2024/8dav_27277_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dav_27277/02_2024/8dav_27277_updated.pdb" } resolution = 3.5 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= -0.017 sd= 1.081 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 Zn 2 6.06 5 P 29 5.49 5 S 156 5.16 5 C 21438 2.51 5 N 5955 2.21 5 O 6668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34248 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5555 Classifications: {'peptide': 712} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 674} Chain breaks: 2 Chain: "B" Number of atoms: 5599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5599 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 680} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4311 Classifications: {'peptide': 555} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 525} Chain breaks: 4 Chain: "D" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4240 Classifications: {'peptide': 547} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 517} Chain breaks: 5 Chain: "E" Number of atoms: 4113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4113 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 502} Chain breaks: 3 Chain: "F" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4284 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 521} Chain breaks: 5 Chain: "G" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3825 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 453} Chain: "H" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 477 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain breaks: 1 Chain: "I" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 298 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "J" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 600 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "K" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 600 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28365 SG CYS G 137 45.745 49.270 92.930 1.00 77.95 S ATOM 28425 SG CYS G 145 49.375 50.017 93.042 1.00 58.37 S ATOM 28452 SG CYS G 148 47.278 50.134 96.007 1.00 56.03 S ATOM 28922 SG CYS G 204 73.882 91.093 114.110 1.00 86.29 S ATOM 29020 SG CYS G 216 74.129 91.033 110.344 1.00 61.09 S ATOM 29041 SG CYS G 219 71.340 92.806 111.935 1.00 66.42 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU K 273 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU K 273 " occ=0.00 residue: pdb=" N ARG K 274 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG K 274 " occ=0.00 residue: pdb=" N GLY K 275 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY K 275 " occ=0.00 residue: pdb=" N GLY K 276 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY K 276 " occ=0.00 Time building chain proxies: 16.21, per 1000 atoms: 0.47 Number of scatterers: 34248 At special positions: 0 Unit cell: (150.024, 169.176, 189.392, 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) Zn 2 29.99 S 156 16.00 P 29 15.00 O 6668 8.00 N 5955 7.00 C 21438 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: 12.39 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 139 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 148 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 137 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 145 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 208 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 219 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 216 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 204 " Number of angles added : 6 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 209 helices and 23 sheets defined 45.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.27 Creating SS restraints... Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.674A pdb=" N LEU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 102 Processing helix chain 'A' and resid 130 through 133 Processing helix chain 'A' and resid 141 through 148 removed outlier: 4.172A pdb=" N LYS A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 220 through 235 removed outlier: 4.149A pdb=" N LEU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.574A pdb=" N LYS A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 316 through 319 No H-bonds generated for 'chain 'A' and resid 316 through 319' Processing helix chain 'A' and resid 329 through 343 Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.795A pdb=" N LYS A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 418 through 439 removed outlier: 4.441A pdb=" N ASP A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.506A pdb=" N SER A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 493 through 508 removed outlier: 4.464A pdb=" N TYR A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Proline residue: A 506 - end of helix Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 534 through 544 Processing helix chain 'A' and resid 554 through 562 Processing helix chain 'A' and resid 569 through 578 Processing helix chain 'A' and resid 589 through 592 removed outlier: 3.707A pdb=" N ILE A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 589 through 592' Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 641 through 644 Processing helix chain 'A' and resid 660 through 670 Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 694 through 717 Processing helix chain 'A' and resid 755 through 763 Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 96 through 102 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 140 through 149 removed outlier: 3.717A pdb=" N LYS B 146 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Proline residue: B 147 - end of helix Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 220 through 233 removed outlier: 4.803A pdb=" N LEU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 237 through 243 Processing helix chain 'B' and resid 261 through 272 Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 292 through 305 Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 330 through 344 Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 418 through 439 removed outlier: 4.073A pdb=" N ASP B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 454 Processing helix chain 'B' and resid 459 through 468 Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 493 through 508 removed outlier: 4.332A pdb=" N TYR B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Proline residue: B 506 - end of helix Processing helix chain 'B' and resid 510 through 516 Processing helix chain 'B' and resid 534 through 544 removed outlier: 4.029A pdb=" N ALA B 538 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 562 Processing helix chain 'B' and resid 569 through 578 Processing helix chain 'B' and resid 589 through 592 Processing helix chain 'B' and resid 609 through 620 Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 641 through 644 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 683 through 688 Processing helix chain 'B' and resid 694 through 717 Processing helix chain 'B' and resid 755 through 763 Processing helix chain 'B' and resid 771 through 785 Processing helix chain 'C' and resid 96 through 102 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 220 through 235 Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 237 through 243 removed outlier: 3.631A pdb=" N LYS C 241 " --> pdb=" O PRO C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 272 Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 291 through 304 Processing helix chain 'C' and resid 316 through 319 No H-bonds generated for 'chain 'C' and resid 316 through 319' Processing helix chain 'C' and resid 330 through 343 removed outlier: 3.941A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 365 through 368 Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.735A pdb=" N LYS C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 412 Processing helix chain 'C' and resid 418 through 438 removed outlier: 4.205A pdb=" N ASP C 438 " --> pdb=" O ARG C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 453 Processing helix chain 'C' and resid 459 through 468 Processing helix chain 'C' and resid 486 through 488 No H-bonds generated for 'chain 'C' and resid 486 through 488' Processing helix chain 'C' and resid 493 through 508 removed outlier: 4.362A pdb=" N GLU C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Proline residue: C 506 - end of helix Processing helix chain 'C' and resid 510 through 516 Processing helix chain 'C' and resid 534 through 544 Processing helix chain 'C' and resid 554 through 562 Processing helix chain 'C' and resid 569 through 578 Processing helix chain 'C' and resid 589 through 592 No H-bonds generated for 'chain 'C' and resid 589 through 592' Processing helix chain 'C' and resid 609 through 618 Processing helix chain 'C' and resid 641 through 644 No H-bonds generated for 'chain 'C' and resid 641 through 644' Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 683 through 688 Processing helix chain 'C' and resid 694 through 717 Processing helix chain 'C' and resid 755 through 764 Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 220 through 235 Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 237 through 243 removed outlier: 3.556A pdb=" N LYS D 241 " --> pdb=" O PRO D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 272 Processing helix chain 'D' and resid 282 through 285 No H-bonds generated for 'chain 'D' and resid 282 through 285' Processing helix chain 'D' and resid 289 through 305 Processing helix chain 'D' and resid 316 through 319 No H-bonds generated for 'chain 'D' and resid 316 through 319' Processing helix chain 'D' and resid 329 through 344 Processing helix chain 'D' and resid 365 through 368 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 406 through 412 Processing helix chain 'D' and resid 418 through 437 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'D' and resid 473 through 475 No H-bonds generated for 'chain 'D' and resid 473 through 475' Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 493 through 508 removed outlier: 3.516A pdb=" N GLU D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) Proline residue: D 506 - end of helix Processing helix chain 'D' and resid 510 through 516 Processing helix chain 'D' and resid 534 through 545 Processing helix chain 'D' and resid 554 through 561 removed outlier: 4.455A pdb=" N SER D 559 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 578 Processing helix chain 'D' and resid 589 through 591 No H-bonds generated for 'chain 'D' and resid 589 through 591' Processing helix chain 'D' and resid 608 through 619 Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 683 through 688 Processing helix chain 'D' and resid 694 through 717 removed outlier: 3.796A pdb=" N LEU D 698 " --> pdb=" O GLY D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 764 Processing helix chain 'D' and resid 771 through 785 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 220 through 235 removed outlier: 4.393A pdb=" N LEU E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 261 through 272 Processing helix chain 'E' and resid 281 through 287 removed outlier: 3.833A pdb=" N LYS E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 306 removed outlier: 3.590A pdb=" N LEU E 296 " --> pdb=" O SER E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 319 No H-bonds generated for 'chain 'E' and resid 316 through 319' Processing helix chain 'E' and resid 330 through 344 removed outlier: 3.863A pdb=" N VAL E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 368 removed outlier: 3.560A pdb=" N ARG E 368 " --> pdb=" O PRO E 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 368' Processing helix chain 'E' and resid 384 through 394 Processing helix chain 'E' and resid 406 through 412 Processing helix chain 'E' and resid 418 through 438 removed outlier: 4.749A pdb=" N ASP E 438 " --> pdb=" O ARG E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 459 through 467 Processing helix chain 'E' and resid 486 through 488 No H-bonds generated for 'chain 'E' and resid 486 through 488' Processing helix chain 'E' and resid 493 through 508 removed outlier: 4.132A pdb=" N TYR E 505 " --> pdb=" O GLU E 501 " (cutoff:3.500A) Proline residue: E 506 - end of helix Processing helix chain 'E' and resid 510 through 515 Processing helix chain 'E' and resid 536 through 545 Processing helix chain 'E' and resid 554 through 562 Processing helix chain 'E' and resid 569 through 578 Processing helix chain 'E' and resid 589 through 592 removed outlier: 3.567A pdb=" N ILE E 592 " --> pdb=" O LEU E 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 589 through 592' Processing helix chain 'E' and resid 608 through 619 Processing helix chain 'E' and resid 636 through 638 No H-bonds generated for 'chain 'E' and resid 636 through 638' Processing helix chain 'E' and resid 641 through 644 Processing helix chain 'E' and resid 660 through 672 Processing helix chain 'E' and resid 682 through 689 removed outlier: 3.867A pdb=" N ALA E 688 " --> pdb=" O ALA E 684 " (cutoff:3.500A) Processing helix chain 'E' and resid 694 through 717 Processing helix chain 'E' and resid 755 through 763 Processing helix chain 'E' and resid 771 through 785 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 202 through 205 No H-bonds generated for 'chain 'F' and resid 202 through 205' Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 220 through 235 removed outlier: 3.983A pdb=" N LEU F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 237 through 243 Processing helix chain 'F' and resid 261 through 272 Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 289 through 306 removed outlier: 4.451A pdb=" N GLU F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 319 No H-bonds generated for 'chain 'F' and resid 316 through 319' Processing helix chain 'F' and resid 329 through 343 removed outlier: 3.520A pdb=" N VAL F 335 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 368 Processing helix chain 'F' and resid 384 through 394 Processing helix chain 'F' and resid 406 through 412 Processing helix chain 'F' and resid 418 through 439 removed outlier: 3.873A pdb=" N ASP F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU F 439 " --> pdb=" O GLU F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 459 through 468 Processing helix chain 'F' and resid 486 through 488 No H-bonds generated for 'chain 'F' and resid 486 through 488' Processing helix chain 'F' and resid 493 through 508 removed outlier: 4.770A pdb=" N TYR F 505 " --> pdb=" O GLU F 501 " (cutoff:3.500A) Proline residue: F 506 - end of helix Processing helix chain 'F' and resid 510 through 516 Processing helix chain 'F' and resid 534 through 544 Processing helix chain 'F' and resid 554 through 562 Processing helix chain 'F' and resid 569 through 578 Processing helix chain 'F' and resid 589 through 592 removed outlier: 3.645A pdb=" N ILE F 592 " --> pdb=" O LEU F 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 589 through 592' Processing helix chain 'F' and resid 609 through 620 Processing helix chain 'F' and resid 636 through 638 No H-bonds generated for 'chain 'F' and resid 636 through 638' Processing helix chain 'F' and resid 641 through 644 Processing helix chain 'F' and resid 660 through 670 Processing helix chain 'F' and resid 683 through 689 Processing helix chain 'F' and resid 694 through 717 Processing helix chain 'F' and resid 755 through 763 Processing helix chain 'F' and resid 771 through 785 Processing helix chain 'G' and resid 117 through 123 Processing helix chain 'G' and resid 156 through 162 Processing helix chain 'G' and resid 169 through 180 removed outlier: 3.891A pdb=" N LYS G 174 " --> pdb=" O HIS G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 242 through 255 Processing helix chain 'G' and resid 300 through 317 removed outlier: 3.895A pdb=" N ARG G 312 " --> pdb=" O LEU G 308 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 364 Processing helix chain 'G' and resid 403 through 408 Processing helix chain 'G' and resid 501 through 512 Processing helix chain 'G' and resid 517 through 523 Processing helix chain 'G' and resid 527 through 536 Processing helix chain 'G' and resid 541 through 552 Processing helix chain 'G' and resid 556 through 564 Processing helix chain 'G' and resid 567 through 578 Processing helix chain 'H' and resid 230 through 233 removed outlier: 3.729A pdb=" N LEU H 233 " --> pdb=" O PRO H 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 230 through 233' Processing helix chain 'H' and resid 244 through 256 removed outlier: 3.805A pdb=" N ARG H 252 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU H 255 " --> pdb=" O SER H 251 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER H 256 " --> pdb=" O ARG H 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 30 Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 156 through 159 Processing helix chain 'K' and resid 223 through 234 Processing helix chain 'K' and resid 238 through 240 No H-bonds generated for 'chain 'K' and resid 238 through 240' Processing helix chain 'K' and resid 256 through 259 No H-bonds generated for 'chain 'K' and resid 256 through 259' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.058A pdb=" N ILE A 80 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE A 51 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU A 82 " --> pdb=" O ILE A 51 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 191 through 193 removed outlier: 7.162A pdb=" N LEU A 127 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL A 175 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 375 through 379 removed outlier: 8.497A pdb=" N VAL A 251 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL A 353 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N MET A 253 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ALA A 355 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLY A 255 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR A 357 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA A 309 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ILE A 354 