Starting phenix.real_space_refine on Tue Sep 24 16:01:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7m_37343/09_2024/8w7m_37343_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7m_37343/09_2024/8w7m_37343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7m_37343/09_2024/8w7m_37343.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7m_37343/09_2024/8w7m_37343.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7m_37343/09_2024/8w7m_37343_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7m_37343/09_2024/8w7m_37343_neut.cif" } resolution = 4.12 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= 0.009 sd= 0.056 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: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 18 5.49 5 Mg 4 5.21 5 S 229 5.16 5 C 32459 2.51 5 N 8757 2.21 5 O 9724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 51196 Number of models: 1 Model: "" Number of chains: 22 Chain: "2" Number of atoms: 4955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4955 Classifications: {'peptide': 627} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 602} Chain breaks: 6 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "3" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4835 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 589} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "4" Number of atoms: 4947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4947 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 598} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 4176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4176 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 507} Chain breaks: 12 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 4837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4837 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 591} Chain breaks: 6 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 5124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5124 Classifications: {'peptide': 657} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 30, 'TRANS': 626} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1602 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 3, 'TRANS': 192} Chain breaks: 1 Chain: "B" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1617 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 1 Chain: "C" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1387 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2004 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain breaks: 2 Chain: "E" Number of atoms: 4591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4591 Classifications: {'peptide': 568} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 552} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3404 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 400} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3380 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3411 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 401} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 160 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "N" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 641 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 78} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "2" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1301 SG CYS 2 341 86.191 104.981 134.408 1.00326.76 S ATOM 1324 SG CYS 2 344 86.470 108.588 132.381 1.00328.60 S ATOM 1482 SG CYS 2 364 89.361 106.701 133.841 1.00327.66 S ATOM 1503 SG CYS 2 367 86.741 108.417 135.982 1.00331.69 S ATOM 11219 SG CYS 4 349 100.544 102.137 168.254 1.00375.19 S ATOM 11240 SG CYS 4 352 102.493 103.585 170.704 1.00369.06 S ATOM 11387 SG CYS 4 371 98.887 103.065 171.636 1.00367.10 S ATOM 11429 SG CYS 4 376 99.992 105.859 169.089 1.00360.25 S ATOM 15874 SG CYS 5 183 63.758 105.227 133.644 1.00243.31 S ATOM 15899 SG CYS 5 186 61.936 108.171 133.572 1.00253.41 S ATOM 16046 SG CYS 5 211 65.409 108.944 133.543 1.00256.56 S ATOM 16074 SG CYS 5 236 64.228 107.218 136.744 1.00265.16 S ATOM 20192 SG CYS 6 311 100.857 104.747 147.167 1.00273.32 S ATOM 20214 SG CYS 6 314 103.132 107.603 146.700 1.00270.00 S ATOM 20371 SG CYS 6 333 102.425 106.214 150.237 1.00270.21 S ATOM 20405 SG CYS 6 338 99.956 108.399 148.223 1.00285.87 S ATOM 25303 SG CYS 7 262 75.943 99.009 177.999 1.00393.18 S ATOM 25326 SG CYS 7 265 72.407 99.906 179.363 1.00387.79 S ATOM 25476 SG CYS 7 284 73.118 99.622 175.698 1.00375.91 S ATOM 25513 SG CYS 7 289 74.483 102.601 177.676 1.00384.22 S Time building chain proxies: 21.06, per 1000 atoms: 0.41 Number of scatterers: 51196 At special positions: 0 Unit cell: (150.52, 195.04, 224.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 229 16.00 P 18 15.00 Mg 4 11.99 O 9724 8.00 N 8757 7.00 C 32459 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 - 3.00 Amino acid : True - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.22 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 903 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 341 " pdb=" ZN 41003 " pdb="ZN ZN 41003 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41003 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41003 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 41003 " - pdb=" SG CYS 4 371 " pdb=" ZN 51600 " pdb="ZN ZN 51600 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 51600 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 51600 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 51600 " - pdb=" SG CYS 5 236 " pdb=" ZN 61600 " pdb="ZN ZN 61600 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61600 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 61600 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61600 " - pdb=" SG CYS 6 333 " pdb=" ZN 7 903 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 262 " Number of angles added : 30 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12180 Finding SS restraints... Secondary structure from input PDB file: 236 helices and 67 sheets defined 47.4% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain '2' and resid 182 through 188 removed outlier: 3.527A pdb=" N ASN 2 188 " --> pdb=" O GLU 2 184 " (cutoff:3.500A) Processing helix chain '2' and resid 193 through 200 removed outlier: 3.553A pdb=" N GLN 2 200 " --> pdb=" O GLU 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 200 through 218 Processing helix chain '2' and resid 225 through 238 Processing helix chain '2' and resid 245 through 252 removed outlier: 3.652A pdb=" N LEU 2 249 " --> pdb=" O ASN 2 245 " (cutoff:3.500A) Processing helix chain '2' and resid 253 through 263 Processing helix chain '2' and resid 263 through 283 removed outlier: 3.784A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 289 Processing helix chain '2' and resid 435 through 443 Processing helix chain '2' and resid 477 through 488 Processing helix chain '2' and resid 492 through 501 Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 548 through 560 Processing helix chain '2' and resid 572 through 577 Processing helix chain '2' and resid 594 through 599 Processing helix chain '2' and resid 615 through 626 Processing helix chain '2' and resid 632 through 636 Processing helix chain '2' and resid 651 through 655 Processing helix chain '2' and resid 670 through 677 Processing helix chain '2' and