Starting phenix.real_space_refine on Thu Feb 22 17:24:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8daw_27278/02_2024/8daw_27278_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8daw_27278/02_2024/8daw_27278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8daw_27278/02_2024/8daw_27278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8daw_27278/02_2024/8daw_27278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8daw_27278/02_2024/8daw_27278_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8daw_27278/02_2024/8daw_27278_updated.pdb" } resolution = 3.6 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= -0.016 sd= 1.098 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 157 5.16 5 C 21813 2.51 5 N 6060 2.21 5 O 6787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34848 Number of models: 1 Model: "" Number of chains: 19 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: "L" 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 48.797 49.156 93.141 1.00 98.79 S ATOM 28425 SG CYS G 145 52.450 49.938 93.137 1.00 77.93 S ATOM 28452 SG CYS G 148 50.393 50.043 96.161 1.00 79.99 S ATOM 28922 SG CYS G 204 76.806 91.382 114.164 1.00103.46 S ATOM 29020 SG CYS G 216 77.041 91.081 110.408 1.00 75.80 S ATOM 29041 SG CYS G 219 74.275 92.965 111.898 1.00 79.10 S Residues with excluded nonbonded symmetry interactions: 3 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: 17.00, per 1000 atoms: 0.49 Number of scatterers: 34848 At special positions: 0 Unit cell: (153.216, 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 157 16.00 P 29 15.00 O 6787 8.00 N 6060 7.00 C 21813 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: 14.11 Conformation dependent library (CDL) restraints added in 6.4 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 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 206 helices and 24 sheets defined 44.5% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.07 Creating SS restraints... Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.553A 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: 4.163A 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: 3.869A 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 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 344 Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 418 through 439 removed outlier: 4.467A pdb=" N ASP A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 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 493 through 508 removed outlier: 4.546A 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 535 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: 3.645A 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 689 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: 3.709A 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 235 removed outlier: 4.716A 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: 4.070A pdb=" N ASP B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 5.384A 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: 4.648A 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: 4.120A 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: 3.682A 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: 4.001A 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: 3.863A 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 437 Processing helix chain 'C' and resid 449 through 454 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: 4.166A pdb=" N GLU C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 4.642A 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 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: 3.648A 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 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' 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 439 removed outlier: 3.784A pdb=" N ASP D 438 " --> pdb=" O ARG D 434 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU D 439 " --> pdb=" O GLU D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 459 through 468 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: 3.786A pdb=" N GLU D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) removed outlier: 4.723A 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 562 removed outlier: 4.129A 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: 3.747A 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: 4.488A 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 282 through 285 No H-bonds generated for 'chain 'E' and resid 282 through 285' Processing helix chain 'E' and resid 291 through 306 removed outlier: 3.753A pdb=" N LEU E 296 " --> pdb=" O SER E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 344 removed outlier: 3.885A pdb=" N VAL E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 362 No H-bonds generated for 'chain 'E' and resid 360 through 362' Processing helix chain 'E' and resid 365 through 368 removed outlier: 3.539A 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 439 removed outlier: 4.798A pdb=" N ASP E 438 " --> pdb=" O ARG E 434 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU E 439 " --> pdb=" O GLU E 435 " (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 493 through 508 removed outlier: 4.331A 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: 3.774A 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 641 through 644 Processing helix chain 'E' and resid 660 through 672 Processing helix chain 'E' and resid 682 through 689 removed outlier: 3.839A pdb=" N ALA E 688 " --> pdb=" O ALA E 684 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR E 689 " --> pdb=" O ILE E 685 " (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: 3.846A 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: 4.428A pdb=" N GLU F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN F 306 " --> pdb=" O GLU F 302 " (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: 3.666A pdb=" N VAL F 335 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 3.702A 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: 3.799A pdb=" N ASP F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) removed outlier: 5.083A 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 467 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: 4.489A 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 545 removed outlier: 3.581A pdb=" N VAL F 545 " --> pdb=" O VAL F 541 " (cutoff:3.500A) 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 591 No H-bonds generated for 'chain 'F' and resid 589 through 591' Processing helix chain 'F' and resid 609 through 620 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: 3.886A 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: 3.879A pdb=" N ARG G 312 " --> pdb=" O LEU G 308 " (cutoff:3.500A) removed outlier: 4.061A 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 565 Processing helix chain 'G' and resid 567 through 578 Processing helix chain 'H' and resid 230 through 232 No H-bonds generated for 'chain 'H' and resid 230 through 232' Processing helix chain 'H' and resid 244 through 256 removed outlier: 3.545A pdb=" N ARG H 252 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU H 255 " --> pdb=" O SER H 251 " (cutoff:3.500A) removed outlier: 4.694A 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 'K' and resid 223 through 234 Processing helix chain 