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 311 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ALA A 356 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE A 313 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE A 275 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE A 312 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE A 277 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASP A 314 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE A 279 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 651 through 655 removed outlier: 8.667A pdb=" N VAL A 524 " --> pdb=" O VAL A 627 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL A 629 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE A 526 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY A 631 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLY A 528 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR A 633 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR A 582 " --> pdb=" O PHE A 628 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE A 630 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A 584 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ALA A 632 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 586 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN A 548 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N PHE A 585 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE A 550 " --> pdb=" O PHE A 585 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 48 through 51 removed outlier: 5.491A pdb=" N ILE B 80 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE B 51 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU B 82 " --> pdb=" O ILE B 51 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 76 through 79 Processing sheet with id= H, first strand: chain 'B' and resid 191 through 193 removed outlier: 7.264A pdb=" N LEU B 127 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 175 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 155 through 157 Processing sheet with id= J, first strand: chain 'B' and resid 375 through 379 removed outlier: 8.470A pdb=" N VAL B 251 " --> pdb=" O VAL B 351 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL B 353 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N MET B 253 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA B 355 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N GLY B 255 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR B 357 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE B 275 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHE B 312 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 651 through 655 removed outlier: 7.141A pdb=" N VAL B 629 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N PHE B 526 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY B 631 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N GLY B 528 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR B 633 " --> pdb=" O GLY B 528 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE B 630 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL B 584 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ALA B 632 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 586 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 550 " --> pdb=" O PHE B 585 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 375 through 379 removed outlier: 3.603A pdb=" N THR C 357 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA C 309 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ILE C 354 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE C 311 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ALA C 356 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE C 313 " --> pdb=" O ALA C 356 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE C 277 " --> pdb=" O PHE C 312 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 524 through 528 removed outlier: 6.551A pdb=" N GLN C 651 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR C 527 " --> pdb=" O GLN C 651 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C 653 " --> pdb=" O TYR C 527 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 375 through 379 removed outlier: 4.131A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N VAL D 251 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL D 353 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N MET D 253 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ALA D 355 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N GLY D 255 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N THR D 357 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 651 through 655 removed outlier: 6.606A pdb=" N THR D 582 " --> pdb=" O PHE D 628 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE D 630 " --> pdb=" O THR D 582 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL D 584 " --> pdb=" O ILE D 630 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ALA D 632 " --> pdb=" O VAL D 584 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU D 586 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ASP D 587 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL D 552 " --> pdb=" O ASP D 587 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 375 through 379 removed outlier: 8.719A pdb=" N VAL E 251 " --> pdb=" O VAL E 351 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL E 353 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N MET E 253 " --> pdb=" O VAL E 353 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ALA E 355 " --> pdb=" O MET E 253 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N GLY E 255 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N THR E 357 " --> pdb=" O GLY E 255 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA E 309 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE E 354 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE E 311 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ALA E 356 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE E 313 " --> pdb=" O ALA E 356 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE E 275 " --> pdb=" O ILE E 310 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE E 312 " --> pdb=" O PHE E 275 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE E 277 " --> pdb=" O PHE E 312 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 651 through 654 removed outlier: 9.254A pdb=" N VAL E 524 " --> pdb=" O VAL E 627 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL E 629 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N PHE E 526 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY E 631 " --> pdb=" O PHE E 526 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR E 582 " --> pdb=" O PHE E 628 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ILE E 630 " --> pdb=" O THR E 582 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL E 584 " --> pdb=" O ILE E 630 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA E 632 " --> pdb=" O VAL E 584 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU E 586 " --> pdb=" O ALA E 632 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN E 548 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE E 585 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE E 550 " --> pdb=" O PHE E 585 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 375 through 379 removed outlier: 3.538A pdb=" N GLY F 255 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA F 309 " --> pdb=" O ASN F 350 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 352 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N PHE F 275 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE F 312 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE F 277 " --> pdb=" O PHE F 312 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 651 through 655 removed outlier: 9.095A pdb=" N VAL F 524 " --> pdb=" O VAL F 627 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL F 629 " --> pdb=" O VAL F 524 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N PHE F 526 " --> pdb=" O VAL F 629 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY F 631 " --> pdb=" O PHE F 526 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N GLY F 528 " --> pdb=" O GLY F 631 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR F 633 " --> pdb=" O GLY F 528 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR F 582 " --> pdb=" O PHE F 628 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE F 630 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL F 584 " --> pdb=" O ILE F 630 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ALA F 632 " --> pdb=" O VAL F 584 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU F 586 " --> pdb=" O ALA F 632 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN F 548 " --> pdb=" O VAL F 583 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE F 585 " --> pdb=" O ASN F 548 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE F 550 " --> pdb=" O PHE F 585 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASP F 587 " --> pdb=" O ILE F 550 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL F 552 " --> pdb=" O ASP F 587 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 236 through 239 removed outlier: 3.657A pdb=" N HIS G 236 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY G 276 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR G 264 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE G 284 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR G 262 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG G 259 " --> pdb=" O THR G 327 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL G 382 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N PHE G 326 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYS G 384 " --> pdb=" O PHE G 326 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 422 through 424 Processing sheet with id= V, first strand: chain 'J' and resid 112 through 116 Processing sheet with id= W, first strand: chain 'K' and resid 212 through 215 1235 hydrogen bonds defined for protein. 