resid 688 through 707 Processing helix chain '2' and resid 747 through 752 Processing helix chain '2' and resid 759 through 774 Processing helix chain '2' and resid 779 through 800 removed outlier: 3.977A pdb=" N LYS 2 785 " --> pdb=" O MET 2 781 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 Processing helix chain '2' and resid 830 through 847 Processing helix chain '2' and resid 849 through 866 removed outlier: 6.200A pdb=" N ARG 2 855 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE 2 863 " --> pdb=" O ARG 2 859 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR 2 864 " --> pdb=" O SER 2 860 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 35 Processing helix chain '3' and resid 35 through 54 removed outlier: 3.888A pdb=" N ARG 3 39 " --> pdb=" O PHE 3 35 " (cutoff:3.500A) Processing helix chain '3' and resid 100 through 107 Processing helix chain '3' and resid 107 through 117 Processing helix chain '3' and resid 117 through 137 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 143 through 150 removed outlier: 3.900A pdb=" N ARG 3 150 " --> pdb=" O ALA 3 146 " (cutoff:3.500A) Processing helix chain '3' and resid 161 through 163 No H-bonds generated for 'chain '3' and resid 161 through 163' Processing helix chain '3' and resid 172 through 176 Processing helix chain '3' and resid 279 through 283 Processing helix chain '3' and resid 343 through 356 removed outlier: 3.619A pdb=" N LYS 3 356 " --> pdb=" O LYS 3 352 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 367 Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 414 through 426 Processing helix chain '3' and resid 438 through 443 Processing helix chain '3' and resid 474 through 478 Processing helix chain '3' and resid 479 through 493 removed outlier: 3.923A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 533 Processing helix chain '3' and resid 536 through 543 Processing helix chain '3' and resid 554 through 570 Processing helix chain '3' and resid 652 through 666 Processing helix chain '3' and resid 672 through 689 Processing helix chain '3' and resid 698 through 716 Processing helix chain '3' and resid 722 through 738 Processing helix chain '4' and resid 186 through 199 Processing helix chain '4' and resid 202 through 210 removed outlier: 3.944A pdb=" N ARG 4 206 " --> pdb=" O LYS 4 202 " (cutoff:3.500A) Processing helix chain '4' and resid 212 through 216 removed outlier: 3.639A pdb=" N ILE 4 216 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) Processing helix chain '4' and resid 217 through 223 Processing helix chain '4' and resid 224 through 237 Processing helix chain '4' and resid 245 through 251 Processing helix chain '4' and resid 251 through 264 removed outlier: 4.213A pdb=" N ASP 4 256 " --> pdb=" O LYS 4 252 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU 4 257 " --> pdb=" O GLN 4 253 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 287 Processing helix chain '4' and resid 292 through 299 Processing helix chain '4' and resid 313 through 317 Processing helix chain '4' and resid 318 through 322 Processing helix chain '4' and resid 422 through 424 No H-bonds generated for 'chain '4' and resid 422 through 424' Processing helix chain '4' and resid 502 through 515 Processing helix chain '4' and resid 517 through 527 removed outlier: 4.119A pdb=" N ALA 4 527 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 546 Processing helix chain '4' and resid 573 through 585 Processing helix chain '4' and resid 597 through 602 Processing helix chain '4' and resid 619 through 625 Processing helix chain '4' and resid 638 through 652 removed outlier: 3.903A pdb=" N GLU 4 647 " --> pdb=" O SER 4 643 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 Processing helix chain '4' and resid 695 through 702 Processing helix chain '4' and resid 713 through 730 Processing helix chain '4' and resid 743 through 758 Processing helix chain '4' and resid 763 through 780 Processing helix chain '4' and resid 794 through 812 Processing helix chain '4' and resid 818 through 833 Processing helix chain '5' and resid 21 through 38 Processing helix chain '5' and resid 44 through 56 Processing helix chain '5' and resid 65 through 72 Processing helix chain '5' and resid 72 through 82 removed outlier: 3.795A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 103 Proline residue: 5 88 - end of helix Processing helix chain '5' and resid 147 through 151 Processing helix chain '5' and resid 152 through 156 Processing helix chain '5' and resid 281 through 283 No H-bonds generated for 'chain '5' and resid 281 through 283' Processing helix chain '5' and resid 350 through 363 Processing helix chain '5' and resid 365 through 374 Processing helix chain '5' and resid 381 through 394 Processing helix chain '5' and resid 420 through 433 Processing helix chain '5' and resid 467 through 472 Processing helix chain '5' and resid 488 through 499 removed outlier: 4.088A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE 5 493 " --> pdb=" O ASP 5 489 " (cutoff:3.500A) Processing helix chain '5' and resid 545 through 550 Processing helix chain '5' and resid 561 through 577 removed outlier: 3.526A pdb=" N ASP 5 565 " --> pdb=" O ASN 5 561 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 610 Processing helix chain '5' and resid 615 through 636 Processing helix chain '5' and resid 649 through 668 Processing helix chain '5' and resid 673 through 693 Processing helix chain '6' and resid 105 through 121 Processing helix chain '6' and resid 134 through 147 Processing helix chain '6' and resid 155 through 161 Processing helix chain '6' and resid 164 through 173 Processing helix chain '6' and resid 173 through 193 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 193 through 198 removed outlier: 3.647A pdb=" N ASN 6 198 " --> pdb=" O PRO 6 194 " (cutoff:3.500A) Processing helix chain '6' and resid 280 through 284 Processing helix chain '6' and resid 384 through 386 No H-bonds generated for 'chain '6' and resid 384 through 386' Processing helix chain '6' and resid 406 through 411 Processing helix chain '6' and resid 501 through 508 Processing helix chain '6' and resid 509 through 522 Processing helix chain '6' and resid 524 through 533 Processing helix chain '6' and resid 540 through 553 Processing helix chain '6' and resid 580 through 592 Processing helix chain '6' and resid 604 through 609 Processing helix chain '6' and resid 626 through 632 Processing helix chain '6' and resid 645 through 659 Processing helix chain '6' and resid 684 through 688 Processing helix chain '6' and resid 694 through 699 removed outlier: 3.504A pdb=" N LEU 6 699 " --> pdb=" O LEU 6 695 " (cutoff:3.500A) Processing helix chain '6' and resid 702 through 708 Processing helix chain '6' and resid 720 through 737 Processing helix chain '6' and resid 738 through 742 Processing helix chain '6' and resid 747 through 761 Processing helix chain '6' and resid 766 through 785 Processing helix chain '6' and resid 796 through 815 Processing helix chain '6' and resid 820 through 836 Processing helix chain '7' and resid 13 through 28 Processing helix chain '7' and resid 61 through 72 Processing helix chain '7' and resid 82 through 96 Processing helix chain '7' and resid 101 through 109 removed outlier: 4.058A pdb=" N GLN 7 107 " --> pdb=" O VAL 7 103 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN 7 108 " --> pdb=" O SER 7 104 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN 7 109 " --> pdb=" O ALA 7 105 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 124 removed outlier: 3.751A pdb=" N PHE 7 113 " --> pdb=" O ASN 7 109 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 151 removed outlier: 3.913A pdb=" N ASN 7 144 " --> pdb=" O ASP 7 140 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN 7 145 " --> pdb=" O VAL 7 141 " (cutoff:3.500A) Processing helix chain '7' and resid 193 through 198 removed outlier: 3.945A pdb=" N THR 7 197 " --> pdb=" O PRO 7 193 " (cutoff:3.500A) Processing helix chain '7' and resid 231 through 235 Processing helix chain '7' and resid 286 through 292 Processing helix chain '7' and resid 338 through 340 No H-bonds generated for 'chain '7' and resid 338 through 340' Processing helix chain '7' and resid 361 through 369 Processing helix chain '7' and resid 395 through 408 removed outlier: 3.709A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 418 Processing helix chain '7' and resid 425 through 438 Processing helix chain '7' and resid 465 through 477 Processing helix chain '7' and resid 489 through 494 Processing helix chain '7' and resid 511 through 516 Processing helix chain '7' and resid 530 through 543 removed outlier: 3.781A pdb=" N GLU 7 539 " --> pdb=" O THR 7 535 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL 7 540 " --> pdb=" O ALA 7 536 " (cutoff:3.500A) Processing helix chain '7' and resid 579 through 585 Processing helix chain '7' and resid 587 through 594 Processing helix chain '7' and resid 605 through 622 Processing helix chain '7' and resid 634 through 647 Processing helix chain '7' and resid 653 through 674 Processing helix chain '7' and resid 676 through 680 Processing helix chain '7' and resid 685 through 704 Processing helix chain '7' and resid 709 through 730 removed outlier: 4.777A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR 7 728 " --> pdb=" O LYS 7 724 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU 7 730 " --> pdb=" O SER 7 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 23 removed outlier: 4.201A pdb=" N GLY A 6 " --> pdb=" O TYR A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 61 Processing helix chain 'A' and resid 66 through 104 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 124 through 143 Processing helix chain 'A' and resid 193 through 202 removed outlier: 4.800A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 12 through 22 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.531A pdb=" N GLN B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 108 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 137 through 161 Processing helix chain 'B' and resid 174 through 200 Proline residue: B 183 - end of helix Processing helix chain 'C' and resid 5 through 14 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.992A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 96 through 101 Processing helix chain 'C' and resid 103 through 115 Processing helix chain 'C' and resid 117 through 141 removed outlier: 3.608A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 169 Processing helix chain 'C' and resid 170 through 193 Processing helix chain 'D' and resid 5 through 15 removed outlier: 3.609A pdb=" N GLU D 15 " --> pdb=" O GLU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 Processing helix chain 'D' and resid 80 through 107 Processing helix chain 'D' and resid 123 through 154 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 170 through 175 Processing helix chain 'D' and resid 176 through 198 Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.701A pdb=" N ALA D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 Processing helix chain 'D' and resid 279 through 289 removed outlier: 4.888A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 6 No H-bonds generated for 'chain 'E' and resid 4 through 6' Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 35 through 53 Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 99 through 104 Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 146 through 152 Processing helix chain 'E' and resid 152 through 165 Processing helix chain 'E' and resid 224 through 241 removed outlier: 4.811A pdb=" N GLU E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 266 through 282 removed outlier: 4.210A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 303 Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 333 through 341 Processing helix chain 'E' and resid 341 through 349 Processing helix chain 'E' and resid 352 through 367 Processing helix chain 'E' and resid 369 through 375 Processing helix chain 'E' and resid 376 through 380 Processing helix chain 'E' and resid 381 through 394 removed outlier: 5.761A pdb=" N GLY E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 405 Processing helix chain 'E' and resid 421 through 435 Processing helix chain 'E' and resid 462 through 485 removed outlier: 3.985A pdb=" N ASP E 485 " --> pdb=" O TRP E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 517 Processing helix chain 'E' and resid 535 through 540 Processing helix chain 'E' and resid 541 through 559 Processing helix chain 'E' and resid 604 through 616 Processing helix chain 'E' and resid 634 through 647 removed outlier: 4.793A pdb=" N SER E 638 " --> pdb=" O ARG E 634 " (cutoff:3.500A) Proline residue: E 639 - end of helix Processing helix chain 'F' and resid 671 through 680 Processing helix chain 'F' and resid 724 through 732 Processing helix chain 'F' and resid 782 through 791 Processing helix chain 'F' and resid 818 through 845 Processing helix chain 'F' and resid 849 through 876 removed outlier: 4.488A pdb=" N GLU F 853 " --> pdb=" O GLY F 849 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 889 Processing helix chain 'F' and resid 891 through 905 Processing helix chain 'F' and resid 907 through 923 Processing helix chain 'G' and resid 671 through 680 Processing helix chain 'G' and resid 724 through 732 Processing helix chain 'G' and resid 782 through 790 Processing helix chain 'G' and resid 818 through 844 Processing helix chain 'G' and resid 850 through 877 Processing helix chain 'G' and resid 878 through 888 Processing helix chain 'G' and resid 891 through 905 removed outlier: 3.642A pdb=" N LEU G 895 " --> pdb=" O GLN G 891 " (cutoff:3.500A) Processing helix chain 'G' and resid 907 through 924 Processing helix chain 'H' and resid 671 through 680 Processing helix chain 'H' and resid 724 through 732 Processing helix chain 'H' and resid 782 through 790 Processing helix chain 'H' and resid 818 through 843 Processing helix chain 'H' and resid 850 through 877 Processing helix chain 'H' and resid 878 through 889 removed outlier: 3.505A pdb=" N LEU H 889 " --> pdb=" O LEU H 885 " (cutoff:3.500A) Processing helix chain 'H' and resid 891 through 905 Processing helix chain 'H' and resid 907 through 924 Processing helix chain 'N' and resid 14 through 25 Proline residue: N 19 - end of helix Processing helix chain 'N' and resid 34 through 48 Processing helix chain 'N' and resid 54 through 69 removed outlier: 4.000A pdb=" N ALA N 58 " --> pdb=" O ARG N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 95 Processing sheet with id=AA1, first strand: chain '2' and resid 241 through 243 Processing sheet with id=AA2, first strand: chain '2' and resid 