'K' and resid 256 through 259 No H-bonds generated for 'chain 'K' and resid 256 through 259' Processing helix chain 'L' and resid 323 through 334 Processing helix chain 'L' and resid 338 through 340 No H-bonds generated for 'chain 'L' and resid 338 through 340' 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 191 through 193 removed outlier: 7.193A pdb=" N LEU A 127 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL A 175 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 375 through 379 removed outlier: 8.614A pdb=" N VAL A 251 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 353 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N MET A 253 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ALA A 355 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLY A 255 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N THR A 357 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA A 309 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE A 354 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 311 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ALA A 356 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE A 313 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE A 275 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE A 312 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE A 277 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ASP A 314 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE A 279 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 651 through 655 removed outlier: 8.642A pdb=" N VAL A 524 " --> pdb=" O VAL A 627 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL A 629 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N PHE A 526 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY A 631 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLY A 528 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR A 633 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR A 582 " --> pdb=" O PHE A 628 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE A 630 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 584 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ALA A 632 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU A 586 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASN A 548 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N PHE A 585 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE A 550 " --> pdb=" O PHE A 585 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 37 through 39 Processing sheet with id= F, first strand: chain 'B' and resid 48 through 51 removed outlier: 5.505A pdb=" N ILE B 80 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE B 51 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 5.738A 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: 7.371A pdb=" N LEU B 127 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 175 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 154 through 157 removed outlier: 3.806A pdb=" N ARG B 154 " --> pdb=" O VAL B 186 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 375 through 379 removed outlier: 8.614A pdb=" N VAL B 251 " --> pdb=" O VAL B 351 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 353 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N MET B 253 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA B 355 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLY B 255 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE B 275 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE B 312 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.617A 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: 3.718A pdb=" N GLN B 651 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 629 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N PHE B 526 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY B 631 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLY B 528 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR B 633 " --> pdb=" O GLY B 528 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE B 630 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 584 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ALA B 632 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU B 586 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.882A 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: 4.120A pdb=" N ARG C 375 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N VAL C 251 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL C 353 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N MET C 253 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA C 355 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLY C 255 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR C 357 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA C 309 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE C 354 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE C 311 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ALA C 356 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE C 313 " --> pdb=" O ALA C 356 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 6.593A 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: 6.677A pdb=" N GLN C 651 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N TYR C 527 " --> pdb=" O GLN C 651 " (cutoff:3.500A) removed outlier: 6.134A 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: 4.172A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL D 251 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 353 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N MET D 253 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ALA D 355 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLY D 255 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR D 357 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 7.302A 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: 6.536A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASP D 587 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 6.905A 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: 8.678A pdb=" N VAL E 251 " --> pdb=" O VAL E 351 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL E 353 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N MET E 253 " --> pdb=" O VAL E 353 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ALA E 355 " --> pdb=" O MET E 253 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLY E 255 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR E 357 " --> pdb=" O GLY E 255 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA E 309 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ILE E 354 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE E 311 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ALA E 356 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE E 313 " --> pdb=" O ALA E 356 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE E 275 " --> pdb=" O ILE E 310 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE E 312 " --> pdb=" O PHE E 275 " (cutoff:3.500A) removed outlier: 6.982A 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: 9.378A pdb=" N VAL E 524 " --> pdb=" O VAL E 627 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL E 629 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N PHE E 526 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY E 631 " --> pdb=" O PHE E 526 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR E 582 " --> pdb=" O PHE E 628 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE E 630 " --> pdb=" O THR E 582 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL E 584 " --> pdb=" O ILE E 630 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ALA E 632 " --> pdb=" O VAL E 584 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU E 586 " --> pdb=" O ALA E 632 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASN E 548 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE E 585 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 6.646A 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: 8.421A pdb=" N VAL F 251 " --> pdb=" O VAL F 351 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL F 353 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N MET F 253 " --> pdb=" O VAL F 353 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ALA F 355 " --> pdb=" O MET F 253 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY F 255 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N THR F 357 " --> pdb=" O GLY F 255 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA F 309 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE F 354 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE F 311 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ALA F 356 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE F 313 " --> pdb=" O ALA F 356 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE F 275 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE F 312 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE F 277 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP F 314 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE F 279 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 651 through 655 removed outlier: 9.084A pdb=" N VAL F 524 " --> pdb=" O VAL F 627 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL F 629 " --> pdb=" O VAL F 524 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE F 526 " --> pdb=" O VAL F 629 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY F 631 " --> pdb=" O PHE F 526 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLY F 528 " --> pdb=" O GLY F 631 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR F 633 " --> pdb=" O GLY F 528 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR F 582 " --> pdb=" O PHE F 628 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE F 630 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL F 584 " --> pdb=" O ILE F 630 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ALA F 632 " --> pdb=" O VAL F 584 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU F 586 " --> pdb=" O ALA F 632 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN F 548 " --> pdb=" O VAL F 583 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N PHE F 585 " --> pdb=" O ASN F 548 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE F 550 " --> pdb=" O PHE F 585 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 467 through 470 removed outlier: 3.557A pdb=" N GLY G 469 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE G 239 " --> pdb=" O GLY G 469 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS G 236 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY G 276 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR G 264 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE G 284 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR G 262 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG G 259 " --> pdb=" O THR G 327 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY G 265 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ARG G 321 " --> pdb=" O GLY G 265 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL G 382 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N PHE G 326 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 6.829A 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 115 removed outlier: 6.692A pdb=" N SER J 165 " --> pdb=" O PHE J 104 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LYS J 106 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU J 167 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 212 through 215 Processing sheet with id= X, first strand: chain 'L' and resid 312 through 315 1256 hydrogen bonds defined for protein. 3648 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: 13.91 Time building geometry restraints manager: 15.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11796 1.34 - 1.46: 6852 1.46 - 1.58: 16447 1.58 - 1.70: 39 1.70 - 1.81: 290 Bond restraints: 35424 Sorted by residual: bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " 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 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 3.03e+01 bond pdb=" C4 ADP D 902 " pdb=" C5 ADP D 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 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 2.98e+01 ... (remaining 35419 not shown) Histogram of bond angle deviations from ideal: 99.45 - 109.48: 2880 109.48 - 119.51: 27754 119.51 - 129.54: 17124 129.54 - 139.57: 153 139.57 - 149.61: 12 Bond angle restraints: 47923 Sorted by residual: angle pdb=" C ILE E 639 " pdb=" N ASP E 640 " pdb=" CA ASP E 640 " ideal model delta sigma weight residual 121.80 149.61 -27.81 2.44e+00 1.68e-01 1.30e+02 angle pdb=" C GLU L 364 " pdb=" N SER L 365 " pdb=" CA SER L 365 " ideal model delta sigma weight residual 121.32 143.96 -22.64 2.10e+00 2.27e-01 1.16e+02 angle pdb=" C LEU B 36 " pdb=" N LEU B 37 " pdb=" CA LEU B 37 " ideal model delta sigma weight residual 121.32 143.64 -22.32 2.10e+00 2.27e-01 1.13e+02 angle pdb=" C PRO E 248 " pdb=" N ARG E 249 " pdb=" CA ARG E 249 " ideal model delta sigma weight residual 122.58 144.56 -21.98 2.07e+00 2.33e-01 1.13e+02 angle pdb=" C GLU E 331 " pdb=" N ARG E 332 " pdb=" CA ARG E 332 " ideal model delta sigma weight residual 121.54 141.36 -19.82 1.91e+00 2.74e-01 1.08e+02 ... (remaining 47918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.11: 21656 33.11 - 66.23: 226 66.23 - 99.34: 25 99.34 - 132.45: 16 132.45 - 165.56: 3 Dihedral angle restraints: 21926 sinusoidal: 9168 harmonic: 12758 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 180.00 140.99 39.01 0 5.00e+00 4.00e-02 6.09e+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 -102.89 -165.56 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O1B ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PB ADP E 901 " pdb=" PA ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 153.01 146.98 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 21923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.346: 5246 0.346 - 0.692: 80 0.692 - 1.038: 0 1.038 - 1.384: 12 1.384 - 1.731: 65 Chirality restraints: 5403 Sorted by residual: chirality pdb=" CG LEU F 589 " pdb=" CB LEU F 589 " pdb=" CD1 LEU F 589 " pdb=" CD2 LEU F 589 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.49e+01 chirality pdb=" CB ILE K 236 " pdb=" CA ILE K 236 " pdb=" CG1 ILE K 236 " pdb=" CG2 ILE K 236 " both_signs ideal model delta sigma weight residual False 2.64 0.92 1.72 2.00e-01 2.50e+01 7.41e+01 chirality pdb=" CG LEU E 339 " pdb=" CB LEU E 339 " pdb=" CD1 LEU E 339 " pdb=" CD2 LEU E 339 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.41e+01 ... (remaining 5400 not