3603 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.72 Time building geometry restraints manager: 13.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11585 1.34 - 1.46: 5476 1.46 - 1.58: 17425 1.58 - 1.69: 45 1.69 - 1.81: 288 Bond restraints: 34819 Sorted by residual: bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C4 ADP A 902 " pdb=" C5 ADP A 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 ADP C 902 " pdb=" C5 ADP C 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP B 902 " pdb=" C5 ADP B 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 ... (remaining 34814 not shown) Histogram of bond angle deviations from ideal: 99.19 - 109.43: 2751 109.43 - 119.68: 27784 119.68 - 129.92: 16417 129.92 - 140.17: 156 140.17 - 150.41: 3 Bond angle restraints: 47111 Sorted by residual: angle pdb=" C GLU E 331 " pdb=" N ARG E 332 " pdb=" CA ARG E 332 " ideal model delta sigma weight residual 120.54 140.12 -19.58 1.35e+00 5.49e-01 2.10e+02 angle pdb=" C MET B 229 " pdb=" N VAL B 230 " pdb=" CA VAL B 230 " ideal model delta sigma weight residual 120.88 137.37 -16.49 1.22e+00 6.72e-01 1.83e+02 angle pdb=" C ASP B 314 " pdb=" N GLU B 315 " pdb=" CA GLU B 315 " ideal model delta sigma weight residual 122.82 140.42 -17.60 1.42e+00 4.96e-01 1.54e+02 angle pdb=" C ARG B 672 " pdb=" N LYS B 673 " pdb=" CA LYS B 673 " ideal model delta sigma weight residual 120.29 137.76 -17.47 1.42e+00 4.96e-01 1.51e+02 angle pdb=" C ILE E 639 " pdb=" N ASP E 640 " pdb=" CA ASP E 640 " ideal model delta sigma weight residual 121.80 150.41 -28.61 2.44e+00 1.68e-01 1.37e+02 ... (remaining 47106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.10: 21262 33.10 - 66.21: 243 66.21 - 99.31: 22 99.31 - 132.41: 16 132.41 - 165.52: 5 Dihedral angle restraints: 21548 sinusoidal: 9006 harmonic: 12542 Sorted by residual: dihedral pdb=" CA ALA F 307 " pdb=" C ALA F 307 " pdb=" N PRO F 308 " pdb=" CA PRO F 308 " ideal model delta harmonic sigma weight residual 180.00 137.12 42.88 0 5.00e+00 4.00e-02 7.36e+01 dihedral pdb=" C2' ADP E 901 " pdb=" C1' ADP E 901 " pdb=" N9 ADP E 901 " pdb=" C4 ADP E 901 " ideal model delta sinusoidal sigma weight residual 91.55 -102.94 -165.52 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C2' ADP A 902 " pdb=" C1' ADP A 902 " pdb=" N9 ADP A 902 " pdb=" C4 ADP A 902 " ideal model delta sinusoidal sigma weight residual 91.55 -122.76 -145.69 1 2.00e+01 2.50e-03 4.38e+01 ... (remaining 21545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.348: 5176 0.348 - 0.695: 63 0.695 - 1.043: 0 1.043 - 1.391: 13 1.391 - 1.738: 54 Chirality restraints: 5306 Sorted by residual: chirality pdb=" CG LEU J 115 " pdb=" CB LEU J 115 " pdb=" CD1 LEU J 115 " pdb=" CD2 LEU J 115 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.55e+01 chirality pdb=" CG LEU F 558 " pdb=" CB LEU F 558 " pdb=" CD1 LEU F 558 " pdb=" CD2 LEU F 558 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.40e+01 chirality pdb=" CG LEU E 234 " pdb=" CB LEU E 234 " pdb=" CD1 LEU E 234 " pdb=" CD2 LEU E 234 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.33e+01 ... (remaining 5303 not shown) Planarity restraints: 6138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 329 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C GLU B 329 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU B 329 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 330 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 506 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C LYS G 506 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS G 506 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR G 507 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 294 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.42e+00 pdb=" C SER F 294 " -0.027 2.00e-02 2.50e+03 pdb=" O SER F 294 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN F 295 " 0.009 2.00e-02 2.50e+03 ... (remaining 6135 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 10 2.03 - 2.75: 4712 2.75 - 3.46: 52701 3.46 - 4.18: 75560 4.18 - 4.90: 138093 Nonbonded interactions: 271076 Sorted by model distance: nonbonded pdb=" NZ LYS I 48 " pdb=" C GLY J 176 " model vdw 1.312 3.350 nonbonded pdb=" NZ LYS J 148 " pdb=" C GLY K 276 " model vdw 1.372 3.350 nonbonded pdb=" OG SER D 559 " pdb=" O GLU D 564 " model vdw 1.934 2.440 nonbonded pdb=" OG1 THR D 754 " pdb=" OE1 GLU D 756 " model vdw 1.941 2.440 nonbonded pdb=" OG1 THR B 66 " pdb=" O CYS B 115 " model vdw 1.991 2.440 ... (remaining 271071 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 33 through 440 or resid 447 through 786 or resid 901 throu \ gh 902)) selection = (chain 'B' and (resid 33 through 786 or resid 901 through 902)) } ncs_group { reference = (chain 'C' and (resid 207 through 440 or resid 447 through 786 or resid 902)) selection = (chain 'D' and (resid 207 through 786 or resid 902)) selection = (chain 'E' and (resid 207 through 786 or resid 902)) selection = (chain 'F' and (resid 207 through 786 or resid 902)) } ncs_group { reference = chain 'J' selection = chain 'K' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 19.230 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 90.370 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 34819 Z= 0.250 Angle : 0.955 28.610 47111 Z= 0.487 Chirality : 0.188 1.738 5306 Planarity : 0.003 0.032 6138 Dihedral : 11.635 165.517 13424 Min Nonbonded Distance : 1.312 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.81 % Rotamer: Outliers : 0.79 % Allowed : 4.13 % Favored : 95.08 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.53 (0.14), residues: 4274 helix: 2.26 (0.12), residues: 1991 sheet: -0.24 (0.23), residues: 551 loop : 0.04 (0.16), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 252 HIS 0.005 0.001 HIS G 236 PHE 0.014 0.001 PHE G 248 TYR 0.017 0.001 TYR G 507 ARG 0.002 0.000 ARG I 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 601 time to evaluate : 4.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 VAL cc_start: 0.7303 (t) cc_final: 0.7019 (t) REVERT: A 561 TRP cc_start: 0.3407 (t-100) cc_final: 0.3132 (t-100) REVERT: A 641 PRO cc_start: 0.8458 (Cg_exo) cc_final: 0.7955 (Cg_endo) REVERT: A 763 LYS cc_start: 0.7770 (mttt) cc_final: 0.7066 (tppt) REVERT: B 115 CYS cc_start: 0.3423 (t) cc_final: 0.3218 (t) REVERT: B 168 MET cc_start: 0.6819 (tpt) cc_final: 0.5415 (ppp) REVERT: B 341 LEU cc_start: 0.8851 (mt) cc_final: 0.8602 (mt) REVERT: B 784 MET cc_start: 0.6987 (mmm) cc_final: 0.6629 (tmm) REVERT: C 331 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7553 (mt-10) REVERT: C 361 ASN cc_start: 0.8217 (t0) cc_final: 0.7914 (t0) REVERT: C 587 ASP cc_start: 0.7341 (t0) cc_final: 0.6743 (t0) REVERT: D 254 TYR cc_start: 0.8607 (p90) cc_final: 0.8342 (p90) REVERT: D 359 ARG cc_start: 0.8216 (mtm110) cc_final: 0.7924 (mtp85) REVERT: D 361 ASN cc_start: 0.7405 (p0) cc_final: 0.6970 (p0) REVERT: D 515 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8555 (tmtt) REVERT: D 575 LYS cc_start: 0.8083 (mttt) cc_final: 0.7807 (mmmm) REVERT: D 646 PRO cc_start: 0.8330 (Cg_exo) cc_final: 0.8039 (Cg_endo) REVERT: E 208 MET cc_start: 0.5902 (tpt) cc_final: 0.4939 (mpp) REVERT: E 339 LEU cc_start: 0.8933 (mp) cc_final: 0.8689 (mt) REVERT: E 644 LEU cc_start: 0.8823 (mm) cc_final: 0.8421 (pp) REVERT: E 775 ARG cc_start: 0.8676 (tmm-80) cc_final: 0.8345 (ttm110) REVERT: E 784 MET cc_start: 0.8073 (mmp) cc_final: 0.7660 (tmm) REVERT: F 587 ASP cc_start: 0.8303 (t0) cc_final: 0.7721 (t0) REVERT: F 753 ILE cc_start: 0.7468 (mp) cc_final: 0.7160 (mt) REVERT: G 208 HIS cc_start: 0.8681 (p-80) cc_final: 0.7960 (p-80) REVERT: G 211 TRP cc_start: 0.8497 (t-100) cc_final: 0.7915 (t-100) REVERT: G 218 LYS cc_start: 0.8698 (ptmt) cc_final: 0.8377 (ptpp) REVERT: I 33 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7290 (mmmt) REVERT: K 204 PHE cc_start: 0.7715 (m-80) cc_final: 0.7367 (m-80) REVERT: K 205 VAL cc_start: 0.7821 (t) cc_final: 0.7612 (m) outliers start: 29 outliers final: 9 residues processed: 617 average time/residue: 0.5374 time to fit residues: 501.3616 Evaluate side-chains 336 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 327 time to evaluate : 3.