Starting phenix.real_space_refine on Thu Feb 22 16:05:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dat_27275/02_2024/8dat_27275_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dat_27275/02_2024/8dat_27275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dat_27275/02_2024/8dat_27275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dat_27275/02_2024/8dat_27275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dat_27275/02_2024/8dat_27275_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dat_27275/02_2024/8dat_27275_updated.pdb" } resolution = 3.8 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= -0.022 sd= 1.089 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 21678 2.51 5 N 6018 2.21 5 O 6751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 34635 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5560 Classifications: {'peptide': 712} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 674} Chain breaks: 2 Chain: "B" Number of atoms: 4361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4361 Classifications: {'peptide': 561} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 531} Chain breaks: 5 Chain: "C" Number of atoms: 5590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5590 Classifications: {'peptide': 716} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 678} Chain breaks: 2 Chain: "D" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4365 Classifications: {'peptide': 561} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 531} Chain breaks: 4 Chain: "E" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4174 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 509} Chain breaks: 2 Chain: "F" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4190 Classifications: {'peptide': 541} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 511} Chain breaks: 2 Chain: "G" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3815 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain: "H" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain breaks: 1 Chain: "J" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 581 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} 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: 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: "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 28493 SG CYS G 137 46.570 46.552 94.504 1.00 85.59 S ATOM 28553 SG CYS G 145 50.237 47.200 94.103 1.00 76.33 S ATOM 28580 SG CYS G 148 48.689 46.859 97.510 1.00 77.07 S ATOM 29050 SG CYS G 204 76.186 88.657 113.339 1.00100.27 S ATOM 29148 SG CYS G 216 76.282 90.588 110.164 1.00 82.25 S ATOM 29169 SG CYS G 219 73.577 91.235 112.527 1.00 80.75 S Time building chain proxies: 17.60, per 1000 atoms: 0.51 Number of scatterers: 34635 At special positions: 0 Unit cell: (151.088, 167.048, 190.456, 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 6751 8.00 N 6018 7.00 C 21678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.45 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 216 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 219 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 204 " Number of angles added : 6 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8210 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 208 helices and 25 sheets defined 45.1% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.94 Creating SS restraints... Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 96 through 102 Processing helix chain 'A' and resid 130 through 133 Processing helix chain 'A' and resid 140 through 149 removed outlier: 4.006A 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 206 removed outlier: 3.787A pdb=" N ASN A 206 " --> pdb=" O ASP A 203 " (cutoff:3.500A) 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 221 through 235 removed outlier: 3.521A pdb=" N MET A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.333A 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 238 through 243 Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 292 through 306 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 345 removed outlier: 4.141A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.596A pdb=" N LYS A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 418 through 439 removed outlier: 4.319A pdb=" N ASP A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 5.287A 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: 4.275A 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 545 removed outlier: 3.763A pdb=" N VAL A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) 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 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 609 through 619 Processing helix chain 'A' and resid 641 through 644 Processing helix chain 'A' and resid 660 through 673 removed outlier: 5.021A pdb=" N LYS A 673 " --> pdb=" O ALA A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 688 Processing helix chain 'A' and resid 694 through 718 Processing helix chain 'A' and resid 755 through 764 removed outlier: 3.706A pdb=" N THR A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'B' and resid 97 through 102 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: 4.092A 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 238 through 243 Processing helix chain 'B' and resid 261 through 272 Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 294 through 305 Processing helix chain 'B' and resid 316 through 319 No H-bonds generated for 'chain 'B' and resid 316 through 319' Processing helix chain 'B' and resid 329 through 345 removed outlier: 3.979A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) 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 412 Processing helix chain 'B' and resid 418 through 439 removed outlier: 4.591A pdb=" N ASP B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 5.789A 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: 4.496A 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 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 591 No H-bonds generated for 'chain 'B' and resid 589 through 591' Processing helix chain 'B' and resid 609 through 619 Processing helix chain 'B' and resid 641 through 644 Processing helix chain 'B' and resid 660 through 670 Processing helix chain 'B' and resid 683 through 689 Processing helix chain 'B' and resid 694 through 718 Processing helix chain 'B' and resid 755 through 762 Processing helix chain 'B' and resid 771 through 786 Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 96 through 102 Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 140 through 149 removed outlier: 4.216A pdb=" N LYS C 146 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Proline residue: C 147 - end of helix Processing helix chain 'C' and resid 202 through 206 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 removed outlier: 4.596A pdb=" N LEU C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 237 through 243 Processing helix chain 'C' and resid 261 through 272 Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 292 through 306 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 329 through 345 removed outlier: 3.927A pdb=" N VAL C 334 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 367 No H-bonds generated for 'chain 'C' and resid 365 through 367' Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 406 through 412 Processing helix chain 'C' and resid 418 through 439 removed outlier: 4.475A pdb=" N ASP C 438 " --> pdb=" O ARG C 434 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 454 Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 493 through 508 removed outlier: 4.721A 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 591 No H-bonds generated for 'chain 'C' and resid 589 through 591' Processing helix chain 'C' and resid 609 through 620 Processing helix chain 'C' and resid 636 through 638 No H-bonds generated for 'chain 'C' and resid 636 through 638' Processing helix chain 'C' and resid 641 through 644 Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 683 through 689 Processing helix chain 'C' and resid 694 through 718 Processing helix chain 'C' and resid 755 through 764 removed outlier: 3.802A pdb=" N THR C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 788 Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 201 through 205 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 removed outlier: 4.125A pdb=" N LEU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 237 through 243 Processing helix chain 'D' and resid 261 through 272 Processing helix chain 'D' and resid 281 through 286 Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 329 through 345 Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 384 through 396 removed outlier: 3.698A pdb=" N LYS D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 412 Processing helix chain 'D' and resid 418 through 439 removed outlier: 4.599A pdb=" N ASP D 438 " --> pdb=" O ARG D 434 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU D 439 " --> pdb=" O GLU D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.584A pdb=" N SER D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) 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 493 through 508 removed outlier: 4.039A 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 