shown) Planarity restraints: 6242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 329 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+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 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C LYS G 506 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS G 506 " 0.012 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=" CB TYR G 507 " 0.019 2.00e-02 2.50e+03 1.23e-02 3.02e+00 pdb=" CG TYR G 507 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR G 507 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR G 507 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR G 507 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR G 507 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR G 507 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR G 507 " 0.004 2.00e-02 2.50e+03 ... (remaining 6239 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 10 2.03 - 2.75: 4745 2.75 - 3.46: 53928 3.46 - 4.18: 77206 4.18 - 4.90: 140500 Nonbonded interactions: 276389 Sorted by model distance: nonbonded pdb=" NZ LYS I 48 " pdb=" C GLY J 176 " model vdw 1.311 3.350 nonbonded pdb=" NZ LYS K 248 " pdb=" C GLY L 376 " model vdw 1.339 3.350 nonbonded pdb=" NZ LYS J 148 " pdb=" C GLY K 276 " model vdw 1.372 3.350 nonbonded pdb=" OG1 THR D 754 " pdb=" OE1 GLU D 756 " model vdw 1.960 2.440 nonbonded pdb=" OG1 THR B 66 " pdb=" O CYS B 115 " model vdw 1.974 2.440 ... (remaining 276384 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' selection = chain 'L' } 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.460 Check model and map are aligned: 0.510 Set scattering table: 0.320 Process input model: 98.260 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.250 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 0.110 35424 Z= 0.242 Angle : 0.983 27.806 47923 Z= 0.494 Chirality : 0.199 1.731 5403 Planarity : 0.003 0.039 6242 Dihedral : 11.527 165.564 13662 Min Nonbonded Distance : 1.311 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.31 % Favored : 94.64 % Rotamer: Outliers : 0.48 % Allowed : 4.27 % Favored : 95.25 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 5.86 % 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: 1.50 (0.14), residues: 4348 helix: 2.37 (0.12), residues: 1985 sheet: -0.29 (0.22), residues: 582 loop : -0.09 (0.16), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 489 HIS 0.003 0.001 HIS G 170 PHE 0.014 0.001 PHE G 248 TYR 0.029 0.001 TYR G 507 ARG 0.004 0.000 ARG G 492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 392 time to evaluate : 4.462 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 56 MET cc_start: -0.2088 (mtt) cc_final: -0.2290 (mpp) REVERT: A 254 TYR cc_start: 0.8642 (p90) cc_final: 0.8347 (p90) REVERT: A 672 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7906 (ttm110) REVERT: B 113 HIS cc_start: 0.8033 (t70) cc_final: 0.7621 (t-90) REVERT: B 153 TYR cc_start: 0.6193 (m-80) cc_final: 0.5657 (t80) REVERT: B 332 ARG cc_start: 0.7112 (mtm110) cc_final: 0.6816 (ttp-170) REVERT: B 398 MET cc_start: 0.8705 (mtt) cc_final: 0.8427 (mtt) REVERT: B 405 ASP cc_start: 0.8367 (t0) cc_final: 0.8042 (t0) REVERT: B 752 TYR cc_start: 0.7835 (p90) cc_final: 0.7304 (p90) REVERT: B 762 MET cc_start: 0.7189 (ptm) cc_final: 0.6939 (ptm) REVERT: B 784 MET cc_start: 0.7982 (mmm) cc_final: 0.7671 (mmp) REVERT: C 301 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7895 (tm-30) REVERT: C 405 ASP cc_start: 0.8288 (t70) cc_final: 0.7909 (t0) REVERT: C 618 MET cc_start: 0.8119 (tmm) cc_final: 0.7869 (tmm) REVERT: D 264 MET cc_start: 0.7921 (ttm) cc_final: 0.7677 (ttm) REVERT: D 314 ASP cc_start: 0.8276 (t0) cc_final: 0.8012 (t0) REVERT: D 560 MET cc_start: 0.6002 (tpp) cc_final: 0.5228 (mpp) REVERT: D 753 ILE cc_start: 0.7134 (mp) cc_final: 0.6649 (tt) REVERT: E 437 MET cc_start: 0.7859 (ptp) cc_final: 0.7647 (ptt) REVERT: E 468 ASN cc_start: 0.8581 (m110) cc_final: 0.8180 (t0) REVERT: E 762 MET cc_start: 0.5085 (ppp) cc_final: 0.4879 (ppp) REVERT: F 311 ILE cc_start: 0.8322 (mt) cc_final: 0.7932 (tt) REVERT: F 343 ASP cc_start: 0.8445 (t0) cc_final: 0.8241 (m-30) REVERT: F 587 ASP cc_start: 0.8349 (t0) cc_final: 0.7940 (t0) REVERT: G 108 TYR cc_start: 0.7658 (m-80) cc_final: 0.7165 (m-80) REVERT: G 315 GLN cc_start: 0.8007 (tt0) cc_final: 0.7735 (tt0) REVERT: G 543 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: G 574 MET cc_start: 0.8476 (tmm) cc_final: 0.8109 (tmm) REVERT: H 258 PHE cc_start: 0.6016 (p90) cc_final: 0.5393 (p90) outliers start: 18 outliers final: 7 residues processed: 408 average time/residue: 0.5297 time to fit residues: 334.9723 Evaluate side-chains 278 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 270 time to evaluate : 4.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain L residue 324 ASP Chi-restraints excluded: chain L residue 355 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 368 optimal weight: 2.9990 chunk 330 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 341 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 395 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 HIS D 236 HIS ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 HIS F 512 GLN F 634 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 528 HIS H 298 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 35424 Z= 0.419 Angle : 0.683 8.151 47923 Z= 0.335 Chirality : 0.046 0.199 5403 Planarity : 0.004 0.045 6242 Dihedral : 10.947 157.243 5028 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 1.63 % Allowed : 7.98 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % 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: 0.94 (0.13), residues: 4348 helix: 1.76 (0.12), residues: 1993 sheet: -0.37 (0.22), residues: 574 loop : -0.27 (0.16), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 561 HIS 0.008 0.001 HIS G 139 PHE 0.025 0.002 PHE E 464 TYR 0.037 0.002 TYR G 507 ARG 0.013 0.001 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 280 time to evaluate : 4.260 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 427 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7467 (tm-30) REVERT: B 113 HIS cc_start: 0.7987 (t70) cc_final: 0.7625 (t70) REVERT: B 332 ARG cc_start: 0.7056 (mtm110) cc_final: 0.6783 (ttp-170) REVERT: B 398 MET cc_start: 0.8751 (mtt) cc_final: 0.8450 (mtt) REVERT: B 752 TYR cc_start: 0.7981 (p90) cc_final: 0.7453 (p90) REVERT: B 784 MET cc_start: 0.7994 (mmm) cc_final: 0.7792 (mmp) REVERT: C 758 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.8107 (t80) REVERT: D 314 ASP cc_start: 0.8391 (t0) cc_final: 0.8142 (t0) REVERT: D 342 MET cc_start: 0.8833 (mmm) cc_final: 0.8632 (mmm) REVERT: D 430 MET cc_start: 0.9009 (tpp) cc_final: 0.8771 (tpp) REVERT: D 560 MET cc_start: 0.6399 (tpp) cc_final: 0.5633 (mpp) REVERT: E 348 ARG cc_start: 0.8279 (ptp90) cc_final: 0.6997 (tpm170) REVERT: E 468 ASN cc_start: 0.8852 (m110) cc_final: 0.8455 (t0) REVERT: E 560 MET cc_start: 0.7522 (mpp) cc_final: 0.6953 (mpp) REVERT: F 254 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.6414 (p90) REVERT: F 311 ILE cc_start: 0.8404 (mt) cc_final: 0.7931 (tt) REVERT: F 343 ASP cc_start: 0.8462 (t0) cc_final: 0.8190 (m-30) REVERT: F 566 GLU cc_start: 0.8122 (mp0) cc_final: 0.7855 (mp0) REVERT: F 587 ASP cc_start: 0.8500 (t0) cc_final: 0.8083 (t0) REVERT: F 758 PHE cc_start: 0.8791 (m-80) cc_final: 0.8575 (m-80) REVERT: G 108 TYR cc_start: 0.7760 (m-80) cc_final: 0.7445 (m-80) REVERT: G 208 HIS cc_start: 0.8164 (p-80) cc_final: 0.7897 (p-80) REVERT: G 543 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: H 258 PHE cc_start: 0.5897 (p90) cc_final: 0.5285 (p90) outliers start: 61 outliers final: 40 residues processed: 324 average time/residue: 0.4524 time to fit residues: 241.2509 Evaluate side-chains 297 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 254 time to evaluate : 4.