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 502 GLN Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 252 ASP Chi-restraints excluded: chain K residue 264 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 3.9990 chunk 325 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 336 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 389 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN B 209 ASN B 270 ASN B 718 GLN C 612 ASN C 622 ASN D 100 ASN ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 ASN ** E 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN F 394 HIS ** F 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 670 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 GLN G 497 GLN J 125 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 34819 Z= 0.488 Angle : 0.738 10.112 47111 Z= 0.363 Chirality : 0.047 0.220 5306 Planarity : 0.005 0.043 6138 Dihedral : 11.034 153.030 4948 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.80 % Favored : 94.13 % Rotamer: Outliers : 2.72 % Allowed : 9.95 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 0.86 (0.13), residues: 4274 helix: 1.59 (0.12), residues: 1980 sheet: -0.46 (0.23), residues: 537 loop : -0.18 (0.16), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 561 HIS 0.014 0.002 HIS F 509 PHE 0.021 0.002 PHE G 260 TYR 0.035 0.002 TYR G 507 ARG 0.009 0.001 ARG E 323 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 321 time to evaluate : 4.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 ARG cc_start: 0.8223 (ttt180) cc_final: 0.8004 (tpp-160) REVERT: B 168 MET cc_start: 0.6767 (tpt) cc_final: 0.5574 (ppp) REVERT: B 332 ARG cc_start: 0.6753 (ttm110) cc_final: 0.6427 (tmm-80) REVERT: B 552 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8721 (m) REVERT: B 784 MET cc_start: 0.7200 (mmm) cc_final: 0.6926 (tmm) REVERT: C 254 TYR cc_start: 0.8758 (p90) cc_final: 0.8223 (p90) REVERT: C 329 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7068 (pm20) REVERT: C 331 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7961 (mt-10) REVERT: C 361 ASN cc_start: 0.8234 (t0) cc_final: 0.7954 (t0) REVERT: C 378 ASP cc_start: 0.8089 (t0) cc_final: 0.7788 (t0) REVERT: C 561 TRP cc_start: 0.7564 (t60) cc_final: 0.7024 (t60) REVERT: C 592 ILE cc_start: 0.7383 (tp) cc_final: 0.6988 (tp) REVERT: C 618 MET cc_start: 0.8519 (tmm) cc_final: 0.8046 (tmm) REVERT: D 100 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7270 (p0) REVERT: D 314 ASP cc_start: 0.8444 (t0) cc_final: 0.8222 (t0) REVERT: D 359 ARG cc_start: 0.8430 (mtm110) cc_final: 0.8009 (mtp85) REVERT: D 361 ASN cc_start: 0.7539 (p0) cc_final: 0.7118 (p0) REVERT: D 646 PRO cc_start: 0.8478 (Cg_exo) cc_final: 0.8160 (Cg_endo) REVERT: E 208 MET cc_start: 0.6081 (tpt) cc_final: 0.4988 (mpp) REVERT: E 282 PRO cc_start: 0.7469 (Cg_exo) cc_final: 0.7202 (Cg_endo) REVERT: E 644 LEU cc_start: 0.8719 (mm) cc_final: 0.8513 (pp) REVERT: E 649 LEU cc_start: 0.7833 (tp) cc_final: 0.7574 (tt) REVERT: E 676 LEU cc_start: 0.8353 (pp) cc_final: 0.8139 (pt) REVERT: E 762 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6695 (tpp) REVERT: E 775 ARG cc_start: 0.8656 (tmm-80) cc_final: 0.8316 (ttm110) REVERT: F 254 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.6984 (p90) REVERT: G 133 LYS cc_start: 0.8382 (tmtt) cc_final: 0.8155 (tppp) REVERT: G 218 LYS cc_start: 0.8720 (ptmt) cc_final: 0.8382 (ptpp) REVERT: I 33 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7519 (mmmt) REVERT: K 204 PHE cc_start: 0.7864 (m-80) cc_final: 0.7485 (m-10) outliers start: 100 outliers final: 43 residues processed: 401 average time/residue: 0.4790 time to fit residues: 308.8151 Evaluate side-chains 321 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 273 time to evaluate : 3.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 624 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 588 GLU Chi-restraints excluded: chain E residue 665 SER Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain F residue 254 TYR Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 282 GLU Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 490 SER Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 265 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 390 optimal weight: 0.8980 chunk 421 optimal weight: 0.6980 chunk 347 optimal weight: 4.9990 chunk 387 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 313 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN B 270 ASN B 638 GLN B 718 GLN D 100 ASN D 295 ASN ** E 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** F 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN K 268 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34819 Z= 0.208 Angle : 0.600 8.090 47111 Z= 0.287 Chirality : 0.042 0.162 5306 Planarity : 0.004 0.049 6138 Dihedral : 10.355 148.258 4938 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.72 % Rotamer: Outliers : 2.12 % Allowed : 11.96 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.06 (0.14), residues: 4274 helix: 1.72 (0.12), residues: 1986 sheet: -0.24 (0.23), residues: 535 loop : -0.07 (0.16), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 252 HIS 0.018 0.001 HIS F 509 PHE 0.016 0.001 PHE G 248 TYR 0.026 0.001 TYR G 507 ARG 0.004 0.000 ARG A 645 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 314 time to evaluate : 4.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 619 ASP cc_start: 0.8843 (t0) cc_final: 0.8639 (t0) REVERT: B 24 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8917 (t) REVERT: B 113 HIS cc_start: 0.7222 (t70) cc_final: 0.6926 (t-90) REVERT: B 168 MET cc_start: 0.6903 (tpt) cc_final: 0.5713 (ppp) REVERT: B 183 TYR cc_start: 0.5742 (p90) cc_final: 0.5204 (p90) REVERT: B 209 ASN cc_start: 0.7687 (OUTLIER) cc_final: 0.7198 (p0) REVERT: B 784 MET cc_start: 0.7319 (mmm) cc_final: 0.7028 (tmm) REVERT: C 329 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6942 (pm20) REVERT: C 331 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7742 (mt-10) REVERT: C 618 MET cc_start: 0.8381 (tmm) cc_final: 0.7962 (tmm) REVERT: D 75 LYS cc_start: 0.7235 (mmmm) cc_final: 0.6859 (tptt) REVERT: D 359 ARG cc_start: 0.8344 (mtm110) cc_final: 0.7938 (mtp85) REVERT: D 361 ASN cc_start: 0.7495 (p0) cc_final: 0.6988 (p0) REVERT: E 208 MET cc_start: 0.6058 (tpt) cc_final: 0.5083 (mpp) REVERT: E 282 PRO cc_start: 0.7179 (Cg_exo) cc_final: 0.6930 (Cg_endo) REVERT: E 676 LEU cc_start: 0.8391 (pp) cc_final: 0.7862 (tp) REVERT: E 775 ARG cc_start: 0.8674 (tmm-80) cc_final: 0.8306 (ttm110) REVERT: F 618 MET cc_start: 0.9092 (ttm) cc_final: 0.8891 (ttp) REVERT: G 126 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7563 (p0) REVERT: G 218 LYS cc_start: 0.8696 (ptmt) cc_final: 0.8354 (ptpp) REVERT: G 574 MET cc_start: 0.8090 (tpt) cc_final: 0.7523 (tpt) REVERT: I 33 LYS cc_start: 0.8159 (mtmm) cc_final: 0.7288 (mmmt) REVERT: K 204 PHE cc_start: 0.7688 (m-80) cc_final: 0.7415 (m-80) REVERT: K 211 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6587 (tttp) outliers start: 78 outliers final: 48 residues processed: 377 average time/residue: 0.4776 time to fit residues: 295.1682 Evaluate side-chains 331 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 278 time to evaluate : 4.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 588 GLU Chi-restraints excluded: chain E residue 665 SER Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 282 GLU Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain H residue 238 MET Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 211 LYS Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 252 ASP Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 3.9990 chunk 293 optimal weight: 9.9990 chunk 202 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 186 optimal weight: 0.4980 chunk 262 optimal weight: 4.9990 chunk 391 optimal weight: 0.6980 chunk 414 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 371 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS B 548 ASN C 622 ASN D 295 ASN F 101 ASN F 613 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34819 Z= 0.169 Angle : 0.575 8.848 47111 Z= 0.272 Chirality : 0.041 0.153 5306 Planarity : 0.004 0.048 6138 Dihedral : 9.768 143.727 4937 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.30 % Rotamer: Outliers : 2.45 % Allowed : 12.42 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.18 (0.14), residues: 4274 helix: 1.79 (0.12), residues: 1983 sheet: -0.11 (0.23), residues: 540 loop : 0.00 (0.16), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 252 HIS 0.010 0.001 HIS F 509 PHE 0.017 0.001 PHE B 149 TYR 0.024 0.001 TYR G 507 ARG 0.012 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 301 time to evaluate : 3.