348 through 352 removed outlier: 5.434A pdb=" N GLY 2 349 " --> pdb=" O PHE 2 339 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE 2 339 " --> pdb=" O GLY 2 349 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL 2 337 " --> pdb=" O LYS 2 379 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LYS 2 379 " --> pdb=" O VAL 2 337 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N PHE 2 339 " --> pdb=" O GLY 2 377 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLY 2 377 " --> pdb=" O PHE 2 339 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N CYS 2 341 " --> pdb=" O VAL 2 375 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N VAL 2 375 " --> pdb=" O CYS 2 341 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N THR 2 449 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU 2 407 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU 2 411 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N SER 2 455 " --> pdb=" O LEU 2 411 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR 2 449 " --> pdb=" O ASN 2 433 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN 2 433 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE 2 451 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS 2 431 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE 2 429 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 563 through 565 removed outlier: 5.895A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL 2 683 " --> pdb=" O LEU 2 540 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU 2 542 " --> pdb=" O VAL 2 683 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 578 through 581 Processing sheet with id=AA5, first strand: chain '2' and resid 629 through 631 Processing sheet with id=AA6, first strand: chain '3' and resid 95 through 99 removed outlier: 3.913A pdb=" N LYS 3 158 " --> pdb=" O ILE 3 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3' and resid 165 through 166 removed outlier: 3.680A pdb=" N GLU 3 183 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS 3 178 " --> pdb=" O PHE 3 298 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE 3 298 " --> pdb=" O LYS 3 178 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ARG 3 291 " --> pdb=" O PRO 3 328 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN 3 293 " --> pdb=" O VAL 3 326 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL 3 326 " --> pdb=" O ASN 3 293 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL 3 295 " --> pdb=" O ASN 3 324 " (cutoff:3.500A) removed outlier: 10.214A pdb=" N SER 3 273 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N ILE 3 321 " --> pdb=" O SER 3 273 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP 3 275 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY 3 323 " --> pdb=" O ASP 3 275 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 194 through 196 Processing sheet with id=AA9, first strand: chain '3' and resid 201 through 203 Processing sheet with id=AB1, first strand: chain '3' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain '3' and resid 431 through 433 removed outlier: 6.942A pdb=" N THR 3 432 " --> pdb=" O ASP 3 473 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL 3 470 " --> pdb=" O ILE 3 513 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ALA 3 515 " --> pdb=" O VAL 3 470 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE 3 472 " --> pdb=" O ALA 3 515 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE 3 405 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ALA 3 516 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N MET 3 407 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU 3 406 " --> pdb=" O PHE 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain '3' and resid 444 through 447 Processing sheet with id=AB4, first strand: chain '3' and resid 494 through 499 removed outlier: 3.809A pdb=" N LYS 3 499 " --> pdb=" O ILE 3 502 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '4' and resid 240 through 244 removed outlier: 6.403A pdb=" N LEU 4 241 " --> pdb=" O ARG 4 304 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR 4 306 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU 4 243 " --> pdb=" O TYR 4 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '4' and resid 355 through 359 removed outlier: 6.772A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '4' and resid 355 through 359 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 339 through 349 current: chain '4' and resid 458 through 468 removed outlier: 6.949A pdb=" N THR 4 436 " --> pdb=" O VAL 4 464 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL 4 466 " --> pdb=" O GLU 4 434 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU 4 434 " --> pdb=" O VAL 4 466 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS 4 468 " --> pdb=" O ARG 4 432 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ARG 4 432 " --> pdb=" O LYS 4 468 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER 4 335 " --> pdb=" O VAL 4 396 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL 4 396 " --> pdb=" O SER 4 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 453 through 454 Processing sheet with id=AB9, first strand: chain '4' and resid 550 through 551 Processing sheet with id=AC1, first strand: chain '4' and resid 588 through 592 removed outlier: 5.956A pdb=" N VAL 4 589 " --> pdb=" O CYS 4 630 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP 4 632 " --> pdb=" O VAL 4 589 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR 4 591 " --> pdb=" O ASP 4 632 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE 4 564 " --> pdb=" O ALA 4 673 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA 4 675 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU 4 566 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS 4 567 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 603 through 606 Processing sheet with id=AC3, first strand: chain '4' and resid 653 through 658 Processing sheet with id=AC4, first strand: chain '5' and resid 60 through 64 Processing sheet with id=AC5, first strand: chain '5' and resid 189 through 193 removed outlier: 5.461A pdb=" N SER 5 174 " --> pdb=" O GLN 5 253 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN 5 253 " --> pdb=" O SER 5 174 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA 5 176 " --> pdb=" O ILE 5 251 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE 5 251 " --> pdb=" O ALA 5 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 189 through 193 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 173 through 183 current: chain '5' and resid 325 through 335 removed outlier: 6.658A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N SER 5 335 " --> pdb=" O ARG 5 291 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ARG 5 291 " --> pdb=" O SER 5 335 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR 5 290 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 398 through 399 Processing sheet with id=AC8, first strand: chain '5' and resid 437 through 438 removed outlier: 6.049A pdb=" N VAL 5 437 " --> pdb=" O CYS 5 478 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL 5 412 " --> pdb=" O ALA 5 521 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '6' and resid 150 through 154 removed outlier: 5.988A pdb=" N ILE 6 151 " --> pdb=" O SER 6 266 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE 6 268 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE 6 153 " --> pdb=" O PHE 6 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain '6' and resid 317 through 322 removed outlier: 5.758A pdb=" N ALA 6 307 " --> pdb=" O ASN 6 320 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU 6 322 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N TYR 6 305 " --> pdb=" O GLU 6 322 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 317 through 322 removed outlier: 5.758A pdb=" N ALA 6 307 " --> pdb=" O ASN 6 320 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU 6 322 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N TYR 6 305 " --> pdb=" O GLU 6 322 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '6' and resid 301 through 311 current: chain '6' and resid 450 through 461 removed outlier: 7.016A pdb=" N THR 6 398 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL 6 459 " --> pdb=" O LYS 6 396 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS 6 396 " --> pdb=" O VAL 6 459 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER 6 461 " --> pdb=" O ARG 6 394 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ARG 6 394 " --> pdb=" O SER 6 461 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL 6 294 " --> pdb=" O GLN 6 362 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN 6 362 " --> pdb=" O VAL 6 294 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 557 through 558 Processing sheet with id=AD4, first strand: chain '6' and resid 596 through 599 removed outlier: 5.778A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS 6 636 " --> pdb=" O LEU 6 679 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA 6 681 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE 6 638 " --> pdb=" O ALA 6 681 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE 6 571 " --> pdb=" O ALA 6 680 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA 6 682 " --> pdb=" O ILE 6 571 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL 6 573 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N CYS 6 572 " --> pdb=" O PHE 6 713 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE 6 715 " --> pdb=" O CYS 6 572 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL 6 574 " --> pdb=" O ILE 6 715 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain '6' and resid 610 through 614 Processing sheet with id=AD6, first strand: chain '6' and resid 661 through 663 Processing sheet with id=AD7, first strand: chain '7' and resid 77 through 81 Processing sheet with id=AD8, first strand: chain '7' and resid 252 through 254 removed outlier: 9.093A pdb=" N THR 7 374 " --> pdb=" O SER 7 330 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN 7 332 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ASN 7 336 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N PHE 7 380 " --> pdb=" O ASN 7 336 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU 7 373 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR 7 352 " --> pdb=" O GLN 7 379 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL 7 381 " --> pdb=" O ASP 7 350 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP 7 350 " --> pdb=" O VAL 7 381 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLN 7 383 " --> pdb=" O ILE 7 348 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ILE 7 348 " --> pdb=" O GLN 7 383 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN 7 237 " --> pdb=" O PHE 7 355 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS 7 314 " --> pdb=" O THR 7 246 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL 7 248 " --> pdb=" O GLU 7 312 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU 7 312 " --> pdb=" O VAL 7 248 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '7' and resid 268 through 272 Processing sheet with id=AE1, first strand: chain '7' and resid 442 through 443 removed outlier: 3.501A pdb=" N LYS 7 442 " --> pdb=" O ILE 7 450 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '7' and resid 481 through 484 removed outlier: 6.073A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL 7 456 " --> pdb=" O ALA 7 565 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ALA 7 567 " --> pdb=" O VAL 7 456 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU 7 458 " --> pdb=" O ALA 7 567 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '7' and resid 495 through 498 Processing sheet with id=AE4, first strand: chain '7' and resid 546 through 548 Processing sheet with id=AE5, first strand: chain 'A' and resid 205 through 206 removed outlier: 3.697A pdb=" N SER E 56 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU E 27 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL E 59 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE E 29 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE E 61 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL E 31 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU E 81 " --> pdb=" O TYR E 121 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE E 120 " --> pdb=" O GLN E 141 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 172 through 175 Processing sheet with id=AE7, first strand: chain 'B' and resid 69 through 72 Processing sheet with id=AE8, first strand: chain 'C' and resid 43 through 47 Processing sheet with id=AE9, first strand: chain 'D' and resid 274 through 278 Processing sheet with id=AF1, first strand: chain 'D' and resid 258 through 260 Processing sheet with id=AF2, first strand: chain 'E' and resid 316 through 322 removed outlier: 3.768A pdb=" N GLY E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 520 through 521 removed outlier: 3.837A pdb=" N VAL E 568 " --> pdb=" O ARG E 526 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA E 570 " --> pdb=" O CYS E 528 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE E 572 " --> pdb=" O LEU E 530 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER E 571 " --> pdb=" O LEU E 580 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 491 through 496 removed outlier: 6.891A pdb=" N VAL F 502 " --> pdb=" O LEU F 494 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N MET F 496 " --> pdb=" O GLY F 500 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY F 500 " --> pdb=" O MET F 496 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 536 through 540 Processing sheet with id=AF6, first strand: chain 'F' and resid 578 through 583 removed outlier: 4.274A pdb=" N THR F 592 " --> pdb=" O TYR F 596 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR F 596 " --> pdb=" O THR F 592 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE F 597 " --> pdb=" O VAL F 609 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL F 609 " --> pdb=" O PHE F 597 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER F 599 " --> pdb=" O PHE F 607 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 620 through 621 removed outlier: 4.185A pdb=" N TYR F 638 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU F 642 " --> pdb=" O TYR F 650 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N TYR F 650 " --> pdb=" O GLU F 642 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 686 through 689 removed outlier: 3.520A pdb=" N LEU F 707 " --> pdb=" O PRO F 695 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU F 704 " --> pdb=" O ILE F 721 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 742 