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain F residue 254 TYR Chi-restraints excluded: chain F residue 472 SER Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain L residue 324 ASP Chi-restraints excluded: chain L residue 361 ILE Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 220 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 chunk 269 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 396 optimal weight: 0.9990 chunk 428 optimal weight: 0.6980 chunk 353 optimal weight: 8.9990 chunk 393 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 318 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 188 GLN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35424 Z= 0.178 Angle : 0.573 7.799 47923 Z= 0.274 Chirality : 0.042 0.149 5403 Planarity : 0.003 0.041 6242 Dihedral : 10.245 149.889 5022 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.79 % Rotamer: Outliers : 1.36 % Allowed : 9.92 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % 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: 1.12 (0.13), residues: 4348 helix: 1.90 (0.12), residues: 1973 sheet: -0.24 (0.22), residues: 579 loop : -0.15 (0.16), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 561 HIS 0.004 0.001 HIS K 268 PHE 0.026 0.001 PHE E 464 TYR 0.029 0.001 TYR G 189 ARG 0.008 0.000 ARG E 434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 278 time to evaluate : 4.343 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 427 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7485 (tm-30) REVERT: B 113 HIS cc_start: 0.7993 (t70) cc_final: 0.7621 (t70) REVERT: B 120 TYR cc_start: 0.5895 (OUTLIER) cc_final: 0.5627 (t80) REVERT: B 287 LYS cc_start: 0.9049 (tttm) cc_final: 0.8699 (tmtt) REVERT: B 398 MET cc_start: 0.8731 (mtt) cc_final: 0.8430 (mtt) REVERT: B 405 ASP cc_start: 0.8280 (t0) cc_final: 0.7998 (t0) REVERT: B 621 MET cc_start: 0.6396 (ppp) cc_final: 0.6124 (ptm) REVERT: B 752 TYR cc_start: 0.7917 (p90) cc_final: 0.7384 (p90) REVERT: C 618 MET cc_start: 0.7803 (tmm) cc_final: 0.7467 (tmm) REVERT: C 758 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.8070 (t80) REVERT: D 314 ASP cc_start: 0.8182 (t0) cc_final: 0.7968 (t0) REVERT: D 342 MET cc_start: 0.8769 (mmm) cc_final: 0.8560 (mmm) REVERT: D 482 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7285 (p) REVERT: D 560 MET cc_start: 0.6323 (tpp) cc_final: 0.5558 (mpp) REVERT: E 285 MET cc_start: 0.6804 (mmp) cc_final: 0.6080 (mtt) REVERT: E 348 ARG cc_start: 0.8281 (ptp90) cc_final: 0.6996 (tpm170) REVERT: E 468 ASN cc_start: 0.8900 (m110) cc_final: 0.8420 (t0) REVERT: F 264 MET cc_start: 0.8476 (ttm) cc_final: 0.7969 (tpp) REVERT: F 311 ILE cc_start: 0.8366 (mt) cc_final: 0.7949 (tt) REVERT: F 343 ASP cc_start: 0.8477 (t0) cc_final: 0.8125 (m-30) REVERT: F 359 ARG cc_start: 0.9096 (tpp-160) cc_final: 0.8667 (mmm-85) REVERT: F 566 GLU cc_start: 0.8097 (mp0) cc_final: 0.7870 (mp0) REVERT: F 571 ASP cc_start: 0.7320 (m-30) cc_final: 0.6741 (m-30) REVERT: F 587 ASP cc_start: 0.8472 (t0) cc_final: 0.7966 (t0) REVERT: G 108 TYR cc_start: 0.7575 (m-80) cc_final: 0.7209 (m-80) REVERT: G 208 HIS cc_start: 0.8151 (p-80) cc_final: 0.7869 (p-80) REVERT: G 543 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: H 258 PHE cc_start: 0.5833 (p90) cc_final: 0.5314 (p90) outliers start: 51 outliers final: 29 residues processed: 314 average time/residue: 0.4685 time to fit residues: 244.0152 Evaluate side-chains 283 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 250 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain L residue 324 ASP Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 391 optimal weight: 0.0050 chunk 298 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 266 optimal weight: 4.9990 chunk 398 optimal weight: 0.7980 chunk 421 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 377 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 35424 Z= 0.194 Angle : 0.563 11.285 47923 Z= 0.268 Chirality : 0.041 0.146 5403 Planarity : 0.003 0.043 6242 Dihedral : 9.762 144.684 5022 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.15 % Rotamer: Outliers : 2.03 % Allowed : 10.70 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % 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: 1.12 (0.13), residues: 4348 helix: 1.85 (0.12), residues: 1974 sheet: -0.13 (0.22), residues: 577 loop : -0.13 (0.16), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 561 HIS 0.004 0.001 HIS K 268 PHE 0.023 0.001 PHE E 464 TYR 0.026 0.001 TYR G 507 ARG 0.004 0.000 ARG D 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 263 time to evaluate : 4.398 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: B 113 HIS cc_start: 0.8011 (t70) cc_final: 0.7459 (t70) REVERT: B 114 PRO cc_start: 0.7510 (Cg_exo) cc_final: 0.7068 (Cg_endo) REVERT: B 287 LYS cc_start: 0.9026 (tttm) cc_final: 0.8695 (tmtt) REVERT: B 398 MET cc_start: 0.8732 (mtt) cc_final: 0.8451 (mtt) REVERT: B 405 ASP cc_start: 0.8250 (t0) cc_final: 0.7991 (t0) REVERT: B 621 MET cc_start: 0.6300 (ppp) cc_final: 0.6074 (ptm) REVERT: B 752 TYR cc_start: 0.7940 (p90) cc_final: 0.7422 (p90) REVERT: C 288 MET cc_start: 0.8219 (mmt) cc_final: 0.7850 (mmt) REVERT: C 583 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8294 (m) REVERT: C 614 LEU cc_start: 0.8799 (tt) cc_final: 0.8494 (mm) REVERT: C 618 MET cc_start: 0.7726 (tmm) cc_final: 0.7161 (tmm) REVERT: C 758 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.8070 (t80) REVERT: D 314 ASP cc_start: 0.8170 (t0) cc_final: 0.7967 (t0) REVERT: D 342 MET cc_start: 0.8784 (mmm) cc_final: 0.8550 (mmm) REVERT: D 482 VAL cc_start: 0.7661 (OUTLIER) cc_final: 0.7135 (p) REVERT: D 560 MET cc_start: 0.6287 (tpp) cc_final: 0.5529 (mpp) REVERT: E 468 ASN cc_start: 0.8908 (m110) cc_final: 0.8463 (t0) REVERT: E 560 MET cc_start: 0.7603 (mpp) cc_final: 0.7273 (mpp) REVERT: F 311 ILE cc_start: 0.8368 (mt) cc_final: 0.7928 (tt) REVERT: F 343 ASP cc_start: 0.8508 (t0) cc_final: 0.8119 (m-30) REVERT: F 587 ASP cc_start: 0.8475 (t0) cc_final: 0.7983 (t0) REVERT: G 108 TYR cc_start: 0.7709 (m-80) cc_final: 0.7360 (m-80) REVERT: G 208 HIS cc_start: 0.8168 (p-80) cc_final: 0.7942 (p-80) REVERT: G 543 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: H 258 PHE cc_start: 0.5793 (p90) cc_final: 0.5355 (p90) REVERT: K 215 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7654 (tt) outliers start: 76 outliers final: 50 residues processed: 323 average time/residue: 0.4451 time to fit residues: 242.5592 Evaluate side-chains 307 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 252 time to evaluate : 4.