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 LYS cc_start: 0.8062 (tppt) cc_final: 0.7689 (ptpp) REVERT: B 24 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8939 (t) REVERT: B 113 HIS cc_start: 0.7223 (t70) cc_final: 0.6885 (t-90) REVERT: B 168 MET cc_start: 0.6926 (tpt) cc_final: 0.5770 (ppp) REVERT: B 183 TYR cc_start: 0.5886 (p90) cc_final: 0.5308 (p90) REVERT: B 480 GLU cc_start: 0.8275 (pm20) cc_final: 0.7663 (pm20) REVERT: B 552 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8483 (m) REVERT: B 784 MET cc_start: 0.7261 (mmm) cc_final: 0.7030 (tmm) REVERT: C 329 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: C 331 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7773 (mt-10) REVERT: C 561 TRP cc_start: 0.7396 (t60) cc_final: 0.7067 (t60) REVERT: C 574 ASP cc_start: 0.8145 (t0) cc_final: 0.7886 (t0) REVERT: C 618 MET cc_start: 0.8252 (tmm) cc_final: 0.7942 (tmm) REVERT: D 75 LYS cc_start: 0.7159 (mmmm) cc_final: 0.6835 (tptt) REVERT: D 359 ARG cc_start: 0.8341 (mtm110) cc_final: 0.7954 (mtp85) REVERT: D 361 ASN cc_start: 0.7447 (p0) cc_final: 0.7015 (p0) REVERT: D 646 PRO cc_start: 0.8395 (Cg_exo) cc_final: 0.8079 (Cg_endo) REVERT: E 208 MET cc_start: 0.6488 (tpt) cc_final: 0.5337 (mpp) REVERT: E 223 MET cc_start: 0.7969 (tpp) cc_final: 0.7689 (tpp) REVERT: E 282 PRO cc_start: 0.7163 (Cg_exo) cc_final: 0.6879 (Cg_endo) REVERT: E 676 LEU cc_start: 0.8383 (pp) cc_final: 0.7882 (tp) REVERT: E 685 ILE cc_start: 0.7544 (mm) cc_final: 0.7239 (mt) REVERT: E 762 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6614 (tpp) REVERT: E 775 ARG cc_start: 0.8678 (tmm-80) cc_final: 0.8327 (ttm110) REVERT: F 254 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.6696 (p90) REVERT: G 133 LYS cc_start: 0.8284 (tmtt) cc_final: 0.8079 (tppp) REVERT: G 218 LYS cc_start: 0.8700 (ptmt) cc_final: 0.8384 (ptpp) REVERT: I 33 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7264 (mmmt) REVERT: K 201 MET cc_start: 0.4694 (tpp) cc_final: 0.4335 (tpt) REVERT: K 204 PHE cc_start: 0.7634 (m-80) cc_final: 0.6986 (m-80) outliers start: 90 outliers final: 55 residues processed: 378 average time/residue: 0.4335 time to fit residues: 270.1150 Evaluate side-chains 336 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 276 time to evaluate : 3.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 519 SER Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain F residue 254 TYR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 282 GLU Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 345 LYS Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 252 ASP Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 308 optimal weight: 0.0770 chunk 171 optimal weight: 4.9990 chunk 353 optimal weight: 7.9990 chunk 286 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 211 optimal weight: 3.9990 chunk 372 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN B 718 GLN C 622 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN D 295 ASN F 432 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 305 ASN G 497 GLN G 570 GLN ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 34819 Z= 0.369 Angle : 0.639 10.290 47111 Z= 0.309 Chirality : 0.043 0.178 5306 Planarity : 0.004 0.050 6138 Dihedral : 9.564 141.879 4937 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.55 % Favored : 94.41 % Rotamer: Outliers : 3.34 % Allowed : 12.64 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 0.98 (0.13), residues: 4274 helix: 1.67 (0.12), residues: 1972 sheet: -0.31 (0.23), residues: 522 loop : -0.13 (0.16), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 486 HIS 0.009 0.001 HIS F 509 PHE 0.020 0.002 PHE F 758 TYR 0.027 0.002 TYR G 507 ARG 0.005 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 283 time to evaluate : 3.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8770 (pt) REVERT: A 285 MET cc_start: 0.8044 (mmm) cc_final: 0.7722 (mmm) REVERT: A 359 ARG cc_start: 0.7876 (mmp-170) cc_final: 0.7653 (mmt180) REVERT: B 26 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8160 (tp) REVERT: B 113 HIS cc_start: 0.7100 (t70) cc_final: 0.6656 (t-90) REVERT: B 168 MET cc_start: 0.7117 (tpt) cc_final: 0.5848 (ppp) REVERT: B 209 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7333 (p0) REVERT: B 329 GLU cc_start: 0.6298 (tp30) cc_final: 0.6013 (tp30) REVERT: B 332 ARG cc_start: 0.6901 (ttm110) cc_final: 0.6521 (tmm-80) REVERT: B 345 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8046 (ttp) REVERT: C 254 TYR cc_start: 0.8717 (p90) cc_final: 0.8123 (p90) REVERT: C 329 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: C 331 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8012 (mt-10) REVERT: C 561 TRP cc_start: 0.7398 (t60) cc_final: 0.7017 (t60) REVERT: C 618 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7741 (tmm) REVERT: D 314 ASP cc_start: 0.8403 (t0) cc_final: 0.8144 (t0) REVERT: D 359 ARG cc_start: 0.8404 (mtm110) cc_final: 0.7861 (mtp-110) REVERT: D 361 ASN cc_start: 0.7508 (p0) cc_final: 0.7241 (p0) REVERT: D 646 PRO cc_start: 0.8490 (Cg_exo) cc_final: 0.8211 (Cg_endo) REVERT: E 208 MET cc_start: 0.6355 (tpt) cc_final: 0.5144 (mpp) REVERT: E 253 MET cc_start: 0.8405 (ptm) cc_final: 0.8125 (ptm) REVERT: E 282 PRO cc_start: 0.7363 (Cg_exo) cc_final: 0.7055 (Cg_endo) REVERT: E 676 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7989 (tp) REVERT: E 775 ARG cc_start: 0.8658 (tmm-80) cc_final: 0.8319 (ttm110) REVERT: F 254 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.6954 (p90) REVERT: G 218 LYS cc_start: 0.8811 (ptmt) cc_final: 0.8435 (ptpp) REVERT: G 574 MET cc_start: 0.8030 (tpt) cc_final: 0.7636 (tpt) REVERT: I 33 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7368 (mmmt) REVERT: K 201 MET cc_start: 0.4637 (tpp) cc_final: 0.4430 (tpt) REVERT: K 204 PHE cc_start: 0.7612 (m-80) cc_final: 0.7366 (m-80) outliers start: 123 outliers final: 81 residues processed: 386 average time/residue: 0.4524 time to fit residues: 288.0427 Evaluate side-chains 359 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 270 time to evaluate : 3.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 653 ILE Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 519 SER Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 588 GLU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 665 SER Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain F residue 254 TYR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 282 GLU Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 345 LYS Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 426 ASN Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 484 SER Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain H residue 238 MET Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 252 ASP Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 5.9990 chunk 373 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 243 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 415 optimal weight: 2.9990 chunk 344 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 217 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN C 361 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34819 Z= 0.165 Angle : 0.584 10.052 47111 Z= 0.276 Chirality : 0.041 0.152 5306 Planarity : 0.004 0.048 6138 Dihedral : 9.190 138.301 4937 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 2.50 % Allowed : 14.16 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.15 (0.14), residues: 4274 helix: 1.77 (0.12), residues: 1974 sheet: -0.10 (0.23), residues: 536 loop : -0.02 (0.16), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 252 HIS 0.008 0.001 HIS F 509 PHE 0.014 0.001 PHE G 248 TYR 0.025 0.001 TYR G 507 ARG 0.003 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 299 time to evaluate : 3.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8049 (mtp) cc_final: 0.7796 (mtp) REVERT: A 245 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8686 (pt) REVERT: A 285 MET cc_start: 0.7944 (mmm) cc_final: 0.7489 (mmm) REVERT: B 113 HIS cc_start: 0.7270 (t70) cc_final: 0.6815 (t-90) REVERT: B 168 MET cc_start: 0.7177 (tpt) cc_final: 0.5967 (ppp) REVERT: B 183 TYR cc_start: 0.5835 (p90) cc_final: 0.5270 (p90) REVERT: B 329 GLU cc_start: 0.6091 (tp30) cc_final: 0.5854 (tp30) REVERT: B 332 ARG cc_start: 0.6764 (ttm110) cc_final: 0.6383 (tmm-80) REVERT: B 345 MET cc_start: 0.8255 (ptm) cc_final: 0.7994 (ttp) REVERT: B 480 GLU cc_start: 0.8220 (pm20) cc_final: 0.7609 (pm20) REVERT: C 254 TYR cc_start: 0.8685 (p90) cc_final: 0.8074 (p90) REVERT: C 329 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7350 (pm20) REVERT: C 331 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7843 (mt-10) REVERT: C 561 TRP cc_start: 0.7397 (t60) cc_final: 0.7113 (t60) REVERT: C 618 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7754 (tmm) REVERT: D 75 LYS cc_start: 0.7065 (mmmm) cc_final: 0.6753 (tptt) REVERT: D 618 MET cc_start: 0.7396 (ttp) cc_final: 0.7138 (ttp) REVERT: D 646 PRO cc_start: 0.8452 (Cg_exo) cc_final: 0.8167 (Cg_endo) REVERT: E 208 MET cc_start: 0.6325 (tpt) cc_final: 0.5129 (mpp) REVERT: E 223 MET cc_start: 0.8263 (tpp) cc_final: 0.7909 (tpp) REVERT: E 282 PRO cc_start: 0.7282 (Cg_exo) cc_final: 0.6986 (Cg_endo) REVERT: E 676 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7963 (tp) REVERT: E 762 MET cc_start: 0.7243 (tpt) cc_final: 