through 748 removed outlier: 6.957A pdb=" N ASN F 753 " --> pdb=" O LEU F 745 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU F 747 " --> pdb=" O THR F 751 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR F 751 " --> pdb=" O LEU F 747 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 491 through 496 removed outlier: 6.471A pdb=" N VAL G 502 " --> pdb=" O LEU G 494 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 539 through 540 Processing sheet with id=AG3, first strand: chain 'G' and resid 578 through 583 removed outlier: 3.697A pdb=" N SER G 580 " --> pdb=" O GLY G 591 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR G 592 " --> pdb=" O TYR G 596 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR G 596 " --> pdb=" O THR G 592 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA G 608 " --> pdb=" O SER G 599 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 615 through 619 removed outlier: 4.335A pdb=" N TYR G 638 " --> pdb=" O GLU G 654 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLU G 642 " --> pdb=" O TYR G 650 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR G 650 " --> pdb=" O GLU G 642 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 686 through 689 removed outlier: 6.344A pdb=" N LEU G 704 " --> pdb=" O ILE G 721 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 740 through 748 removed outlier: 6.992A pdb=" N ASN G 753 " --> pdb=" O LEU G 745 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU G 747 " --> pdb=" O THR G 751 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR G 751 " --> pdb=" O LEU G 747 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 491 through 495 removed outlier: 5.786A pdb=" N ARG H 491 " --> pdb=" O LYS H 506 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS H 506 " --> pdb=" O ARG H 491 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR H 493 " --> pdb=" O THR H 504 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR H 504 " --> pdb=" O TYR H 493 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR H 495 " --> pdb=" O VAL H 502 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 536 through 539 Processing sheet with id=AG9, first strand: chain 'H' and resid 578 through 583 removed outlier: 3.607A pdb=" N SER H 580 " --> pdb=" O GLY H 591 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN H 601 " --> pdb=" O PRO H 606 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 615 through 621 removed outlier: 6.561A pdb=" N VAL H 628 " --> pdb=" O VAL H 616 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU H 618 " --> pdb=" O PHE H 626 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE H 626 " --> pdb=" O LEU H 618 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA H 620 " --> pdb=" O ARG H 624 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG H 624 " --> pdb=" O ALA H 620 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 615 through 621 removed outlier: 6.561A pdb=" N VAL H 628 " --> pdb=" O VAL H 616 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU H 618 " --> pdb=" O PHE H 626 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE H 626 " --> pdb=" O LEU H 618 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA H 620 " --> pdb=" O ARG H 624 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG H 624 " --> pdb=" O ALA H 620 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 684 through 687 removed outlier: 4.114A pdb=" N GLY H 699 " --> pdb=" O THR H 703 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR H 703 " --> pdb=" O GLY H 699 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU H 722 " --> pdb=" O LEU H 704 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU H 706 " --> pdb=" O PRO H 720 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N SER H 708 " --> pdb=" O TRP H 718 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TRP H 718 " --> pdb=" O SER H 708 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 743 through 748 removed outlier: 6.415A pdb=" N ASN H 753 " --> pdb=" O LEU H 745 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU H 747 " --> pdb=" O THR H 751 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR H 751 " --> pdb=" O LEU H 747 " (cutoff:3.500A) 2531 hydrogen bonds defined for protein. 7245 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: 22.91 Time building geometry restraints manager: 12.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 16969 1.36 - 1.51: 13406 1.51 - 1.65: 21388 1.65 - 1.80: 223 1.80 - 1.95: 146 Bond restraints: 52132 Sorted by residual: bond pdb=" N THR E 594 " pdb=" CA THR E 594 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.09e-02 8.42e+03 8.94e+00 bond pdb=" N GLU 7 634 " pdb=" CA GLU 7 634 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.46e-02 4.69e+03 8.81e+00 bond pdb=" N ILE 3 91 " pdb=" CA ILE 3 91 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.20e-02 6.94e+03 8.29e+00 bond pdb=" N ILE 7 230 " pdb=" CA ILE 7 230 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.22e-02 6.72e+03 8.27e+00 bond pdb=" N ILE 7 220 " pdb=" CA ILE 7 220 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.08e+00 ... (remaining 52127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 69586 2.05 - 4.10: 910 4.10 - 6.16: 56 6.16 - 8.21: 4 8.21 - 10.26: 1 Bond angle restraints: 70557 Sorted by residual: angle pdb=" C ASP 3 280 " pdb=" CA ASP 3 280 " pdb=" CB ASP 3 280 " ideal model delta sigma weight residual 116.54 110.86 5.68 1.15e+00 7.56e-01 2.44e+01 angle pdb=" N PRO 7 626 " pdb=" CA PRO 7 626 " pdb=" C PRO 7 626 " ideal model delta sigma weight residual 111.14 104.32 6.82 1.56e+00 4.11e-01 1.91e+01 angle pdb=" N ILE E 524 " pdb=" CA ILE E 524 " pdb=" C ILE E 524 " ideal model delta sigma weight residual 113.53 109.25 4.28 9.80e-01 1.04e+00 1.91e+01 angle pdb=" C ASN H 622 " pdb=" CA ASN H 622 " pdb=" CB ASN H 622 " ideal model delta sigma weight residual 116.63 111.71 4.92 1.16e+00 7.43e-01 1.80e+01 angle pdb=" CA VAL 7 633 " pdb=" C VAL 7 633 " pdb=" O VAL 7 633 " ideal model delta sigma weight residual 121.59 117.38 4.21 1.03e+00 9.43e-01 1.67e+01 ... (remaining 70552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 31236 34.86 - 69.72: 512 69.72 - 104.58: 73 104.58 - 139.44: 3 139.44 - 174.31: 2 Dihedral angle restraints: 31826 sinusoidal: 13076 harmonic: 18750 Sorted by residual: dihedral pdb=" C5' ADP 31001 " pdb=" O5' ADP 31001 " pdb=" PA ADP 31001 " pdb=" O2A ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 114.31 -174.31 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP 31001 " pdb=" O3A ADP 31001 " pdb=" PA ADP 31001 " pdb=" PB ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 83.64 -143.64 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" O1B ADP 31001 " pdb=" O3A ADP 31001 " pdb=" PB ADP 31001 " pdb=" PA ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 61.27 -121.28 1 2.00e+01 2.50e-03 3.65e+01 ... (remaining 31823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 6655 0.045 - 0.091: 976 0.091 - 0.136: 415 0.136 - 0.181: 15 0.181 - 0.227: 4 Chirality restraints: 8065 Sorted by residual: chirality pdb=" CA ILE E 595 " pdb=" N ILE E 595 " pdb=" C ILE E 595 " pdb=" CB ILE E 595 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ILE 7 220 " pdb=" N ILE 7 220 " pdb=" C ILE 7 220 " pdb=" CB ILE 7 220 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CA