544 Processing helix chain 'D' and resid 554 through 562 Processing helix chain 'D' and resid 569 through 578 Processing helix chain 'D' and resid 589 through 592 No H-bonds generated for 'chain 'D' and resid 589 through 592' Processing helix chain 'D' and resid 609 through 619 Processing helix chain 'D' and resid 641 through 644 Processing helix chain 'D' and resid 660 through 670 Processing helix chain 'D' and resid 683 through 689 Processing helix chain 'D' and resid 694 through 718 Processing helix chain 'D' and resid 755 through 763 Processing helix chain 'D' and resid 771 through 786 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: 4.210A 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 237 through 243 removed outlier: 3.687A pdb=" N LYS E 241 " --> pdb=" O PRO E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 272 Processing helix chain 'E' and resid 281 through 286 Processing helix chain 'E' and resid 292 through 304 Processing helix chain 'E' and resid 316 through 319 No H-bonds generated for 'chain 'E' and resid 316 through 319' Processing helix chain 'E' and resid 331 through 345 removed outlier: 3.914A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 367 No H-bonds generated for 'chain 'E' and resid 365 through 367' Processing helix chain 'E' and resid 384 through 396 removed outlier: 3.869A pdb=" N LYS E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 412 Processing helix chain 'E' and resid 418 through 439 removed outlier: 4.592A pdb=" N ASP E 438 " --> pdb=" O ARG E 434 " (cutoff:3.500A) removed outlier: 5.637A 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 468 Processing helix chain 'E' and resid 473 through 475 No H-bonds generated for 'chain 'E' and resid 473 through 475' Processing helix chain 'E' and resid 493 through 508 removed outlier: 4.211A 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 516 Processing helix chain 'E' and resid 534 through 544 Processing helix chain 'E' and resid 554 through 561 Processing helix chain 'E' and resid 569 through 578 Processing helix chain 'E' and resid 589 through 592 No H-bonds generated for 'chain 'E' and resid 589 through 592' Processing helix chain 'E' and resid 609 through 619 Processing helix chain 'E' and resid 636 through 638 No H-bonds generated for 'chain 'E' and resid 636 through 638' Processing helix chain 'E' and resid 641 through 644 Processing helix chain 'E' and resid 660 through 673 removed outlier: 4.889A pdb=" N LYS E 673 " --> pdb=" O ALA E 669 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 689 Processing helix chain 'E' and resid 694 through 718 Processing helix chain 'E' and resid 755 through 764 Processing helix chain 'E' and resid 771 through 786 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: 4.655A 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 292 through 305 Processing helix chain 'F' and resid 316 through 318 No H-bonds generated for 'chain 'F' and resid 316 through 318' Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 329 through 345 Processing helix chain 'F' and resid 365 through 367 No H-bonds generated for 'chain 'F' and resid 365 through 367' Processing helix chain 'F' and resid 384 through 396 removed outlier: 3.570A pdb=" N LYS F 396 " --> pdb=" O ARG F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 412 Processing helix chain 'F' and resid 418 through 439 removed outlier: 4.304A pdb=" N ASP F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) removed outlier: 5.583A 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 473 through 475 No H-bonds generated for 'chain 'F' and resid 473 through 475' Processing helix chain 'F' and resid 493 through 508 removed outlier: 4.030A pdb=" N TYR F 505 " --> pdb=" O GLU F 501 " (cutoff:3.500A) Proline residue: F 506 - end of helix Processing helix chain 'F' and resid 510 through 516 Processing helix chain 'F' and resid 534 through 544 Processing helix chain 'F' and resid 554 through 562 Processing helix chain 'F' and resid 569 through 578 Processing helix chain 'F' and resid 589 through 591 No H-bonds generated for 'chain 'F' and resid 589 through 591' Processing helix chain 'F' and resid 609 through 619 Processing helix chain 'F' and resid 641 through 644 Processing helix chain 'F' and resid 660 through 671 Processing helix chain 'F' and resid 683 through 687 Processing helix chain 'F' and resid 694 through 718 Processing helix chain 'F' and resid 755 through 764 removed outlier: 4.136A pdb=" N THR F 764 " --> pdb=" O GLU F 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 771 through 787 Processing helix chain 'G' and resid 117 through 124 Processing helix chain 'G' and resid 156 through 161 Processing helix chain 'G' and resid 169 through 179 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 removed outlier: 3.880A pdb=" N PHE G 248 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 317 removed outlier: 3.820A pdb=" N GLN G 309 " --> pdb=" O ASN G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 363 Processing helix chain 'G' and resid 403 through 410 removed outlier: 4.097A pdb=" N THR G 410 " --> pdb=" O GLU G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 462 No H-bonds generated for 'chain 'G' and resid 460 through 462' Processing helix chain 'G' and resid 501 through 507 Processing helix chain 'G' and resid 510 through 514 removed outlier: 3.750A pdb=" N SER G 514 " --> pdb=" O ASN G 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 510 through 514' Processing helix chain 'G' and resid 517 through 524 removed outlier: 4.133A pdb=" N GLU G 522 " --> pdb=" O ASN G 518 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS G 523 " --> pdb=" O LEU G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 527 through 536 Processing helix chain 'G' and resid 541 through 551 Processing helix chain 'G' and resid 557 through 565 Processing helix chain 'G' and resid 567 through 578 Processing helix chain 'H' and resid 244 through 252 Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 156 through 159 No H-bonds generated for 'chain 'J' and resid 156 through 159' 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 356 through 359 No H-bonds generated for 'chain 'L' and resid 356 through 359' Processing sheet with id= A, first strand: chain 'A' and resid 91 through 94 removed outlier: 7.735A pdb=" N CYS A 92 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU A 37 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 94 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP A 39 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 36 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 110 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 191 through 193 removed outlier: 7.268A pdb=" N LEU A 127 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL A 175 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 154 through 156 removed outlier: 4.249A pdb=" N ARG A 154 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 186 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.822A pdb=" N MET A 253 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA A 309 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE A 354 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 311 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ALA A 356 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE A 313 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE A 275 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N PHE A 312 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE A 277 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 651 through 655 removed outlier: 3.673A pdb=" N GLY A 528 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR A 582 " --> pdb=" O PHE A 628 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A 630 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 584 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ALA A 632 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 586 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN A 548 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N PHE A 585 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 550 " --> pdb=" O PHE A 585 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 375 through 379 removed outlier: 6.659A pdb=" N ALA B 309 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE B 354 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE B 311 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE B 275 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE B 312 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASP B 314 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B 279 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 651 through 655 removed outlier: 4.392A pdb=" N GLN B 651 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL B 524 " --> pdb=" O VAL B 627 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 629 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE B 526 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY B 631 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N GLY B 528 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR B 633 " --> pdb=" O GLY B 528 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR B 582 " --> pdb=" O