0.6596 (tpp) REVERT: E 775 ARG cc_start: 0.8653 (tmm-80) cc_final: 0.8320 (ttm110) REVERT: F 254 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6824 (p90) REVERT: G 218 LYS cc_start: 0.8759 (ptmt) cc_final: 0.8381 (ptpp) REVERT: G 574 MET cc_start: 0.8011 (tpt) cc_final: 0.7697 (tpt) REVERT: I 33 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7364 (mmmt) REVERT: K 204 PHE cc_start: 0.7227 (m-80) cc_final: 0.6962 (m-80) outliers start: 92 outliers final: 64 residues processed: 373 average time/residue: 0.4619 time to fit residues: 279.5474 Evaluate side-chains 348 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 279 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 692 PHE Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 519 SER Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 588 GLU Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain F residue 254 TYR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 282 GLU Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 345 LYS Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 426 ASN Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 484 SER Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 252 ASP Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 303 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 349 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 chunk 413 optimal weight: 0.8980 chunk 258 optimal weight: 0.9980 chunk 252 optimal weight: 0.9980 chunk 190 optimal weight: 20.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 ASN C 651 GLN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 34819 Z= 0.368 Angle : 0.652 9.031 47111 Z= 0.316 Chirality : 0.043 0.179 5306 Planarity : 0.004 0.049 6138 Dihedral : 9.193 136.741 4937 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.90 % Favored : 94.08 % Rotamer: Outliers : 3.04 % Allowed : 14.65 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 0.95 (0.14), residues: 4274 helix: 1.67 (0.12), residues: 1955 sheet: -0.37 (0.23), residues: 521 loop : -0.13 (0.16), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 486 HIS 0.008 0.001 HIS G 236 PHE 0.019 0.002 PHE G 248 TYR 0.027 0.002 TYR G 507 ARG 0.014 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 281 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8761 (pt) REVERT: A 323 ARG cc_start: 0.8255 (ttt180) cc_final: 0.7829 (tpt170) REVERT: A 359 ARG cc_start: 0.8207 (mmt180) cc_final: 0.7882 (tpp80) REVERT: B 113 HIS cc_start: 0.7247 (t70) cc_final: 0.6782 (t-90) REVERT: B 168 MET cc_start: 0.7209 (tpt) cc_final: 0.5962 (ppp) REVERT: B 208 MET cc_start: 0.6998 (mmt) cc_final: 0.6715 (mmm) REVERT: B 345 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8110 (ttp) REVERT: C 254 TYR cc_start: 0.8720 (p90) cc_final: 0.8197 (p90) REVERT: C 329 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7407 (pm20) REVERT: C 331 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8037 (mt-10) REVERT: C 561 TRP cc_start: 0.7445 (t60) cc_final: 0.7190 (t60) REVERT: C 592 ILE cc_start: 0.7667 (tp) cc_final: 0.7358 (tp) REVERT: C 618 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7769 (tmm) REVERT: D 646 PRO cc_start: 0.8571 (Cg_exo) cc_final: 0.8296 (Cg_endo) REVERT: E 208 MET cc_start: 0.6360 (tpt) cc_final: 0.5144 (mpp) REVERT: E 231 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7346 (mt-10) REVERT: E 282 PRO cc_start: 0.7456 (Cg_exo) cc_final: 0.7138 (Cg_endo) REVERT: E 676 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8025 (tp) REVERT: E 775 ARG cc_start: 0.8675 (tmm-80) cc_final: 0.8336 (ttm110) REVERT: F 254 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.7068 (p90) REVERT: F 315 GLU cc_start: 0.7559 (tp30) cc_final: 0.7247 (tp30) REVERT: F 672 ARG cc_start: 0.8215 (mmp-170) cc_final: 0.7769 (ttp80) REVERT: G 218 LYS cc_start: 0.8831 (ptmt) cc_final: 0.8460 (ptpp) REVERT: G 574 MET cc_start: 0.8029 (tpt) cc_final: 0.7709 (tpt) REVERT: I 33 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7475 (mmmt) REVERT: K 204 PHE cc_start: 0.7362 (m-80) cc_final: 0.7090 (m-80) outliers start: 112 outliers final: 80 residues processed: 372 average time/residue: 0.4575 time to fit residues: 280.0531 Evaluate side-chains 361 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 275 time to evaluate : 3.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 692 PHE Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 653 ILE Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 519 SER Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 588 GLU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 683 THR Chi-restraints excluded: chain F residue 254 TYR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 345 LYS Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 426 ASN Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 484 SER Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 252 ASP Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 246 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 262 optimal weight: 5.9990 chunk 281 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 325 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN K 260 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 34819 Z= 0.370 Angle : 0.656 9.689 47111 Z= 0.318 Chirality : 0.044 0.196 5306 Planarity : 0.004 0.053 6138 Dihedral : 9.116 135.141 4937 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 3.18 % Allowed : 14.81 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 0.80 (0.13), residues: 4274 helix: 1.53 (0.12), residues: 1961 sheet: -0.44 (0.23), residues: 528 loop : -0.19 (0.16), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 544 HIS 0.007 0.001 HIS G 236 PHE 0.017 0.002 PHE G 260 TYR 0.044 0.002 TYR G 189 ARG 0.011 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 278 time to evaluate : 4.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8801 (pt) REVERT: A 323 ARG cc_start: 0.8248 (ttt180) cc_final: 0.7809 (tpt170) REVERT: B 113 HIS cc_start: 0.7178 (t70) cc_final: 0.6730 (t-90) REVERT: B 168 MET cc_start: 0.7368 (tpt) cc_final: 0.6194 (ppp) REVERT: B 208 MET cc_start: 0.7035 (mmt) cc_final: 0.6765 (mmm) REVERT: B 223 MET cc_start: 0.8593 (mmm) cc_final: 0.8303 (tpt) REVERT: B 345 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8147 (ttp) REVERT: C 254 TYR cc_start: 0.8725 (p90) cc_final: 0.8183 (p90) REVERT: C 329 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: C 331 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7997 (mt-10) REVERT: C 561 TRP cc_start: 0.7450 (t60) cc_final: 0.7150 (t60) REVERT: C 592 ILE cc_start: 0.7652 (tp) cc_final: 0.7303 (tp) REVERT: C 618 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7647 (tmm) REVERT: D 646 PRO cc_start: 0.8686 (Cg_exo) cc_final: 0.8433 (Cg_endo) REVERT: E 208 MET cc_start: 0.6471 (tpt) cc_final: 0.5328 (mpp) REVERT: E 231 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7407 (mt-10) REVERT: E 282 PRO cc_start: 0.7570 (Cg_exo) cc_final: 0.7261 (Cg_endo) REVERT: E 676 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8041 (tp) REVERT: E 775 ARG cc_start: 0.8650 (tmm-80) cc_final: 0.8326 (ttm110) REVERT: F 74 ARG cc_start: 0.5938 (mpt180) cc_final: 0.4883 (mtm-85) REVERT: F 254 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.7148 (p90) REVERT: F 521 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8510 (t) REVERT: G 218 LYS cc_start: 0.8824 (ptmt) cc_final: 0.8461 (ptpp) REVERT: G 574 MET cc_start: 0.8043 (tpt) cc_final: 0.7696 (tpt) REVERT: I 33 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7462 (mmmt) REVERT: K 204 PHE cc_start: 0.7344 (m-80) cc_final: 0.7038 (m-80) REVERT: K 270 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7703 (m) outliers start: 117 outliers final: 85 residues processed: 373 average time/residue: 0.4515 time to fit residues: 277.9212 Evaluate side-chains 363 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 270 time to evaluate : 4.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 692 PHE Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 653 ILE Chi-restraints excluded: chain D residue 655 VAL Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 519 SER Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 588 GLU Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 665 SER Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 683 THR Chi-restraints excluded: chain F residue 254 TYR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 521 SER Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 426 ASN Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 484 SER Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 1.9990 chunk 396 optimal weight: 0.5980 chunk 361 optimal weight: 0.6980 chunk 385 optimal weight: 0.3980 chunk 231 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 302 optimal weight: 0.0970 chunk 118 optimal weight: 4.9990 chunk 348 optimal weight: 8.9990 chunk 364 optimal weight: 0.6980 chunk 383 optimal weight: 0.0050 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN C 361 ASN F 101 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 GLN G 497 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34819 Z= 0.150 Angle : 0.606 10.937 47111 Z= 0.286 Chirality : 0.041 0.157 5306 Planarity : 0.004 0.045 6138 Dihedral : 8.612 130.466 4937 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.23 % Favored : 95.74 % Rotamer: Outliers : 1.77 % Allowed : 16.28 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.05 (0.14), residues: 4274 helix: 1.69 (0.12), residues: 1970 sheet: -0.18 (0.23), residues: 522 loop : -0.06 (0.16), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 252 HIS 0.005 0.001 HIS F 509 PHE 0.013 0.001 PHE G 248 TYR 0.025 0.001 TYR G 507 ARG 0.010 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 300 time to evaluate : 4.