ILE E 601 " pdb=" N ILE E 601 " pdb=" C ILE E 601 " pdb=" CB ILE E 601 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 8062 not shown) Planarity restraints: 9000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS 7 620 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C HIS 7 620 " 0.036 2.00e-02 2.50e+03 pdb=" O HIS 7 620 " -0.014 2.00e-02 2.50e+03 pdb=" N MET 7 621 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA 3 368 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO 3 369 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO 3 369 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO 3 369 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 5 87 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO 5 88 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO 5 88 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO 5 88 " -0.026 5.00e-02 4.00e+02 ... (remaining 8997 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 478 2.44 - 3.05: 40239 3.05 - 3.67: 88224 3.67 - 4.28: 128100 4.28 - 4.90: 202842 Nonbonded interactions: 459883 Sorted by model distance: nonbonded pdb=" O1B AGS 41001 " pdb="MG MG 41002 " model vdw 1.822 2.170 nonbonded pdb=" O2A AGS 41001 " pdb="MG MG 41002 " model vdw 1.847 2.170 nonbonded pdb="MG MG 7 901 " pdb=" O3B AGS 7 902 " model vdw 1.861 2.170 nonbonded pdb=" O PRO G 481 " pdb=" OG1 THR G 495 " model vdw 1.898 3.040 nonbonded pdb="MG MG 7 901 " pdb=" O3A AGS 7 902 " model vdw 1.900 2.170 ... (remaining 459878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 474 through 663 or resid 670 through 789 or (resid 790 and \ (name N or name CA or name C or name O or name CB )) or resid 814 through 892 o \ r (resid 893 through 894 and (name N or name CA or name C or name O or name CB ) \ ) or resid 895 through 901 or (resid 902 and (name N or name CA or name C or nam \ e O or name CB )) or resid 903 through 911 or (resid 912 and (name N or name CA \ or name C or name O or name CB )) or resid 913 through 923)) selection = (chain 'G' and (resid 474 through 789 or (resid 790 and (name N or name CA or na \ me C or name O or name CB )) or resid 814 through 901 or (resid 902 and (name N \ or name CA or name C or name O or name CB )) or resid 903 through 909 or (resid \ 910 and (name N or name CA or name C or name O or name CB )) or resid 911 throug \ h 923)) selection = (chain 'H' and (resid 474 through 663 or resid 670 through 892 or (resid 893 thr \ ough 894 and (name N or name CA or name C or name O or name CB )) or resid 895 t \ hrough 909 or (resid 910 and (name N or name CA or name C or name O or name CB ) \ ) or resid 911 or (resid 912 and (name N or name CA or name C or name O or name \ CB )) or resid 913 through 923)) } 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: 3.060 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: 0.070 Extract box with map and model: 1.500 Check model and map are aligned: 0.290 Set scattering table: 0.380 Process input model: 100.380 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 0.051 52132 Z= 0.202 Angle : 0.576 10.259 70557 Z= 0.343 Chirality : 0.039 0.227 8065 Planarity : 0.004 0.055 9000 Dihedral : 14.047 174.306 19646 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.53 % Rotamer: Outliers : 0.55 % Allowed : 0.19 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.11), residues: 6264 helix: 1.04 (0.10), residues: 2701 sheet: -1.37 (0.16), residues: 1019 loop : -0.75 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 53 HIS 0.005 0.001 HIS 4 386 PHE 0.021 0.001 PHE 3 543 TYR 0.022 0.001 TYR G 862 ARG 0.012 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 4.501 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: 2 783 MET cc_start: 0.8773 (mtp) cc_final: 0.8399 (mtp) REVERT: 3 386 MET cc_start: 0.9044 (tpp) cc_final: 0.8775 (tpp) REVERT: 3 407 MET cc_start: 0.9321 (pmm) cc_final: 0.9091 (pmm) REVERT: 5 65 MET cc_start: 0.9639 (mmp) cc_final: 0.9116 (mmm) REVERT: 5 182 MET cc_start: 0.9651 (tpp) cc_final: 0.9271 (tpp) REVERT: 5 252 ASP cc_start: 0.8970 (m-30) cc_final: 0.8535 (p0) REVERT: 5 276 MET cc_start: 0.9004 (mpp) cc_final: 0.8712 (mpp) REVERT: 6 143 MET cc_start: 0.9542 (tpt) cc_final: 0.9304 (tpp) REVERT: 6 629 MET cc_start: 0.9557 (mmp) cc_final: 0.9223 (mmm) REVERT: 7 64 MET cc_start: 0.9310 (mmp) cc_final: 0.8837 (mmm) REVERT: 7 222 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8174 (m) REVERT: 7 498 MET cc_start: 0.9527 (tpt) cc_final: 0.9239 (tpp) REVERT: 7 541 MET cc_start: 0.9446 (ptm) cc_final: 0.8800 (ppp) REVERT: 7 623 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.6542 (t0) REVERT: 7 652 MET cc_start: 0.6895 (ppp) cc_final: 0.6421 (ppp) REVERT: 7 707 MET cc_start: 0.9336 (ppp) cc_final: 0.9080 (ppp) REVERT: A 100 MET cc_start: 0.9321 (mmt) cc_final: 0.8842 (mmm) REVERT: C 16 PHE cc_start: 0.9454 (m-80) cc_final: 0.9162 (m-80) REVERT: C 159 ASN cc_start: 0.8424 (t0) cc_final: 0.8010 (t0) REVERT: C 191 MET cc_start: 0.9394 (tmm) cc_final: 0.9169 (tmm) REVERT: D 84 MET cc_start: 0.9400 (mpp) cc_final: 0.9168 (mpp) REVERT: E 44 MET cc_start: 0.9531 (mtp) cc_final: 0.9175 (mtp) REVERT: E 362 MET cc_start: 0.9698 (tmm) cc_final: 0.9056 (tmm) REVERT: F 477 MET cc_start: 0.9279 (mmm) cc_final: 0.9013 (mmm) REVERT: F 778 MET cc_start: 0.8928 (mmp) cc_final: 0.7971 (mmm) REVERT: G 778 MET cc_start: 0.8660 (mmp) cc_final: 0.8443 (mmm) REVERT: H 477 MET cc_start: 0.8543 (mmm) cc_final: 0.8304 (mmm) REVERT: H 778 MET cc_start: 0.9026 (mmp) cc_final: 0.8391 (mmp) REVERT: N 65 GLN cc_start: 0.8570 (tp40) cc_final: 0.8295 (tp-100) outliers start: 31 outliers final: 11 residues processed: 205 average time/residue: 0.5378 time to fit residues: 195.4594 Evaluate side-chains 167 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 4.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 533 optimal weight: 7.9990 chunk 479 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 chunk 163 optimal weight: 4.9990 chunk 323 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 495 optimal weight: 0.0770 chunk 191 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 chunk 368 optimal weight: 9.9990 chunk 573 optimal weight: 30.0000 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 653 ASN 2 760 GLN ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 46 GLN ** 3 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 349 ASN 3 670 GLN 4 266 GLN 4 327 ASN ** 4 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 726 ASN 5 145 GLN 5 188 HIS 5 273 ASN 6 649 GLN ** 7 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 112 HIS 7 209 GLN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 GLN A 122 ASN B 82 GLN D 81 HIS D 160 GLN ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 ASN E 493 ASN E 497 GLN F 622 ASN F 843 ASN F 877 GLN ** G 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 52132 Z= 0.304 Angle : 0.656 9.510 70557 Z= 0.345 Chirality : 0.043 0.174 8065 Planarity : 0.005 0.051 9000 Dihedral : 7.080 167.550 7088 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 0.21 % Allowed : 3.53 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.11), residues: 6264 helix: 1.11 (0.10), residues: 2812 sheet: -1.25 (0.15), residues: 1057 loop : -0.63 (0.13), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 743 HIS 0.009 0.001 HIS 4 354 PHE 0.029 0.002 PHE 6 584 TYR 0.026 0.002 