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 472 SER Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 309 THR Chi-restraints excluded: chain L residue 324 ASP Chi-restraints excluded: chain L residue 361 ILE Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 350 optimal weight: 0.3980 chunk 239 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 313 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 359 optimal weight: 0.2980 chunk 291 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 378 optimal weight: 0.5980 chunk 106 optimal weight: 0.5980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35424 Z= 0.142 Angle : 0.548 10.226 47923 Z= 0.257 Chirality : 0.041 0.226 5403 Planarity : 0.003 0.041 6242 Dihedral : 9.305 139.282 5022 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 1.89 % Allowed : 11.63 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % 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: 1.24 (0.13), residues: 4348 helix: 1.89 (0.12), residues: 1973 sheet: 0.01 (0.22), residues: 578 loop : -0.03 (0.16), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 561 HIS 0.003 0.001 HIS K 268 PHE 0.022 0.001 PHE E 464 TYR 0.022 0.001 TYR G 507 ARG 0.003 0.000 ARG G 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 271 time to evaluate : 3.863 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 427 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7991 (tp30) REVERT: A 560 MET cc_start: 0.7355 (mtt) cc_final: 0.7077 (mtt) REVERT: B 113 HIS cc_start: 0.8013 (t70) cc_final: 0.7478 (t70) REVERT: B 114 PRO cc_start: 0.7494 (Cg_exo) cc_final: 0.7049 (Cg_endo) REVERT: B 287 LYS cc_start: 0.9034 (tttm) cc_final: 0.8678 (tmtt) REVERT: B 359 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8766 (ptp90) REVERT: B 398 MET cc_start: 0.8724 (mtt) cc_final: 0.8435 (mtt) REVERT: B 405 ASP cc_start: 0.8283 (t0) cc_final: 0.8036 (t0) REVERT: B 437 MET cc_start: 0.7501 (tpp) cc_final: 0.7257 (tpp) REVERT: B 621 MET cc_start: 0.6214 (ppp) cc_final: 0.5961 (ptm) REVERT: B 752 TYR cc_start: 0.7992 (p90) cc_final: 0.7493 (p90) REVERT: C 583 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8299 (m) REVERT: C 614 LEU cc_start: 0.8816 (tt) cc_final: 0.8475 (mm) REVERT: C 618 MET cc_start: 0.7718 (tmm) cc_final: 0.7388 (tmm) REVERT: C 758 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.8051 (t80) REVERT: D 314 ASP cc_start: 0.8115 (t0) cc_final: 0.7889 (t0) REVERT: D 342 MET cc_start: 0.8743 (mmm) cc_final: 0.8509 (mmm) REVERT: D 482 VAL cc_start: 0.7624 (OUTLIER) cc_final: 0.7117 (p) REVERT: D 560 MET cc_start: 0.6227 (tpp) cc_final: 0.5461 (mpp) REVERT: E 468 ASN cc_start: 0.8826 (m110) cc_final: 0.8451 (t0) REVERT: E 560 MET cc_start: 0.7592 (mpp) cc_final: 0.7253 (mpp) REVERT: F 343 ASP cc_start: 0.8426 (t0) cc_final: 0.8026 (m-30) REVERT: F 587 ASP cc_start: 0.8492 (t0) cc_final: 0.8023 (t0) REVERT: F 758 PHE cc_start: 0.8718 (m-80) cc_final: 0.8448 (m-80) REVERT: G 108 TYR cc_start: 0.7580 (m-80) cc_final: 0.7277 (m-80) REVERT: G 208 HIS cc_start: 0.8158 (p-80) cc_final: 0.7928 (p-80) REVERT: G 543 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: G 555 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7150 (mp0) REVERT: H 258 PHE cc_start: 0.5710 (p90) cc_final: 0.5317 (p90) REVERT: K 215 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7538 (tt) outliers start: 71 outliers final: 41 residues processed: 328 average time/residue: 0.4271 time to fit residues: 233.7756 Evaluate side-chains 301 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 254 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 472 SER Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 501 TYR Chi-restraints excluded: chain G residue 533 ILE Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain L residue 324 ASP Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 141 optimal weight: 9.9990 chunk 379 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 247 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 421 optimal weight: 0.6980 chunk 350 optimal weight: 0.7980 chunk 195 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35424 Z= 0.179 Angle : 0.557 12.632 47923 Z= 0.262 Chirality : 0.041 0.251 5403 Planarity : 0.003 0.059 6242 Dihedral : 8.992 135.681 5022 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.40 % Rotamer: Outliers : 2.03 % Allowed : 12.06 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % 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: 1.24 (0.14), residues: 4348 helix: 1.91 (0.12), residues: 1977 sheet: 0.00 (0.22), residues: 579 loop : -0.04 (0.16), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 561 HIS 0.004 0.001 HIS K 268 PHE 0.020 0.001 PHE E 464 TYR 0.025 0.001 TYR G 507 ARG 0.006 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 259 time to evaluate : 4.372 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 427 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7979 (tp30) REVERT: A 560 MET cc_start: 0.7255 (mtt) cc_final: 0.6981 (mtt) REVERT: B 113 HIS cc_start: 0.8091 (t70) cc_final: 0.7622 (t-90) REVERT: B 114 PRO cc_start: 0.7523 (Cg_exo) cc_final: 0.7192 (Cg_endo) REVERT: B 287 LYS cc_start: 0.9005 (tttm) cc_final: 0.8774 (tmtt) REVERT: B 359 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8761 (ptp90) REVERT: B 398 MET cc_start: 0.8735 (mtt) cc_final: 0.8445 (mtt) REVERT: B 405 ASP cc_start: 0.8311 (t0) cc_final: 0.8083 (t0) REVERT: B 621 MET cc_start: 0.6237 (ppp) cc_final: 0.5982 (ptm) REVERT: B 752 TYR cc_start: 0.7984 (p90) cc_final: 0.7480 (p90) REVERT: C 618 MET cc_start: 0.7905 (tmm) cc_final: 0.7463 (tmm) REVERT: C 758 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.8056 (t80) REVERT: D 314 ASP cc_start: 0.8144 (t0) cc_final: 0.7919 (t0) REVERT: D 342 MET cc_start: 0.8808 (mmm) cc_final: 0.8572 (mmm) REVERT: D 482 VAL cc_start: 0.7607 (OUTLIER) cc_final: 0.7076 (p) REVERT: D 560 MET cc_start: 0.6210 (tpp) cc_final: 0.5370 (mpp) REVERT: E 468 ASN cc_start: 0.8868 (m110) cc_final: 0.8492 (t0) REVERT: E 560 MET cc_start: 0.7606 (mpp) cc_final: 0.7264 (mpp) REVERT: F 343 ASP cc_start: 0.8429 (t0) cc_final: 0.8064 (m-30) REVERT: F 587 ASP cc_start: 0.8476 (t0) cc_final: 0.7956 (t0) REVERT: F 758 PHE cc_start: 0.8721 (m-80) cc_final: 0.8449 (m-80) REVERT: G 108 TYR cc_start: 0.7625 (m-80) cc_final: 0.7242 (m-80) REVERT: G 208 HIS cc_start: 0.8194 (p-80) cc_final: 0.7977 (p-80) REVERT: G 543 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: H 258 PHE cc_start: 0.5668 (p90) cc_final: 0.5320 (p90) REVERT: K 215 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7556 (tt) outliers start: 76 outliers final: 52 residues processed: 320 average time/residue: 0.4490 time to fit residues: 240.5483 Evaluate side-chains 308 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 251 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 472 SER Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 501 TYR Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain L residue 324 ASP Chi-restraints excluded: chain L residue 361 ILE Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 406 optimal weight: 0.0170 chunk 47 optimal weight: 4.9990 chunk 240 optimal weight: 0.5980 chunk 308 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 355 optimal weight: 8.9990 chunk 235 optimal weight: 9.9990 chunk 420 optimal weight: 5.9990 chunk 262 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 overall best weight: 2.