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ARG cc_start: 0.6334 (mpp-170) cc_final: 0.5787 (mpt-90) REVERT: A 245 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8713 (pt) REVERT: A 323 ARG cc_start: 0.8120 (ttt180) cc_final: 0.7864 (tpt170) REVERT: A 359 ARG cc_start: 0.8160 (mmt180) cc_final: 0.7770 (mtp85) REVERT: A 561 TRP cc_start: 0.3233 (t-100) cc_final: 0.2519 (t-100) REVERT: B 113 HIS cc_start: 0.7362 (t70) cc_final: 0.6896 (t-90) REVERT: B 168 MET cc_start: 0.7352 (tpt) cc_final: 0.6240 (ppp) REVERT: B 208 MET cc_start: 0.7061 (mmt) cc_final: 0.6769 (mmm) REVERT: B 223 MET cc_start: 0.8495 (mmm) cc_final: 0.8191 (tpt) REVERT: B 329 GLU cc_start: 0.6038 (tp30) cc_final: 0.5788 (tp30) REVERT: B 332 ARG cc_start: 0.6743 (ttm110) cc_final: 0.6396 (tmm-80) REVERT: C 254 TYR cc_start: 0.8677 (p90) cc_final: 0.8225 (p90) REVERT: C 329 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: C 331 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7799 (mt-10) REVERT: C 430 MET cc_start: 0.8927 (tpp) cc_final: 0.8601 (tpp) REVERT: C 561 TRP cc_start: 0.7428 (t60) cc_final: 0.7165 (t60) REVERT: C 618 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7760 (tmm) REVERT: C 619 ASP cc_start: 0.7954 (t0) cc_final: 0.7641 (m-30) REVERT: D 75 LYS cc_start: 0.7002 (mmmm) cc_final: 0.6732 (tptt) REVERT: D 646 PRO cc_start: 0.8599 (Cg_exo) cc_final: 0.8326 (Cg_endo) REVERT: E 208 MET cc_start: 0.6333 (tpt) cc_final: 0.5295 (mpp) REVERT: E 231 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7159 (mt-10) REVERT: E 282 PRO cc_start: 0.7436 (Cg_exo) cc_final: 0.7141 (Cg_endo) REVERT: E 676 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8118 (tp) REVERT: E 775 ARG cc_start: 0.8622 (tmm-80) cc_final: 0.8299 (ttm110) REVERT: F 74 ARG cc_start: 0.5902 (mpt180) cc_final: 0.4827 (mtm-85) REVERT: F 521 SER cc_start: 0.8767 (OUTLIER) cc_final: 0.8367 (t) REVERT: G 218 LYS cc_start: 0.8778 (ptmt) cc_final: 0.8416 (ptpp) REVERT: G 574 MET cc_start: 0.7966 (tpt) cc_final: 0.7716 (tpt) REVERT: I 33 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7358 (mmmt) REVERT: K 204 PHE cc_start: 0.7183 (m-80) cc_final: 0.6738 (m-10) outliers start: 65 outliers final: 44 residues processed: 347 average time/residue: 0.4737 time to fit residues: 267.2670 Evaluate side-chains 327 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 278 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 519 SER Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 521 SER Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 345 LYS Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 426 ASN Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 484 SER Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 0.8980 chunk 407 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 193 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 chunk 427 optimal weight: 0.9980 chunk 393 optimal weight: 0.5980 chunk 340 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 chunk 262 optimal weight: 5.9990 chunk 208 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 34819 Z= 0.156 Angle : 0.596 11.949 47111 Z= 0.279 Chirality : 0.041 0.149 5306 Planarity : 0.004 0.046 6138 Dihedral : 8.237 126.132 4936 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.52 % Favored : 95.46 % Rotamer: Outliers : 1.44 % Allowed : 16.49 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.14 (0.14), residues: 4274 helix: 1.78 (0.12), residues: 1971 sheet: -0.09 (0.23), residues: 538 loop : -0.05 (0.16), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 252 HIS 0.003 0.001 HIS A 757 PHE 0.012 0.001 PHE G 260 TYR 0.024 0.001 TYR G 507 ARG 0.009 0.000 ARG A 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8548 Ramachandran restraints generated. 4274 Oldfield, 0 Emsley, 4274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 299 time to evaluate : 4.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ARG cc_start: 0.6445 (mpp-170) cc_final: 0.5887 (mpt-90) REVERT: A 245 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8722 (pt) REVERT: A 323 ARG cc_start: 0.8133 (ttt180) cc_final: 0.7852 (tpt170) REVERT: A 359 ARG cc_start: 0.8080 (mmt180) cc_final: 0.7697 (mtp85) REVERT: A 561 TRP cc_start: 0.3258 (t-100) cc_final: 0.2552 (t-100) REVERT: B 113 HIS cc_start: 0.7307 (t70) cc_final: 0.6872 (t-90) REVERT: B 168 MET cc_start: 0.7374 (tpt) cc_final: 0.6275 (ppp) REVERT: B 183 TYR cc_start: 0.5972 (p90) cc_final: 0.5371 (p90) REVERT: B 208 MET cc_start: 0.7204 (mmt) cc_final: 0.6850 (mmm) REVERT: B 223 MET cc_start: 0.8543 (mmm) cc_final: 0.8166 (tpt) REVERT: C 254 TYR cc_start: 0.8712 (p90) cc_final: 0.8245 (p90) REVERT: C 298 LYS cc_start: 0.8549 (mttt) cc_final: 0.8075 (pttp) REVERT: C 329 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7448 (pm20) REVERT: C 331 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7798 (mt-10) REVERT: C 561 TRP cc_start: 0.7423 (t60) cc_final: 0.7177 (t60) REVERT: C 574 ASP cc_start: 0.8359 (t0) cc_final: 0.8063 (t0) REVERT: C 592 ILE cc_start: 0.7552 (tp) cc_final: 0.7218 (tp) REVERT: C 618 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7766 (tmm) REVERT: C 619 ASP cc_start: 0.8035 (t0) cc_final: 0.7674 (m-30) REVERT: C 784 MET cc_start: 0.6414 (mmp) cc_final: 0.6166 (mmm) REVERT: D 75 LYS cc_start: 0.6978 (mmmm) cc_final: 0.6719 (tptt) REVERT: E 208 MET cc_start: 0.6285 (tpt) cc_final: 0.5233 (mpp) REVERT: E 282 PRO cc_start: 0.7462 (Cg_exo) cc_final: 0.7167 (Cg_endo) REVERT: E 676 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8132 (tp) REVERT: E 775 ARG cc_start: 0.8622 (tmm-80) cc_final: 0.8297 (ttm110) REVERT: F 74 ARG cc_start: 0.6167 (mpt180) cc_final: 0.4918 (mtm-85) REVERT: F 521 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8365 (t) REVERT: F 588 GLU cc_start: 0.8565 (mp0) cc_final: 0.8271 (mp0) REVERT: F 672 ARG cc_start: 0.8084 (mmp-170) cc_final: 0.7740 (ttp80) REVERT: G 126 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7493 (p0) REVERT: G 218 LYS cc_start: 0.8785 (ptmt) cc_final: 0.8392 (ptpp) REVERT: G 574 MET cc_start: 0.7943 (tpt) cc_final: 0.7708 (tpt) REVERT: I 33 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7340 (mmmt) outliers start: 53 outliers final: 40 residues processed: 338 average time/residue: 0.4881 time to fit residues: 271.0348 Evaluate side-chains 329 residues out of total 3681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 283 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 519 SER Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 521 SER Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 707 TYR Chi-restraints excluded: chain F residue 750 VAL Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 345 LYS Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 426 ASN Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 484 SER Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain K residue 271 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 7.9990 chunk 362 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 313 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 340 optimal weight: 0.0370 chunk 142 optimal weight: 7.9990 chunk 350 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.136662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.098407 restraints weight = 91847.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.097615 restraints weight = 57300.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.097676 restraints weight = 40175.111| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34819 Z= 0.170 Angle : 0.600 11.872 47111 Z= 0.282 Chirality : 0.041 0.145 5306 Planarity : 0.004 0.046 6138 Dihedral : 8.050 122.939 4935 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.38 % Favored : 95.60 % Rotamer: Outliers : 1.55 % Allowed : 16.58 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.05 % Twisted Proline : 0.45 % 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: 1.19 (0.14), residues: 4274 helix: 1.81 (0.12), residues: 1977 sheet: -0.02 (0.23), residues: 539 loop : -0.03 (0.16), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 252 HIS 0.004 0.001 HIS A 757 PHE 0.017 0.001 PHE G 260 TYR 0.023 0.001 TYR G 507 ARG 0.009 0.000 ARG A 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6727.67 seconds wall clock time: 124 minutes 37.58 seconds (7477.58 seconds total)