PHE B 628 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE B 630 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 584 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA B 632 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU B 586 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN B 548 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N PHE B 585 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE B 550 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASP B 587 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 552 " --> pdb=" O ASP B 587 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= I, first strand: chain 'C' and resid 177 through 179 removed outlier: 6.436A pdb=" N ILE C 191 " --> pdb=" O ILE C 124 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 154 through 157 removed outlier: 3.842A pdb=" N ARG C 154 " --> pdb=" O VAL C 186 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 161 through 166 removed outlier: 3.639A pdb=" N PHE C 162 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 376 through 379 removed outlier: 8.366A pdb=" N VAL C 377 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU C 252 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE C 379 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR C 254 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N VAL C 251 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL C 353 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N MET C 253 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA C 355 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLY C 255 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR C 357 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA C 309 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE C 354 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE C 311 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ALA C 356 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE C 313 " --> pdb=" O ALA C 356 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 651 through 654 removed outlier: 7.074A pdb=" N THR C 582 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE C 630 " --> pdb=" O THR C 582 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 584 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA C 632 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 586 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN C 548 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE C 585 " --> pdb=" O ASN C 548 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE C 550 " --> pdb=" O PHE C 585 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 375 through 379 removed outlier: 4.084A pdb=" N ARG D 375 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N VAL D 251 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL D 353 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N MET D 253 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA D 355 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLY D 255 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N THR D 357 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA D 309 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE D 354 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE D 313 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE D 275 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE D 277 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP D 314 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 279 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 651 through 654 removed outlier: 4.342A pdb=" N GLN D 651 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N VAL D 524 " --> pdb=" O VAL D 627 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 629 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE D 526 " --> pdb=" O VAL D 629 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY D 631 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR D 582 " --> pdb=" O PHE D 628 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE D 630 " --> pdb=" O THR D 582 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL D 584 " --> pdb=" O ILE D 630 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ALA D 632 " --> pdb=" O VAL D 584 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU D 586 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 375 through 379 removed outlier: 3.693A pdb=" N ARG E 375 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL E 353 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N MET E 253 " --> pdb=" O VAL E 353 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ALA E 355 " --> pdb=" O MET E 253 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLY E 255 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR E 357 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 652 through 654 removed outlier: 8.526A pdb=" N ILE E 653 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU E 525 " --> pdb=" O ILE E 653 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL E 524 " --> pdb=" O VAL E 627 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL E 629 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE E 526 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY E 631 " --> pdb=" O PHE E 526 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR E 582 " --> pdb=" O PHE E 628 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE E 630 " --> pdb=" O THR E 582 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL E 584 " --> pdb=" O ILE E 630 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA E 632 " --> pdb=" O VAL E 584 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU E 586 " --> pdb=" O ALA E 632 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN E 548 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE E 585 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE E 550 " --> pdb=" O PHE E 585 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 375 through 379 removed outlier: 3.779A pdb=" N ARG F 375 " --> pdb=" O GLY F 250 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL F 251 " --> pdb=" O VAL F 351 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL F 353 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N MET F 253 " --> pdb=" O VAL F 353 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA F 355 " --> pdb=" O MET F 253 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLY F 255 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR F 357 " --> pdb=" O GLY F 255 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA F 309 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE F 354 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE F 311 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA F 356 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE F 313 " --> pdb=" O ALA F 356 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE F 275 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N PHE F 312 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE F 277 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASP F 314 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 6.679A 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: 4.082A pdb=" N GLY F 528 " --> pdb=" O THR F 633 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR F 582 " --> pdb=" O PHE F 628 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE F 630 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL F 584 " --> pdb=" O ILE F 630 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ALA F 632 " --> pdb=" O VAL F 584 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU F 586 " --> pdb=" O ALA F 632 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASN F 548 " --> pdb=" O VAL F 583 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N PHE F 585 " --> pdb=" O ASN F 548 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE F 550 " --> pdb=" O PHE F 585 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 224 through 226 Processing sheet with id= U, first strand: chain 'G' and resid 467 through 470 removed outlier: 3.939A pdb=" N GLY G 276 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR G 264 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE G 284 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR G 262 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL G 382 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N PHE G 326 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS G 384 " --> pdb=" O PHE G 326 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER G 398 " --> pdb=" O LEU G 466 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU G 466 " --> pdb=" O SER G 398 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 414 through 416 removed outlier: 3.543A pdb=" N PHE G 457 " --> pdb=" O ALA G 423 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= X, first strand: chain 'K' and resid 212 through 216 removed outlier: 5.718A pdb=" N SER K 265 " --> pdb=" O PHE K 204 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS K 206 " --> pdb=" O SER K 265 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU K 267 " --> pdb=" O LYS K 206 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 312 through 316 removed outlier: 5.399A pdb=" N SER L 365 " --> pdb=" O PHE L 304 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS L 306 " --> pdb=" O SER L 365 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU L 367 " --> pdb=" O LYS L 306 " (cutoff:3.500A) 1263 hydrogen bonds defined for protein. 