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 HIS ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 35424 Z= 0.333 Angle : 0.631 10.569 47923 Z= 0.306 Chirality : 0.043 0.233 5403 Planarity : 0.004 0.041 6242 Dihedral : 8.875 132.401 5022 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 2.24 % Allowed : 12.43 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.02 % 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: 0.97 (0.13), residues: 4348 helix: 1.73 (0.12), residues: 1977 sheet: -0.21 (0.23), residues: 573 loop : -0.22 (0.16), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 561 HIS 0.006 0.001 HIS K 268 PHE 0.025 0.002 PHE E 464 TYR 0.037 0.002 TYR G 507 ARG 0.005 0.000 ARG D 323 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 252 time to evaluate : 4.360 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 560 MET cc_start: 0.7407 (mtt) cc_final: 0.7103 (mtt) REVERT: B 113 HIS cc_start: 0.8223 (t70) cc_final: 0.7725 (t-90) REVERT: B 114 PRO cc_start: 0.7572 (Cg_exo) cc_final: 0.7238 (Cg_endo) REVERT: B 332 ARG cc_start: 0.6966 (mtm110) cc_final: 0.6732 (ttp-170) REVERT: B 359 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8812 (ptp90) REVERT: B 398 MET cc_start: 0.8760 (mtt) cc_final: 0.8469 (mtt) REVERT: B 437 MET cc_start: 0.7730 (tpp) cc_final: 0.7472 (tpp) REVERT: B 621 MET cc_start: 0.6215 (ppp) cc_final: 0.5719 (ptm) REVERT: B 752 TYR cc_start: 0.7988 (p90) cc_final: 0.7541 (p90) REVERT: C 287 LYS cc_start: 0.8241 (pttm) cc_final: 0.7633 (pttt) REVERT: C 618 MET cc_start: 0.8053 (tmm) cc_final: 0.7705 (tmm) REVERT: C 758 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.8088 (t80) REVERT: D 314 ASP cc_start: 0.8271 (t0) cc_final: 0.8061 (t0) REVERT: D 342 MET cc_start: 0.8898 (mmm) cc_final: 0.8596 (mmm) REVERT: D 482 VAL cc_start: 0.7650 (OUTLIER) cc_final: 0.7112 (p) REVERT: D 560 MET cc_start: 0.6253 (tpp) cc_final: 0.5385 (mpp) REVERT: D 756 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7358 (pm20) REVERT: E 254 TYR cc_start: 0.8085 (p90) cc_final: 0.7740 (p90) REVERT: E 464 PHE cc_start: 0.8455 (t80) cc_final: 0.8111 (t80) REVERT: E 560 MET cc_start: 0.7567 (mpp) cc_final: 0.7155 (mpp) REVERT: E 784 MET cc_start: 0.7630 (mmp) cc_final: 0.7108 (mmm) REVERT: F 254 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.6848 (p90) REVERT: F 311 ILE cc_start: 0.8352 (mt) cc_final: 0.7957 (tt) REVERT: F 343 ASP cc_start: 0.8544 (t0) cc_final: 0.8153 (m-30) REVERT: F 587 ASP cc_start: 0.8524 (t0) cc_final: 0.7944 (t0) REVERT: G 108 TYR cc_start: 0.7810 (m-80) cc_final: 0.7451 (m-80) REVERT: G 543 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: H 258 PHE cc_start: 0.5631 (p90) cc_final: 0.5323 (p90) REVERT: K 215 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7678 (tt) outliers start: 84 outliers final: 60 residues processed: 316 average time/residue: 0.4934 time to fit residues: 262.5144 Evaluate side-chains 309 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 242 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain F residue 254 TYR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 472 SER Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain L residue 309 THR Chi-restraints excluded: chain L residue 324 ASP Chi-restraints excluded: chain L residue 361 ILE Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 259 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 250 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 267 optimal weight: 6.9990 chunk 286 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 330 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 ASN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 35424 Z= 0.416 Angle : 0.675 10.506 47923 Z= 0.332 Chirality : 0.044 0.200 5403 Planarity : 0.004 0.042 6242 Dihedral : 8.810 129.246 5022 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.91 % Favored : 94.04 % Rotamer: Outliers : 2.43 % Allowed : 12.48 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.02 % 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: 0.54 (0.13), residues: 4348 helix: 1.40 (0.12), residues: 1979 sheet: -0.52 (0.23), residues: 572 loop : -0.44 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 561 HIS 0.007 0.001 HIS G 139 PHE 0.040 0.002 PHE E 464 TYR 0.043 0.002 TYR G 507 ARG 0.006 0.001 ARG G 492 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 243 time to evaluate : 4.671 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: B 113 HIS cc_start: 0.8132 (t70) cc_final: 0.7606 (t-90) REVERT: B 114 PRO cc_start: 0.7623 (Cg_exo) cc_final: 0.7289 (Cg_endo) REVERT: B 332 ARG cc_start: 0.7046 (mtm110) cc_final: 0.6639 (ttp-170) REVERT: B 359 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8806 (ptp90) REVERT: B 398 MET cc_start: 0.8785 (mtt) cc_final: 0.8481 (mtt) REVERT: B 752 TYR cc_start: 0.8026 (p90) cc_final: 0.7554 (p90) REVERT: C 287 LYS cc_start: 0.8216 (pttm) cc_final: 0.7599 (pttt) REVERT: C 618 MET cc_start: 0.8169 (tmm) cc_final: 0.7875 (tmm) REVERT: C 758 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.8084 (t80) REVERT: D 314 ASP cc_start: 0.8347 (t0) cc_final: 0.8111 (t0) REVERT: D 323 ARG cc_start: 0.6453 (mmt90) cc_final: 0.6189 (mmt-90) REVERT: D 342 MET cc_start: 0.8930 (mmm) cc_final: 0.8626 (mmm) REVERT: D 432 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8863 (tm-30) REVERT: D 482 VAL cc_start: 0.7725 (OUTLIER) cc_final: 0.7222 (p) REVERT: D 756 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: E 229 MET cc_start: 0.8347 (tmm) cc_final: 0.7877 (ttt) REVERT: E 560 MET cc_start: 0.7550 (mpp) cc_final: 0.7140 (mpp) REVERT: E 639 ILE cc_start: 0.6043 (mm) cc_final: 0.5207 (pt) REVERT: F 254 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.6719 (p90) REVERT: F 311 ILE cc_start: 0.8426 (mt) cc_final: 0.7989 (tt) REVERT: F 343 ASP cc_start: 0.8675 (t0) cc_final: 0.8300 (m-30) REVERT: F 587 ASP cc_start: 0.8558 (t0) cc_final: 0.7964 (t0) REVERT: G 121 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7753 (mm-30) REVERT: G 543 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: G 574 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8148 (tmm) REVERT: K 215 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7645 (tt) outliers start: 91 outliers final: 67 residues processed: 318 average time/residue: 0.4627 time to fit residues: 246.7458 Evaluate side-chains 310 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 234 time to evaluate : 4.