3687 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: 12.19 Time building geometry restraints manager: 15.37 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: 11722 1.34 - 1.46: 6664 1.46 - 1.58: 16497 1.58 - 1.69: 46 1.69 - 1.81: 290 Bond restraints: 35219 Sorted by residual: bond pdb=" C4 ADP A 902 " pdb=" C5 ADP A 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C5 ADP A 902 " pdb=" C6 ADP A 902 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C5 ADP C 901 " pdb=" C6 ADP C 901 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 35214 not shown) Histogram of bond angle deviations from ideal: 99.40 - 107.50: 1439 107.50 - 115.61: 21746 115.61 - 123.72: 23714 123.72 - 131.82: 704 131.82 - 139.93: 48 Bond angle restraints: 47651 Sorted by residual: angle pdb=" N ILE F 592 " pdb=" CA ILE F 592 " pdb=" C ILE F 592 " ideal model delta sigma weight residual 112.96 108.95 4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" CA THR B 24 " pdb=" C THR B 24 " pdb=" O THR B 24 " ideal model delta sigma weight residual 122.36 117.61 4.75 1.21e+00 6.83e-01 1.54e+01 angle pdb=" PA ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PB ADP A 902 " ideal model delta sigma weight residual 120.50 131.99 -11.49 3.00e+00 1.11e-01 1.47e+01 angle pdb=" CA ARG C 235 " pdb=" C ARG C 235 " pdb=" O ARG C 235 " ideal model delta sigma weight residual 120.42 117.03 3.39 1.06e+00 8.90e-01 1.02e+01 angle pdb=" C2' ADP A 902 " pdb=" C3' ADP A 902 " pdb=" C4' ADP A 902 " ideal model delta sigma weight residual 111.00 101.49 9.51 3.00e+00 1.11e-01 1.01e+01 ... (remaining 47646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 21521 34.25 - 68.50: 242 68.50 - 102.75: 14 102.75 - 137.00: 9 137.00 - 171.26: 2 Dihedral angle restraints: 21788 sinusoidal: 9108 harmonic: 12680 Sorted by residual: dihedral pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " pdb=" O2A ADP E 902 " ideal model delta sinusoidal sigma weight residual -60.00 111.26 -171.26 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2' ADP C 901 " pdb=" C1' ADP C 901 " pdb=" N9 ADP C 901 " pdb=" C4 ADP C 901 " ideal model delta sinusoidal sigma weight residual 91.55 -120.81 -147.64 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" C2' ADP A 902 " pdb=" C1' ADP A 902 " pdb=" N9 ADP A 902 " pdb=" C4 ADP A 902 " ideal model delta sinusoidal sigma weight residual 91.55 -132.68 -135.77 1 2.00e+01 2.50e-03 4.12e+01 ... (remaining 21785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4829 0.070 - 0.139: 509 0.139 - 0.209: 10 0.209 - 0.278: 7 0.278 - 0.348: 9 Chirality restraints: 5364 Sorted by residual: chirality pdb=" CA ASN G 510 " pdb=" N ASN G 510 " pdb=" C ASN G 510 " pdb=" CB ASN G 510 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C2' ATP E 901 " pdb=" C1' ATP E 901 " pdb=" C3' ATP E 901 " pdb=" O2' ATP E 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2' ATP B 901 " pdb=" C1' ATP B 901 " pdb=" C3' ATP B 901 " pdb=" O2' ATP B 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 5361 not shown) Planarity restraints: 6206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 505 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO E 506 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 506 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 506 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 234 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C LEU C 234 " 0.025 2.00e-02 2.50e+03 pdb=" O LEU C 234 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG C 235 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 554 " -0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO B 555 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 555 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 555 " -0.020 5.00e-02 4.00e+02 ... (remaining 6203 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 10 2.05 - 2.76: 6158 2.76 - 3.47: 52176 3.47 - 4.19: 76605 4.19 - 4.90: 141087 Nonbonded interactions: 276036 Sorted by model distance: nonbonded pdb=" NZ LYS J 148 " pdb=" C GLY K 276 " model vdw 1.335 3.350 nonbonded pdb=" NZ LYS K 248 " pdb=" C GLY L 376 " model vdw 1.353 3.350 nonbonded pdb=" O ILE G 167 " pdb=" OG SER G 171 " model vdw 1.958 2.440 nonbonded pdb=" OG1 THR E 262 " pdb=" O3G ATP E 901 " model vdw 1.963 2.440 nonbonded pdb=" OG1 THR B 262 " pdb=" O3G ATP B 901 " model vdw 1.977 2.440 ... (remaining 276031 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 786 or resid 902)) selection = (chain 'C' and (resid 33 through 786 or resid 902)) } ncs_group { reference = (chain 'B' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'D' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'E' and (resid 208 through 787 or resid 901 through 902)) selection = (chain 'F' and (resid 208 through 787 or resid 901 through 902)) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 201 through 273) selection = (chain 'L' and resid 301 through 373) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.220 Check model and map are aligned: 0.560 Set scattering table: 0.340 Process input model: 96.150 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 35219 Z= 0.187 Angle : 0.527 11.489 47651 Z= 0.250 Chirality : 0.043 0.348 5364 Planarity : 0.003 0.040 6206 Dihedral : 11.089 171.256 13578 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.97 % Favored : 95.01 % Rotamer: Outliers : 1.34 % Allowed : 4.62 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.14), residues: 4330 helix: 2.38 (0.12), residues: 2065 sheet: -0.13 (0.21), residues: 615 loop : 0.32 (0.17), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 561 HIS 0.002 0.001 HIS G 528 PHE 0.009 0.001 PHE G 527 TYR 0.010 0.001 TYR B 254 ARG 0.002 0.000 ARG K 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 492 time to evaluate : 3.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 TYR cc_start: 0.6902 (m-80) cc_final: 0.6682 (m-10) REVERT: A 161 HIS cc_start: 0.6251 (m90) cc_final: 0.5967 (m-70) REVERT: A 173 PHE cc_start: 0.7196 (m-80) cc_final: 0.6187 (m-80) REVERT: A 223 MET cc_start: 0.8727 (mmm) cc_final: 0.8389 (mmm) REVERT: A 283 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 302 GLU cc_start: 0.8854 (tt0) cc_final: 0.8651 (mt-10) REVERT: B 283 GLU cc_start: 0.7317 (tt0) cc_final: 0.7109 (tt0) REVERT: B 504 GLU cc_start: 0.8652 (tt0) cc_final: 0.8266 (mm-30) REVERT: B 571 ASP cc_start: 0.8347 (t0) cc_final: 0.8073 (t0) REVERT: C 345 MET cc_start: 0.8054 (ptp) cc_final: 0.7749 (ptt) REVERT: C 571 ASP cc_start: 0.8588 (t0) cc_final: 0.8377 (t0) REVERT: D 301 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7552 (tm-30) REVERT: D 493 ASP cc_start: 0.8206 (m-30) cc_final: 0.7606 (t70) REVERT: D 522 LYS cc_start: 0.8471 (tttt) cc_final: 0.8214 (tptm) REVERT: D 628 PHE cc_start: 0.8315 (m-80) cc_final: 0.7968 (m-10) REVERT: E 315 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8438 (mt-10) REVERT: E 346 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7750 (ptmt) REVERT: E 440 ILE cc_start: 0.7487 (mt) cc_final: 0.7285 (tt) REVERT: F 253 MET cc_start: 0.8321 (mtp) cc_final: 0.7871 (mtp) REVERT: F 323 ARG cc_start: 0.7778 (tpp-160) cc_final: 0.6789 (tpt90) REVERT: F 346 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7860 (mmtt) REVERT: F 437 MET cc_start: 0.7998 (tmm) cc_final: 0.7599 (tpp) REVERT: F 560 MET cc_start: 0.8073 (mtt) cc_final: 0.7848 (mtt) REVERT: G 138 LYS cc_start: 0.9156 (ptmm) cc_final: 0.8934 (pttm) REVERT: G 142 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8466 (pmm-80) REVERT: G 257 MET cc_start: 0.8445 (mmp) cc_final: 0.7569 (mmp) REVERT: G 378 SER cc_start: 0.7703 (m) cc_final: 0.7310 (t) REVERT: G 406 GLU cc_start: 0.8338 (tt0) cc_final: 0.8060 (tt0) outliers start: 50 outliers final: 11 residues processed: 529 average time/residue: 0.5279 time to fit residues: 431.9287 Evaluate side-chains 312 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 298 time to evaluate : 4.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 638 GLN Chi-restraints excluded: chain D residue 249 ARG Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 572 LEU Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 366 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 340 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 206 optimal weight: 0.1980 chunk 253 optimal weight: 6.9990 chunk 394 optimal weight: 5.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 HIS C 432 GLN C 548 ASN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 305 ASN G 361 HIS ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 35219 Z= 0.342 Angle : 0.629 8.248 47651 Z= 0.308 Chirality : 0.044 0.158 5364 Planarity : 0.004 0.052 6206 Dihedral : 9.854 175.401 5024 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.80 % Rotamer: Outliers : 1.93 % Allowed : 8.08 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.13), residues: 4330 helix: 1.94 (0.12), residues: 2070 sheet: -0.12 (0.21), residues: 613 loop : 0.19 (0.17), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 486 HIS 0.013 0.001 HIS C 719 PHE 0.018 0.002 PHE D 275 TYR 0.021 0.002 TYR G 439 ARG 0.009 0.001 ARG D 348 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 299 time to evaluate : 3.990 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 158 LYS cc_start: 0.8073 (tptp) cc_final: 0.7831 (tppt) REVERT: A 161 HIS cc_start: 0.6194 (m90) cc_final: 0.5964 (m-70) REVERT: A 173 PHE cc_start: 0.7360 (m-80) cc_final: 0.6525 (m-80) REVERT: A 283 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7897 (tm-30) REVERT: A 331 GLU cc_start: 0.7430 (pm20) cc_final: 0.7192 (pm20) REVERT: A 440 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7213 (mm) REVERT: B 283 GLU cc_start: 0.7510 (tt0) cc_final: 0.7292 (tt0) REVERT: B 571 ASP cc_start: 0.8534 (t0) cc_final: 0.8178 (t0) REVERT: B 621 MET cc_start: 0.8554 (tpp) cc_final: 0.8350 (tpp) REVERT: C 56 MET cc_start: 0.6154 (ptt) cc_final: 0.5690 (tmm) REVERT: C 215 ASP cc_start: 0.8924 (t0) cc_final: 0.8676 (t0) REVERT: C 571 ASP cc_start: 0.8776 (t0) cc_final: 0.8408 (t0) REVERT: D 208 MET cc_start: 0.6197 (tpp) cc_final: 0.5069 (tpt) REVERT: D 285 MET cc_start: 0.9011 (mmm) cc_final: 0.8539 (mmm) REVERT: D 301 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7774 (tm-30) REVERT: D 427 GLU cc_start: 0.8828 (tp30) cc_final: 0.8393 (tt0) REVERT: D 522 LYS cc_start: 0.8402 (tttt) cc_final: 0.8044 (tptm) REVERT: D 628 PHE cc_start: 0.8230 (m-80) cc_final: 0.7927 (m-10) REVERT: E 346 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7663 (ptmm) REVERT: E 699 TYR cc_start: 0.8577 (t80) cc_final: 0.8038 (t80) REVERT: F 323 ARG cc_start: 0.7844 (tpp-160) cc_final: 0.6917 (tpt90) REVERT: F 346 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7635 (mmtt) REVERT: F 560 MET cc_start: 0.8156 (mtt) cc_final: 0.7944 (mtt) REVERT: G 142 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8461 (ptt-90) REVERT: G 233 MET cc_start: 0.8966 (mmm) cc_final: 0.8710 (mmm) REVERT: G 257 MET cc_start: 0.8471 (mmp) cc_final: 0.7650 (mmp) REVERT: G 378 SER cc_start: 0.7913 (m) cc_final: 0.7558 (t) REVERT: G 406 GLU cc_start: 0.8376 (tt0) cc_final: 0.7995 (tm-30) REVERT: G 422 MET cc_start: 0.8626 (mmt) cc_final: 0.8197 (mmt) REVERT: G 440 MET cc_start: 0.8352 (ttm) cc_final: 0.7862 (mtp) REVERT: H 252 ARG cc_start: 0.5983 (mmt-90) cc_final: 0.4909 (mtm110) outliers start: 72 outliers final: 41 residues processed: 356 average time/residue: 0.4703 time to fit residues: 273.0160 Evaluate side-chains 307 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 262 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 626 ASN Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 472 ASN Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 506 LYS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 548 ILE Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 301 MET Chi-restraints excluded: chain L residue 344 ILE Chi-restraints excluded: chain L residue 354 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 219 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 328 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 394 optimal weight: 4.9990 chunk 426 optimal weight: 4.9990 chunk 351 optimal weight: 6.9990 chunk 391 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 316 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 313 GLN G 362 GLN ** G 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 35219 Z= 0.447 Angle : 0.677 10.083 47651 Z= 0.337 Chirality : 0.045 0.159 5364 Planarity : 0.005 0.064 6206 Dihedral : 9.559 161.728 5012 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.80 % Favored : 94.16 % Rotamer: Outliers : 2.74 % Allowed : 9.91 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.13), residues: 4330 helix: 1.44 (0.12), residues: 2073 sheet: -0.31 (0.21), residues: 622 loop : -0.08 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 486 HIS 0.014 0.001 HIS C 719 PHE 0.022 0.002 PHE D 275 TYR 0.023 0.002 TYR G 439 ARG 0.005 0.001 ARG G 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 264 time to evaluate : 3.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 HIS cc_start: 0.6324 (m90) cc_final: 0.6058 (m-70) REVERT: A 173 PHE cc_start: 0.7258 (m-80) cc_final: 0.6566 (m-80) REVERT: A 283 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7883 (tm-30) REVERT: A 437 MET cc_start: 0.7838 (tmm) cc_final: 0.7553 (tpt) REVERT: A 440 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7198 (mm) REVERT: B 571 ASP cc_start: 0.8600 (t0) cc_final: 0.8228 (t0) REVERT: B 621 MET cc_start: 0.8915 (tpp) cc_final: 0.8414 (tpp) REVERT: B 762 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.6949 (tmm) REVERT: C 56 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5781 (tmm) REVERT: C 215 ASP cc_start: 0.9037 (t0) cc_final: 0.8736 (t0) REVERT: C 437 MET cc_start: 0.8350 (tpp) cc_final: 0.8112 (tpp) REVERT: C 571 ASP cc_start: 0.8874 (t0) cc_final: 0.8455 (t0) REVERT: D 522 LYS cc_start: 0.8528 (tttt) cc_final: 0.8080 (tptm) REVERT: D 615 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8987 (mm) REVERT: D 628 PHE cc_start: 0.8297 (m-80) cc_final: 0.8021 (m-10) REVERT: E 331 GLU cc_start: 0.8663 (mp0) cc_final: 0.8409 (mp0) REVERT: E 332 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8240 (ttm-80) REVERT: E 346 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7663 (ptmm) REVERT: E 489 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7950 (p) REVERT: E 497 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8659 (mp0) REVERT: E 621 MET cc_start: 0.7274 (ppp) cc_final: 0.6978 (ppp) REVERT: E 699 TYR cc_start: 0.8601 (t80) cc_final: 0.8080 (t80) REVERT: F 430 MET cc_start: 0.9022 (tpp) cc_final: 0.8692 (tpp) REVERT: F 560 MET cc_start: 0.8179 (mtt) cc_final: 0.7941 (mtt) REVERT: F 588 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: G 257 MET cc_start: 0.8471 (mmp) cc_final: 0.7644 (mmp) REVERT: G 378 SER cc_start: 0.8371 (m) cc_final: 0.8041 (t) REVERT: G 406 GLU cc_start: 0.8457 (tt0) cc_final: 0.8164 (tm-30) REVERT: G 422 MET cc_start: 0.8604 (mmt) cc_final: 0.8190 (mmt) REVERT: J 140 GLN cc_start: 0.5311 (OUTLIER) cc_final: 0.5022 (pm20) outliers start: 102 outliers final: 61 residues processed: 341 average time/residue: 0.4365 time to fit residues: 250.6999 Evaluate side-chains 318 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 247 time to evaluate : 3.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 497 GLU Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 626 ASN Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 500 ASP Chi-restraints excluded: chain G residue 506 LYS Chi-restraints excluded: chain G residue 518 ASN Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 548 ILE Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain J residue 140 GLN Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 325 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 390 optimal weight: 0.8980 chunk 296 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 188 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 396 optimal weight: 4.9990 chunk 419 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 375 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN E 327 ASN G 289 GLN G 362 GLN ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 325 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 35219 Z= 0.159 Angle : 0.557 9.690 47651 Z= 0.267 Chirality : 0.042 0.215 5364 Planarity : 0.004 0.062 6206 Dihedral : 8.984 155.953 5008 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.55 % Favored : 95.43 % Rotamer: Outliers : 1.88 % Allowed : 11.20 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.13), residues: 4330 helix: 1.66 (0.12), residues: 2053 sheet: -0.06 (0.21), residues: 614 loop : 0.03 (0.16), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 486 HIS 0.014 0.001 HIS C 719 PHE 0.013 0.001 PHE H 300 TYR 0.018 0.001 TYR G 439 ARG 0.004 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 299 time to evaluate : 4.521 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 158 LYS cc_start: 0.8173 (tptp) cc_final: 0.7656 (tptt) REVERT: A 161 HIS cc_start: 0.6316 (m90) cc_final: 0.6109 (m-70) REVERT: A 173 PHE cc_start: 0.7350 (m-80) cc_final: 0.6608 (m-80) REVERT: A 283 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 331 GLU cc_start: 0.7399 (pm20) cc_final: 0.7193 (pm20) REVERT: A 437 MET cc_start: 0.7654 (tmm) cc_final: 0.7389 (tpt) REVERT: A 440 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7270 (mm) REVERT: B 259 THR cc_start: 0.9145 (p) cc_final: 0.8876 (t) REVERT: B 301 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7924 (tm-30) REVERT: B 571 ASP cc_start: 0.8512 (t0) cc_final: 0.8044 (t0) REVERT: B 621 MET cc_start: 0.8798 (tpp) cc_final: 0.8457 (tpp) REVERT: C 56 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5792 (tmm) REVERT: C 215 ASP cc_start: 0.8947 (t0) cc_final: 0.8704 (t0) REVERT: C 342 MET cc_start: 0.9283 (mmm) cc_final: 0.9062 (mmt) REVERT: C 437 MET cc_start: 0.8395 (tpp) cc_final: 0.8121 (tpp) REVERT: C 571 ASP cc_start: 0.8694 (t0) cc_final: 0.8318 (t0) REVERT: D 208 MET cc_start: 0.6302 (tpp) cc_final: 0.5021 (tpt) REVERT: D 304 GLU cc_start: 0.8254 (tp30) cc_final: 0.8035 (tp30) REVERT: D 522 LYS cc_start: 0.8560 (tttt) cc_final: 0.8056 (tptm) REVERT: D 628 PHE cc_start: 0.8201 (m-80) cc_final: 0.7980 (m-10) REVERT: E 346 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7406 (ptmm) REVERT: E 497 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8683 (mp0) REVERT: E 621 MET cc_start: 0.7229 (ppp) cc_final: 0.6877 (ppp) REVERT: E 699 TYR cc_start: 0.8506 (t80) cc_final: 0.7970 (t80) REVERT: F 323 ARG cc_start: 0.7792 (tpp-160) cc_final: 0.6754 (tpt90) REVERT: F 325 LYS cc_start: 0.7119 (tppt) cc_final: 0.6435 (mmmt) REVERT: F 430 MET cc_start: 0.8943 (tpp) cc_final: 0.8641 (tpp) REVERT: F 560 MET cc_start: 0.8187 (mtt) cc_final: 0.7948 (mtt) REVERT: F 588 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: G 257 MET cc_start: 0.8446 (mmp) cc_final: 0.7681 (mmp) REVERT: G 378 SER cc_start: 0.7874 (m) cc_final: 0.7602 (t) REVERT: G 406 GLU cc_start: 0.8402 (tt0) cc_final: 0.8187 (tm-30) REVERT: G 422 MET cc_start: 0.8626 (mmt) cc_final: 0.8230 (mmt) REVERT: J 136 ILE cc_start: 0.8053 (mm) cc_final: 0.7808 (tp) REVERT: L 351 GLU cc_start: 0.7446 (pm20) cc_final: 0.6851 (tp30) REVERT: L 352 ASP cc_start: 0.7243 (m-30) cc_final: 0.6873 (t0) outliers start: 70 outliers final: 35 residues processed: 354 average time/residue: 0.4419 time to fit residues: 262.7561 Evaluate side-chains 310 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 270 time to evaluate : 3.