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 432 GLN Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain F residue 254 TYR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 472 SER Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 521 HIS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 574 MET Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain L residue 309 THR Chi-restraints excluded: chain L residue 324 ASP Chi-restraints excluded: chain L residue 361 ILE Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 382 optimal weight: 0.6980 chunk 402 optimal weight: 0.5980 chunk 367 optimal weight: 0.0070 chunk 391 optimal weight: 0.2980 chunk 235 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 chunk 307 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 353 optimal weight: 8.9990 chunk 370 optimal weight: 1.9990 chunk 390 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35424 Z= 0.151 Angle : 0.587 10.216 47923 Z= 0.280 Chirality : 0.041 0.187 5403 Planarity : 0.003 0.042 6242 Dihedral : 8.319 124.334 5022 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.28 % Favored : 95.68 % Rotamer: Outliers : 1.71 % Allowed : 13.50 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % 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: 0.88 (0.13), residues: 4348 helix: 1.65 (0.12), residues: 1973 sheet: -0.30 (0.22), residues: 576 loop : -0.23 (0.16), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 561 HIS 0.004 0.001 HIS K 268 PHE 0.025 0.001 PHE E 464 TYR 0.026 0.001 TYR G 507 ARG 0.005 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 255 time to evaluate : 4.320 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 208 MET cc_start: 0.8352 (tmm) cc_final: 0.8117 (tmm) REVERT: A 427 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7568 (tm-30) REVERT: A 560 MET cc_start: 0.7574 (mtt) cc_final: 0.7331 (mtt) REVERT: B 113 HIS cc_start: 0.8168 (t70) cc_final: 0.7650 (t-90) REVERT: B 114 PRO cc_start: 0.7576 (Cg_exo) cc_final: 0.7243 (Cg_endo) REVERT: B 359 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8811 (ptp90) REVERT: B 398 MET cc_start: 0.8780 (mtt) cc_final: 0.8546 (mtt) REVERT: B 437 MET cc_start: 0.7801 (tpp) cc_final: 0.7533 (tpp) REVERT: B 752 TYR cc_start: 0.7949 (p90) cc_final: 0.7548 (p90) REVERT: C 614 LEU cc_start: 0.8922 (tt) cc_final: 0.8586 (mm) REVERT: C 618 MET cc_start: 0.8032 (tmm) cc_final: 0.7530 (tmm) REVERT: C 758 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.8065 (t80) REVERT: D 342 MET cc_start: 0.8881 (mmm) cc_final: 0.8582 (mmm) REVERT: D 482 VAL cc_start: 0.7600 (OUTLIER) cc_final: 0.7093 (p) REVERT: D 756 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: E 621 MET cc_start: 0.7075 (tpp) cc_final: 0.6865 (tpp) REVERT: E 784 MET cc_start: 0.7650 (mmp) cc_final: 0.7138 (mmm) REVERT: F 311 ILE cc_start: 0.8359 (mt) cc_final: 0.7983 (tt) REVERT: F 343 ASP cc_start: 0.8509 (t0) cc_final: 0.8099 (m-30) REVERT: F 587 ASP cc_start: 0.8520 (t0) cc_final: 0.8028 (t0) REVERT: K 215 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7544 (tt) outliers start: 64 outliers final: 43 residues processed: 308 average time/residue: 0.4580 time to fit residues: 234.0858 Evaluate side-chains 291 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 243 time to evaluate : 3.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 306 ASN Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain L residue 309 THR Chi-restraints excluded: chain L residue 324 ASP Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 257 optimal weight: 0.9990 chunk 414 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 287 optimal weight: 7.9990 chunk 434 optimal weight: 3.9990 chunk 399 optimal weight: 1.9990 chunk 345 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 267 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 668 ASN ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 HIS ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 35424 Z= 0.318 Angle : 0.634 11.412 47923 Z= 0.307 Chirality : 0.043 0.193 5403 Planarity : 0.004 0.041 6242 Dihedral : 8.293 122.519 5019 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 1.63 % Allowed : 13.76 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % 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: 0.76 (0.13), residues: 4348 helix: 1.56 (0.12), residues: 1979 sheet: -0.38 (0.23), residues: 572 loop : -0.31 (0.16), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 561 HIS 0.005 0.001 HIS K 268 PHE 0.022 0.001 PHE E 464 TYR 0.034 0.001 TYR G 507 ARG 0.004 0.000 ARG C 375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8696 Ramachandran restraints generated. 4348 Oldfield, 0 Emsley, 4348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 241 time to evaluate : 4.234 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 560 MET cc_start: 0.7550 (mtt) cc_final: 0.7291 (mtt) REVERT: B 113 HIS cc_start: 0.8189 (t70) cc_final: 0.7676 (t-90) REVERT: B 114 PRO cc_start: 0.7588 (Cg_exo) cc_final: 0.7255 (Cg_endo) REVERT: B 359 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8805 (ptp90) REVERT: B 398 MET cc_start: 0.8777 (mtt) cc_final: 0.8476 (mtt) REVERT: B 437 MET cc_start: 0.7933 (tpp) cc_final: 0.7693 (tpp) REVERT: B 752 TYR cc_start: 0.7965 (p90) cc_final: 0.7553 (p90) REVERT: C 280 ASN cc_start: 0.7365 (m-40) cc_final: 0.7073 (m-40) REVERT: C 287 LYS cc_start: 0.8268 (pttm) cc_final: 0.7620 (pttp) REVERT: C 614 LEU cc_start: 0.8856 (tt) cc_final: 0.8516 (mm) REVERT: C 618 MET cc_start: 0.8013 (tmm) cc_final: 0.7500 (tmm) REVERT: C 758 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.8067 (t80) REVERT: D 342 MET cc_start: 0.8909 (mmm) cc_final: 0.8598 (mmm) REVERT: D 482 VAL cc_start: 0.7681 (OUTLIER) cc_final: 0.7171 (p) REVERT: D 756 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: E 288 MET cc_start: 0.4692 (mmt) cc_final: 0.4115 (mpp) REVERT: E 560 MET cc_start: 0.7536 (mpp) cc_final: 0.7162 (mpp) REVERT: E 621 MET cc_start: 0.7141 (tpp) cc_final: 0.6908 (tpp) REVERT: E 639 ILE cc_start: 0.5934 (mm) cc_final: 0.5091 (pt) REVERT: E 784 MET cc_start: 0.7661 (mmp) cc_final: 0.7153 (mmm) REVERT: F 311 ILE cc_start: 0.8366 (mt) cc_final: 0.7972 (tt) REVERT: F 343 ASP cc_start: 0.8616 (t0) cc_final: 0.8203 (m-30) REVERT: F 587 ASP cc_start: 0.8562 (t0) cc_final: 0.8004 (t0) REVERT: K 215 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7661 (tt) outliers start: 61 outliers final: 51 residues processed: 290 average time/residue: 0.4541 time to fit residues: 220.7079 Evaluate side-chains 292 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 236 time to evaluate : 3.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 306 ASN Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 509 HIS Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 626 ASN Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain L residue 309 THR Chi-restraints excluded: chain L residue 324 ASP Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 274 optimal weight: 3.9990 chunk 368 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 318 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 346 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 355 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.122388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.085949 restraints weight = 99837.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.085885 restraints weight = 58536.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085984 restraints weight = 44067.791| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 35424 Z= 0.343 Angle : 0.655 11.874 47923 Z= 0.320 Chirality : 0.043 0.182 5403 Planarity : 0.004 0.042 6242 Dihedral : 8.323 118.439 5019 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 1.79 % Allowed : 13.71 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.86 % Cis-general : 0.05 % Twisted Proline : 0.45 % Twisted General : 0.02 % 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: 0.56 (0.13), residues: 4348 helix: 1.39 (0.12), residues: 1977 sheet: -0.52 (0.23), residues: 572 loop : -0.39 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 561 HIS 0.006 0.001 HIS G 208 PHE 0.026 0.002 PHE E 464 TYR 0.039 0.002 TYR G 507 ARG 0.004 0.000 ARG C 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6238.33 seconds wall clock time: 115 minutes 26.42 seconds (6926.42 seconds total)