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 497 GLU Chi-restraints excluded: chain E residue 608 ASP Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 626 ASN Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 608 ASP Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 506 LYS Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 349 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 312 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 357 optimal weight: 7.9990 chunk 289 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 376 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 GLN ** C 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 468 ASN G 362 GLN H 249 ASN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 202 GLN ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 35219 Z= 0.438 Angle : 0.680 8.316 47651 Z= 0.337 Chirality : 0.045 0.190 5364 Planarity : 0.005 0.102 6206 Dihedral : 8.957 148.341 5004 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.86 % Rotamer: Outliers : 3.22 % Allowed : 11.79 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.13), residues: 4330 helix: 1.34 (0.12), residues: 2057 sheet: -0.36 (0.21), residues: 607 loop : -0.20 (0.16), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 486 HIS 0.016 0.001 HIS C 719 PHE 0.024 0.002 PHE D 275 TYR 0.022 0.002 TYR G 439 ARG 0.005 0.001 ARG C 717 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 255 time to evaluate : 3.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 PHE cc_start: 0.7151 (m-80) cc_final: 0.6649 (m-80) REVERT: A 283 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 437 MET cc_start: 0.7850 (tmm) cc_final: 0.7582 (tpt) REVERT: A 440 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7389 (mm) REVERT: A 784 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6409 (mpp) REVERT: B 331 GLU cc_start: 0.8248 (mp0) cc_final: 0.7962 (mt-10) REVERT: B 543 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8271 (p) REVERT: B 571 ASP cc_start: 0.8622 (t0) cc_final: 0.8176 (t0) REVERT: B 621 MET cc_start: 0.9059 (tpp) cc_final: 0.8486 (tpp) REVERT: C 56 MET cc_start: 0.6176 (OUTLIER) cc_final: 0.5921 (ptt) REVERT: C 215 ASP cc_start: 0.9026 (t0) cc_final: 0.8766 (t0) REVERT: C 342 MET cc_start: 0.9355 (mmm) cc_final: 0.9129 (mmt) REVERT: C 437 MET cc_start: 0.8445 (tpp) cc_final: 0.8229 (tpp) REVERT: C 571 ASP cc_start: 0.8879 (t0) cc_final: 0.8466 (t0) REVERT: D 283 GLU cc_start: 0.8338 (tt0) cc_final: 0.8057 (tt0) REVERT: D 285 MET cc_start: 0.8903 (tpp) cc_final: 0.8389 (tpp) REVERT: D 522 LYS cc_start: 0.8572 (tttt) cc_final: 0.8064 (tptm) REVERT: D 628 PHE cc_start: 0.8310 (m-80) cc_final: 0.8061 (m-10) REVERT: E 331 GLU cc_start: 0.8642 (mp0) cc_final: 0.8409 (mp0) REVERT: E 346 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7713 (ptmm) REVERT: E 497 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8699 (mp0) REVERT: E 621 MET cc_start: 0.7303 (ppp) cc_final: 0.6997 (ppp) REVERT: F 323 ARG cc_start: 0.7880 (tpp-160) cc_final: 0.7039 (tpt90) REVERT: F 325 LYS cc_start: 0.7244 (tppt) cc_final: 0.6550 (mmmt) REVERT: F 430 MET cc_start: 0.8985 (tpp) cc_final: 0.8632 (tpp) REVERT: F 560 MET cc_start: 0.8197 (mtt) cc_final: 0.7970 (mtt) REVERT: F 588 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: G 257 MET cc_start: 0.8473 (mmp) cc_final: 0.7473 (mmp) REVERT: G 406 GLU cc_start: 0.8428 (tt0) cc_final: 0.8216 (tm-30) REVERT: G 422 MET cc_start: 0.8586 (mmt) cc_final: 0.8200 (mmt) REVERT: H 238 MET cc_start: 0.8446 (ttm) cc_final: 0.8221 (tpp) outliers start: 120 outliers final: 77 residues processed: 350 average time/residue: 0.4479 time to fit residues: 264.5976 Evaluate side-chains 330 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 246 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 345 MET Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 497 GLU Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 617 GLU Chi-restraints excluded: chain E residue 626 ASN Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 608 ASP Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 506 LYS Chi-restraints excluded: chain G residue 518 ASN Chi-restraints excluded: chain G residue 548 ILE Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 258 ASP Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 325 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 141 optimal weight: 4.9990 chunk 377 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 246 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 419 optimal weight: 4.9990 chunk 348 optimal weight: 0.6980 chunk 194 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 138 optimal weight: 8.9990 chunk 220 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN C 638 GLN ** C 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 GLN G 362 GLN ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 GLN K 202 GLN ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35219 Z= 0.160 Angle : 0.563 10.305 47651 Z= 0.270 Chirality : 0.042 0.202 5364 Planarity : 0.004 0.065 6206 Dihedral : 8.526 146.190 5002 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.18 % Favored : 95.80 % Rotamer: Outliers : 2.01 % Allowed : 13.24 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.13), residues: 4330 helix: 1.54 (0.12), residues: 2059 sheet: -0.16 (0.21), residues: 617 loop : -0.07 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 486 HIS 0.012 0.001 HIS A 161 PHE 0.015 0.001 PHE H 300 TYR 0.017 0.001 TYR B 752 ARG 0.011 0.000 ARG B 323 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 279 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 PHE cc_start: 0.7214 (m-80) cc_final: 0.6944 (m-80) REVERT: A 223 MET cc_start: 0.8836 (mmm) cc_final: 0.8225 (mmm) REVERT: A 283 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7851 (tm-30) REVERT: A 437 MET cc_start: 0.7804 (tmm) cc_final: 0.7538 (tmm) REVERT: A 784 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6246 (mpp) REVERT: B 223 MET cc_start: 0.8927 (mmm) cc_final: 0.8725 (tpt) REVERT: B 301 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7889 (tm-30) REVERT: B 389 GLU cc_start: 0.8665 (tt0) cc_final: 0.8463 (tt0) REVERT: B 571 ASP cc_start: 0.8522 (t0) cc_final: 0.8077 (t0) REVERT: B 621 MET cc_start: 0.8931 (tpp) cc_final: 0.8568 (tpp) REVERT: C 56 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5960 (ptt) REVERT: C 215 ASP cc_start: 0.8963 (t0) cc_final: 0.8695 (t0) REVERT: C 342 MET cc_start: 0.9295 (mmm) cc_final: 0.9075 (mmm) REVERT: C 437 MET cc_start: 0.8447 (tpp) cc_final: 0.8216 (tpp) REVERT: C 571 ASP cc_start: 0.8700 (t0) cc_final: 0.8282 (t0) REVERT: D 208 MET cc_start: 0.6344 (tpp) cc_final: 0.4920 (tpt) REVERT: D 522 LYS cc_start: 0.8577 (tttt) cc_final: 0.8019 (tptm) REVERT: D 628 PHE cc_start: 0.8199 (m-80) cc_final: 0.7976 (m-10) REVERT: E 346 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7614 (ptmt) REVERT: E 497 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8742 (mp0) REVERT: E 621 MET cc_start: 0.7272 (ppp) cc_final: 0.6973 (ppp) REVERT: F 323 ARG cc_start: 0.7803 (tpp-160) cc_final: 0.6777 (tpt90) REVERT: F 325 LYS cc_start: 0.7192 (tppt) cc_final: 0.6858 (mtmt) REVERT: F 430 MET cc_start: 0.8889 (tpp) cc_final: 0.8587 (tpp) REVERT: F 560 MET cc_start: 0.8148 (mtt) cc_final: 0.7933 (mtt) REVERT: F 588 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: G 233 MET cc_start: 0.9163 (mmm) cc_final: 0.8884 (mmm) REVERT: G 257 MET cc_start: 0.8450 (mmp) cc_final: 0.7673 (mmp) REVERT: G 352 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8278 (p) REVERT: G 370 LYS cc_start: 0.9012 (ttpt) cc_final: 0.8771 (ttmt) REVERT: G 378 SER cc_start: 0.7909 (m) cc_final: 0.7496 (t) REVERT: G 406 GLU cc_start: 0.8355 (tt0) cc_final: 0.8073 (tm-30) REVERT: L 348 LYS cc_start: 0.6700 (mmmt) cc_final: 0.5940 (mttp) REVERT: L 351 GLU cc_start: 0.7507 (pm20) cc_final: 0.6938 (tp30) outliers start: 75 outliers final: 46 residues processed: 340 average time/residue: 0.4350 time to fit residues: 249.3215 Evaluate side-chains 313 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 261 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 661 ASN Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 497 GLU Chi-restraints excluded: chain E residue 626 ASN Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 608 ASP Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 506 LYS Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 140 GLN Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 404 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 306 optimal weight: 4.9990 chunk 237 optimal weight: 0.7980 chunk 353 optimal weight: 7.9990 chunk 234 optimal weight: 0.7980 chunk 418 optimal weight: 0.0040 chunk 261 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN ** C 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 GLN G 305 ASN ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 GLN ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35219 Z= 0.189 Angle : 0.561 9.976 47651 Z= 0.268 Chirality : 0.041 0.151 5364 Planarity : 0.004 0.063 6206 Dihedral : 8.292 143.349 4999 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.78 % Favored : 95.20 % Rotamer: Outliers : 1.91 % Allowed : 13.99 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.13), residues: 4330 helix: 1.58 (0.12), residues: 2072 sheet: -0.10 (0.21), residues: 613 loop : -0.06 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 486 HIS 0.008 0.001 HIS C 719 PHE 0.012 0.001 PHE D 275 TYR 0.014 0.001 TYR G 439 ARG 0.004 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 268 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8098 (tppt) cc_final: 0.7773 (mmtt) REVERT: A 173 PHE cc_start: 0.7226 (m-80) cc_final: 0.7019 (m-80) REVERT: A 223 MET cc_start: 0.8888 (mmm) cc_final: 0.8292 (mmm) REVERT: A 283 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 437 MET cc_start: 0.7835 (tmm) cc_final: 0.7578 (tmm) REVERT: B 223 MET cc_start: 0.8924 (mmm) cc_final: 0.8662 (tpt) REVERT: B 301 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7887 (tm-30) REVERT: B 389 GLU cc_start: 0.8728 (tt0) cc_final: 0.8507 (tt0) REVERT: B 571 ASP cc_start: 0.8539 (t0) cc_final: 0.8101 (t0) REVERT: B 621 MET cc_start: 0.8916 (tpp) cc_final: 0.8553 (tpp) REVERT: C 56 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5949 (ptt) REVERT: C 215 ASP cc_start: 0.8968 (t0) cc_final: 0.8698 (t0) REVERT: C 342 MET cc_start: 0.9277 (mmm) cc_final: 0.9066 (mmm) REVERT: C 437 MET cc_start: 0.8423 (tpp) cc_final: 0.8173 (tpp) REVERT: C 571 ASP cc_start: 0.8663 (t0) cc_final: 0.8273 (t0) REVERT: D 208 MET cc_start: 0.6525 (tpp) cc_final: 0.5256 (tpt) REVERT: D 522 LYS cc_start: 0.8613 (tttt) cc_final: 0.8025 (tptm) REVERT: D 628 PHE cc_start: 0.8203 (m-80) cc_final: 0.7971 (m-10) REVERT: E 331 GLU cc_start: 0.8606 (mp0) cc_final: 0.8381 (mp0) REVERT: E 497 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8740 (mp0) REVERT: E 621 MET cc_start: 0.7413 (ppp) cc_final: 0.7162 (ppp) REVERT: F 253 MET cc_start: 0.8459 (mtp) cc_final: 0.8162 (mtp) REVERT: F 323 ARG cc_start: 0.7780 (tpp-160) cc_final: 0.6893 (tpt90) REVERT: F 325 LYS cc_start: 0.7188 (tppt) cc_final: 0.6779 (mtmt) REVERT: F 430 MET cc_start: 0.8872 (tpp) cc_final: 0.8561 (tpp) REVERT: F 560 MET cc_start: 0.8175 (mtt) cc_final: 0.7959 (mtt) REVERT: F 588 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7425 (pm20) REVERT: G 233 MET cc_start: 0.9118 (mmm) cc_final: 0.8861 (mmm) REVERT: G 257 MET cc_start: 0.8443 (mmp) cc_final: 0.7639 (mmp) REVERT: G 352 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8316 (p) REVERT: G 370 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8806 (ttmt) REVERT: G 378 SER cc_start: 0.7978 (m) cc_final: 0.7586 (t) REVERT: G 406 GLU cc_start: 0.8343 (tt0) cc_final: 0.8055 (tm-30) REVERT: J 130 ILE cc_start: 0.8430 (mt) cc_final: 0.8033 (pt) REVERT: L 348 LYS cc_start: 0.6842 (mmmt) cc_final: 0.6071 (mttp) REVERT: L 351 GLU cc_start: 0.7490 (pm20) cc_final: 0.6919 (tp30) outliers start: 71 outliers final: 56 residues processed: 325 average time/residue: 0.4113 time to fit residues: 226.1475 Evaluate side-chains 318 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 258 time to evaluate : 3.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 661 ASN Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 497 GLU Chi-restraints excluded: chain E residue 626 ASN Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 608 ASP Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 506 LYS Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 140 GLN Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 258 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 249 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 265 optimal weight: 0.0370 chunk 284 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 328 optimal weight: 3.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 GLN ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 GLN ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35219 Z= 0.228 Angle : 0.577 11.302 47651 Z= 0.276 Chirality : 0.042 0.281 5364 Planarity : 0.004 0.063 6206 Dihedral : 8.197 141.656 4995 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.94 % Favored : 95.03 % Rotamer: Outliers : 2.09 % Allowed : 13.86 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.13), residues: 4330 helix: 1.58 (0.12), residues: 2072 sheet: -0.12 (0.21), residues: 614 loop : -0.08 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 486 HIS 0.006 0.001 HIS C 719 PHE 0.014 0.001 PHE D 275 TYR 0.015 0.001 TYR G 439 ARG 0.003 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 265 time to evaluate : 4.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 437 MET cc_start: 0.7857 (tmm) cc_final: 0.7592 (tmm) REVERT: B 223 MET cc_start: 0.8945 (mmm) cc_final: 0.8664 (tpt) REVERT: B 301 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7921 (tm-30) REVERT: B 389 GLU cc_start: 0.8728 (tt0) cc_final: 0.8458 (tt0) REVERT: B 543 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8160 (p) REVERT: B 571 ASP cc_start: 0.8561 (t0) cc_final: 0.8088 (t0) REVERT: B 621 MET cc_start: 0.8953 (tpp) cc_final: 0.8598 (tpp) REVERT: C 56 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5887 (ptt) REVERT: C 215 ASP cc_start: 0.8989 (t0) cc_final: 0.8718 (t0) REVERT: C 342 MET cc_start: 0.9291 (mmm) cc_final: 0.9074 (mmm) REVERT: C 398 MET cc_start: 0.9295 (mmt) cc_final: 0.9007 (mmt) REVERT: C 571 ASP cc_start: 0.8696 (t0) cc_final: 0.8270 (t0) REVERT: D 208 MET cc_start: 0.6301 (tpp) cc_final: 0.5075 (tpt) REVERT: D 522 LYS cc_start: 0.8632 (tttt) cc_final: 0.8025 (tptm) REVERT: D 628 PHE cc_start: 0.8215 (m-80) cc_final: 0.7982 (m-10) REVERT: E 497 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8729 (mp0) REVERT: E 621 MET cc_start: 0.7421 (ppp) cc_final: 0.7167 (ppp) REVERT: F 253 MET cc_start: 0.8476 (mtp) cc_final: 0.8236 (mtp) REVERT: F 323 ARG cc_start: 0.7727 (tpp-160) cc_final: 0.6854 (tpt90) REVERT: F 325 LYS cc_start: 0.7180 (tppt) cc_final: 0.6794 (mtmt) REVERT: F 430 MET cc_start: 0.8889 (tpp) cc_final: 0.8565 (tpp) REVERT: F 560 MET cc_start: 0.8172 (mtt) cc_final: 0.7969 (mtt) REVERT: F 588 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7410 (pm20) REVERT: G 233 MET cc_start: 0.9071 (mmm) cc_final: 0.8812 (mmm) REVERT: G 257 MET cc_start: 0.8459 (mmp) cc_final: 0.7628 (mmp) REVERT: G 352 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8386 (p) REVERT: G 378 SER cc_start: 0.8078 (m) cc_final: 0.7696 (t) REVERT: G 406 GLU cc_start: 0.8319 (tt0) cc_final: 0.8049 (tm-30) REVERT: J 130 ILE cc_start: 0.8393 (mt) cc_final: 0.7976 (pt) REVERT: L 348 LYS cc_start: 0.6850 (mmmt) cc_final: 0.6075 (mttp) REVERT: L 351 GLU cc_start: 0.7455 (pm20) cc_final: 0.6887 (tp30) outliers start: 78 outliers final: 64 residues processed: 329 average time/residue: 0.4297 time to fit residues: 240.3435 Evaluate side-chains 323 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 254 time to evaluate : 4.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 661 ASN Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 497 GLU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 626 ASN Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 608 ASP Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 506 LYS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 140 GLN Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 339 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 380 optimal weight: 2.9990 chunk 400 optimal weight: 0.9990 chunk 365 optimal weight: 0.5980 chunk 389 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 306 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 352 optimal weight: 5.9990 chunk 368 optimal weight: 2.9990 chunk 388 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 GLN ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35219 Z= 0.244 Angle : 0.595 12.424 47651 Z= 0.283 Chirality : 0.042 0.254 5364 Planarity : 0.004 0.064 6206 Dihedral : 8.152 140.737 4995 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.17 % Favored : 94.80 % Rotamer: Outliers : 2.26 % Allowed : 14.02 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.13), residues: 4330 helix: 1.57 (0.12), residues: 2071 sheet: -0.12 (0.21), residues: 613 loop : -0.09 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 486 HIS 0.006 0.001 HIS C 719 PHE 0.014 0.001 PHE D 275 TYR 0.015 0.001 TYR G 439 ARG 0.003 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 256 time to evaluate : 4.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8078 (tppt) cc_final: 0.7760 (mmtt) REVERT: A 283 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7891 (tm-30) REVERT: A 437 MET cc_start: 0.7861 (tmm) cc_final: 0.7604 (tmm) REVERT: A 784 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6241 (mpp) REVERT: B 223 MET cc_start: 0.8959 (mmm) cc_final: 0.8658 (tpt) REVERT: B 301 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7938 (tm-30) REVERT: B 389 GLU cc_start: 0.8727 (tt0) cc_final: 0.8424 (tt0) REVERT: B 543 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8152 (p) REVERT: B 571 ASP cc_start: 0.8569 (t0) cc_final: 0.8098 (t0) REVERT: B 621 MET cc_start: 0.8972 (tpp) cc_final: 0.8574 (tpp) REVERT: C 56 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5872 (ptt) REVERT: C 215 ASP cc_start: 0.8998 (t0) cc_final: 0.8735 (t0) REVERT: C 342 MET cc_start: 0.9298 (mmm) cc_final: 0.9081 (mmt) REVERT: C 398 MET cc_start: 0.9297 (mmt) cc_final: 0.9012 (mmt) REVERT: C 571 ASP cc_start: 0.8700 (t0) cc_final: 0.8265 (t0) REVERT: D 208 MET cc_start: 0.6389 (tpp) cc_final: 0.5255 (tpt) REVERT: D 522 LYS cc_start: 0.8647 (tttt) cc_final: 0.8027 (tptm) REVERT: D 628 PHE cc_start: 0.8220 (m-80) cc_final: 0.7988 (m-10) REVERT: E 455 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8215 (mt) REVERT: E 497 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8732 (mp0) REVERT: E 621 MET cc_start: 0.7540 (ppp) cc_final: 0.7266 (ppp) REVERT: F 253 MET cc_start: 0.8445 (mtp) cc_final: 0.8183 (mtp) REVERT: F 323 ARG cc_start: 0.7734 (tpp-160) cc_final: 0.6857 (tpt90) REVERT: F 325 LYS cc_start: 0.7181 (tppt) cc_final: 0.6806 (mtmt) REVERT: F 430 MET cc_start: 0.8878 (tpp) cc_final: 0.8556 (tpp) REVERT: F 588 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: G 257 MET cc_start: 0.8461 (mmp) cc_final: 0.7627 (mmp) REVERT: G 352 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8415 (p) REVERT: G 367 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8762 (p0) REVERT: G 378 SER cc_start: 0.8083 (m) cc_final: 0.7503 (t) REVERT: G 406 GLU cc_start: 0.8300 (tt0) cc_final: 0.8046 (tm-30) REVERT: J 130 ILE cc_start: 0.8414 (mt) cc_final: 0.8001 (pt) REVERT: K 204 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: L 348 LYS cc_start: 0.6897 (mmmt) cc_final: 0.6104 (mttp) REVERT: L 351 GLU cc_start: 0.7479 (pm20) cc_final: 0.6964 (tp30) outliers start: 84 outliers final: 68 residues processed: 321 average time/residue: 0.4189 time to fit residues: 229.2702 Evaluate side-chains 330 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 253 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 661 ASN Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 497 GLU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 626 ASN Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 608 ASP Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 506 LYS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 140 GLN Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 204 PHE Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain L residue 339 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 255 optimal weight: 6.9990 chunk 412 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 286 optimal weight: 0.0000 chunk 432 optimal weight: 6.9990 chunk 397 optimal weight: 0.0060 chunk 344 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 265 optimal weight: 0.0980 chunk 211 optimal weight: 0.8980 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 GLN ** K 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 35219 Z= 0.142 Angle : 0.571 11.815 47651 Z= 0.269 Chirality : 0.041 0.263 5364 Planarity : 0.004 0.062 6206 Dihedral : 7.955 138.124 4995 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.30 % Favored : 95.68 % Rotamer: Outliers : 1.64 % Allowed : 14.82 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.13), residues: 4330 helix: 1.69 (0.12), residues: 2060 sheet: 0.06 (0.21), residues: 624 loop : 0.06 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 486 HIS 0.006 0.001 HIS C 719 PHE 0.014 0.001 PHE B 312 TYR 0.014 0.001 TYR G 439 ARG 0.012 0.000 ARG G 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8660 Ramachandran restraints generated. 4330 Oldfield, 0 Emsley, 4330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 276 time to evaluate : 4.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8048 (tppt) cc_final: 0.7764 (mmtt) REVERT: A 283 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7827 (tm-30) REVERT: A 412 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8207 (tm-30) REVERT: A 784 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.6098 (mpp) REVERT: B 223 MET cc_start: 0.8982 (mmm) cc_final: 0.8689 (tpt) REVERT: B 301 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7886 (tm-30) REVERT: B 359 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7947 (ttm-80) REVERT: B 398 MET cc_start: 0.9043 (pmm) cc_final: 0.8757 (mtm) REVERT: B 571 ASP cc_start: 0.8497 (t0) cc_final: 0.8004 (t0) REVERT: B 621 MET cc_start: 0.8908 (tpp) cc_final: 0.8349 (tpp) REVERT: C 215 ASP cc_start: 0.8930 (t0) cc_final: 0.8696 (t0) REVERT: C 342 MET cc_start: 0.9258 (mmm) cc_final: 0.9018 (mmm) REVERT: C 398 MET cc_start: 0.9285 (mmt) cc_final: 0.9059 (mmt) REVERT: C 571 ASP cc_start: 0.8601 (t0) cc_final: 0.8185 (t0) REVERT: D 208 MET cc_start: 0.6291 (tpp) cc_final: 0.5159 (tpt) REVERT: D 345 MET cc_start: 0.8120 (tmm) cc_final: 0.7820 (tmm) REVERT: D 522 LYS cc_start: 0.8653 (tttt) cc_final: 0.8041 (tptm) REVERT: D 628 PHE cc_start: 0.8137 (m-80) cc_final: 0.7912 (m-10) REVERT: E 223 MET cc_start: 0.8744 (mmm) cc_final: 0.8135 (mtp) REVERT: E 455 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8217 (mt) REVERT: E 497 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8716 (mp0) REVERT: E 621 MET cc_start: 0.7511 (ppp) cc_final: 0.7234 (ppp) REVERT: F 253 MET cc_start: 0.8338 (mtp) cc_final: 0.7929 (mtp) REVERT: F 323 ARG cc_start: 0.7748 (tpp-160) cc_final: 0.6834 (tpt90) REVERT: F 430 MET cc_start: 0.8773 (tpp) cc_final: 0.8475 (tpp) REVERT: F 588 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: G 205 HIS cc_start: 0.6157 (OUTLIER) cc_final: 0.5875 (m90) REVERT: G 233 MET cc_start: 0.9054 (mmm) cc_final: 0.8733 (mmm) REVERT: G 257 MET cc_start: 0.8441 (mmp) cc_final: 0.7664 (mmp) REVERT: G 352 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8230 (p) REVERT: G 378 SER cc_start: 0.7767 (m) cc_final: 0.7432 (t) REVERT: G 406 GLU cc_start: 0.8262 (tt0) cc_final: 0.8016 (tm-30) REVERT: L 348 LYS cc_start: 0.6601 (mmmt) cc_final: 0.5935 (mtmt) REVERT: L 349 GLN cc_start: 0.6959 (pp30) cc_final: 0.6753 (pp30) REVERT: L 351 GLU cc_start: 0.7409 (pm20) cc_final: 0.6771 (tp30) outliers start: 61 outliers final: 47 residues processed: 325 average time/residue: 0.4524 time to fit residues: 250.3842 Evaluate side-chains 309 residues out of total 3724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 255 time to evaluate : 3.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 497 GLU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 626 ASN Chi-restraints excluded: chain E residue 769 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain F residue 588 GLU Chi-restraints excluded: chain F residue 608 ASP Chi-restraints excluded: chain F residue 769 VAL Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 485 THR Chi-restraints excluded: chain G residue 506 LYS Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 140 GLN Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 215 LEU Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 273 optimal weight: 9.9990 chunk 366 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 317 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 344 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 354 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 GLN ** K 241 GLN ** 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 = 0.3671 r_free = 0.3671 target = 0.101079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.079571 restraints weight = 107072.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.079739 restraints weight = 58898.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.081086 restraints weight = 47876.635| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35219 Z= 0.229 Angle : 0.596 12.204 47651 Z= 0.282 Chirality : 0.042 0.250 5364 Planarity : 0.004 0.059 6206 Dihedral : 7.963 137.629 4995 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.99 % Favored : 94.99 % Rotamer: Outliers : 1.88 % Allowed : 14.82 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.13), residues: 4330 helix: 1.66 (0.12), residues: 2071 sheet: -0.01 (0.21), residues: 614 loop : -0.01 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 486 HIS 0.003 0.001 HIS G 468 PHE 0.020 0.001 PHE G 509 TYR 0.014 0.001 TYR G 439 ARG 0.004 0.000 ARG G 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6505.62 seconds wall clock time: 119 minutes 47.43 seconds (7187.43 seconds total)