TYR G 922 ARG 0.007 0.001 ARG H 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 4.494 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: 2 783 MET cc_start: 0.8890 (mtp) cc_final: 0.8522 (mtp) REVERT: 3 136 MET cc_start: 0.9242 (tmm) cc_final: 0.8840 (ppp) REVERT: 3 386 MET cc_start: 0.9177 (tpp) cc_final: 0.8871 (tpp) REVERT: 3 407 MET cc_start: 0.9316 (pmm) cc_final: 0.9103 (pmm) REVERT: 3 561 ILE cc_start: 0.9564 (OUTLIER) cc_final: 0.9216 (tp) REVERT: 4 847 MET cc_start: 0.8582 (ppp) cc_final: 0.8030 (mmm) REVERT: 5 65 MET cc_start: 0.9641 (mmp) cc_final: 0.9283 (mmp) REVERT: 5 182 MET cc_start: 0.9501 (tpp) cc_final: 0.9180 (tpp) REVERT: 5 252 ASP cc_start: 0.8925 (m-30) cc_final: 0.8674 (p0) REVERT: 5 393 MET cc_start: 0.9168 (tpp) cc_final: 0.8381 (tpp) REVERT: 6 143 MET cc_start: 0.9697 (tpt) cc_final: 0.9355 (tpp) REVERT: 6 373 MET cc_start: 0.9094 (ppp) cc_final: 0.8877 (ppp) REVERT: 6 629 MET cc_start: 0.9562 (mmp) cc_final: 0.9279 (mmm) REVERT: 6 709 PHE cc_start: 0.9091 (m-10) cc_final: 0.8743 (m-80) REVERT: 7 64 MET cc_start: 0.9381 (mmp) cc_final: 0.9055 (mmm) REVERT: 7 459 MET cc_start: 0.9433 (tpt) cc_final: 0.9218 (tpp) REVERT: 7 498 MET cc_start: 0.9444 (tpt) cc_final: 0.9206 (tpp) REVERT: 7 529 MET cc_start: 0.8569 (tmm) cc_final: 0.8176 (tmm) REVERT: 7 541 MET cc_start: 0.9193 (ptm) cc_final: 0.8927 (ptm) REVERT: 7 652 MET cc_start: 0.7363 (ppp) cc_final: 0.7088 (ppp) REVERT: A 100 MET cc_start: 0.9251 (mmt) cc_final: 0.8887 (mmm) REVERT: C 16 PHE cc_start: 0.9465 (m-80) cc_final: 0.9162 (m-80) REVERT: C 159 ASN cc_start: 0.8575 (t0) cc_final: 0.8053 (t0) REVERT: D 84 MET cc_start: 0.9336 (mpp) cc_final: 0.9062 (mpp) REVERT: D 129 MET cc_start: 0.9356 (mmp) cc_final: 0.9080 (mmm) REVERT: E 1 MET cc_start: 0.8791 (tmm) cc_final: 0.8508 (tmm) REVERT: E 44 MET cc_start: 0.9420 (mtp) cc_final: 0.8955 (mtp) REVERT: E 362 MET cc_start: 0.9707 (tmm) cc_final: 0.9137 (tmm) REVERT: E 366 MET cc_start: 0.9169 (mmp) cc_final: 0.8864 (mmm) REVERT: E 380 MET cc_start: 0.8975 (mmp) cc_final: 0.8614 (mmm) REVERT: F 477 MET cc_start: 0.9308 (mmm) cc_final: 0.8976 (mmm) REVERT: F 774 MET cc_start: 0.8928 (mpp) cc_final: 0.8627 (mpp) REVERT: F 778 MET cc_start: 0.8567 (mmp) cc_final: 0.8002 (mmm) REVERT: H 477 MET cc_start: 0.8578 (mmm) cc_final: 0.8322 (mmm) REVERT: H 778 MET cc_start: 0.8901 (mmp) cc_final: 0.8172 (mmm) REVERT: N 65 GLN cc_start: 0.9008 (tp40) cc_final: 0.8680 (tp-100) outliers start: 12 outliers final: 1 residues processed: 179 average time/residue: 0.4636 time to fit residues: 149.5775 Evaluate side-chains 157 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 318 optimal weight: 20.0000 chunk 178 optimal weight: 20.0000 chunk 477 optimal weight: 9.9990 chunk 390 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 574 optimal weight: 7.9990 chunk 621 optimal weight: 7.9990 chunk 512 optimal weight: 20.0000 chunk 570 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 461 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 196 ASN 4 253 GLN 4 386 HIS ** 4 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 145 GLN 5 253 GLN 6 156 GLN 6 458 HIS 6 649 GLN 7 107 GLN 7 625 GLN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN B 196 HIS ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 ASN E 319 ASN F 510 GLN F 673 ASN ** F 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 916 ASN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 52132 Z= 0.292 Angle : 0.611 11.406 70557 Z= 0.322 Chirality : 0.041 0.169 8065 Planarity : 0.005 0.080 9000 Dihedral : 7.084 173.231 7088 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 6264 helix: 1.22 (0.10), residues: 2815 sheet: -1.37 (0.15), residues: 1067 loop : -0.52 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 74 HIS 0.006 0.001 HIS 4 354 PHE 0.031 0.002 PHE 6 584 TYR 0.024 0.002 TYR G 922 ARG 0.007 0.001 ARG 4 642 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 4.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8921 (mtp) cc_final: 0.8620 (mtp) REVERT: 3 136 MET cc_start: 0.9226 (tmm) cc_final: 0.8805 (ppp) REVERT: 3 261 MET cc_start: 0.8922 (tpp) cc_final: 0.8649 (tpp) REVERT: 3 386 MET cc_start: 0.9216 (tpp) cc_final: 0.8884 (tpp) REVERT: 3 561 ILE cc_start: 0.9626 (OUTLIER) cc_final: 0.9328 (tp) REVERT: 4 314 MET cc_start: 0.8175 (ppp) cc_final: 0.7679 (ppp) REVERT: 4 847 MET cc_start: 0.8511 (ppp) cc_final: 0.7979 (mmm) REVERT: 5 65 MET cc_start: 0.9613 (mmp) cc_final: 0.9100 (mmm) REVERT: 5 182 MET cc_start: 0.9544 (tpp) cc_final: 0.9242 (tpp) REVERT: 5 276 MET cc_start: 0.9121 (mpp) cc_final: 0.8881 (mpp) REVERT: 5 393 MET cc_start: 0.9104 (tpp) cc_final: 0.8129 (tpp) REVERT: 6 143 MET cc_start: 0.9664 (tpt) cc_final: 0.9354 (tpp) REVERT: 6 373 MET cc_start: 0.9203 (ppp) cc_final: 0.8959 (ppp) REVERT: 6 629 MET cc_start: 0.9596 (mmp) cc_final: 0.9352 (mmm) REVERT: 7 64 MET cc_start: 0.9434 (mmp) cc_final: 0.9070 (mmm) REVERT: 7 498 MET cc_start: 0.9444 (tpt) cc_final: 0.9189 (tpp) REVERT: 7 529 MET cc_start: 0.8740 (tmm) cc_final: 0.8325 (tmm) REVERT: 7 541 MET cc_start: 0.9248 (ptm) cc_final: 0.8943 (ptm) REVERT: A 100 MET cc_start: 0.9287 (mmt) cc_final: 0.8936 (mmm) REVERT: C 16 PHE cc_start: 0.9436 (m-80) cc_final: 0.9119 (m-80) REVERT: C 79 MET cc_start: 0.8962 (ptm) cc_final: 0.8720 (ptm) REVERT: C 159 ASN cc_start: 0.8487 (t0) cc_final: 0.7893 (t0) REVERT: D 84 MET cc_start: 0.9480 (mpp) cc_final: 0.9148 (mpp) REVERT: D 218 MET cc_start: 0.9456 (mtp) cc_final: 0.9251 (mtp) REVERT: E 1 MET cc_start: 0.8800 (tmm) cc_final: 0.8463 (tmm) REVERT: E 44 MET cc_start: 0.9399 (mtp) cc_final: 0.8978 (mtp) REVERT: E 362 MET cc_start: 0.9665 (tmm) cc_final: 0.9075 (tmm) REVERT: E 380 MET cc_start: 0.8908 (mmp) cc_final: 0.8588 (mmm) REVERT: F 477 MET cc_start: 0.9233 (mmm) cc_final: 0.8952 (mmm) REVERT: F 778 MET cc_start: 0.8715 (mmp) cc_final: 0.8141 (mmm) REVERT: H 774 MET cc_start: 0.8552 (mpp) cc_final: 0.8215 (mpp) REVERT: H 778 MET cc_start: 0.8723 (mmp) cc_final: 0.8306 (mmm) REVERT: N 65 GLN cc_start: 0.9108 (tp40) cc_final: 0.8791 (tp-100) REVERT: N 80 ASP cc_start: 0.8616 (p0) cc_final: 0.8324 (p0) REVERT: N 81 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8555 (pp30) outliers start: 5 outliers final: 0 residues processed: 173 average time/residue: 0.4735 time to fit residues: 147.4409 Evaluate side-chains 157 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 568 optimal weight: 20.0000 chunk 432 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 274 optimal weight: 0.9990 chunk 386 optimal weight: 10.0000 chunk 577 optimal weight: 8.9990 chunk 610 optimal weight: 0.5980 chunk 301 optimal weight: 7.9990 chunk 546 optimal weight: 30.0000 chunk 164 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 710 ASN ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 49 GLN 7 271 GLN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 555 GLN F 761 HIS ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 52132 Z= 0.235 Angle : 0.575 11.041 70557 Z= 0.302 Chirality : 0.041 0.214 8065 Planarity : 0.004 0.062 9000 Dihedral : 7.042 173.660 7088 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.52 % Rotamer: Outliers : 0.02 % Allowed : 2.54 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.11), residues: 6264 helix: 1.39 (0.10), residues: 2816 sheet: -1.23 (0.16), residues: 1059 loop : -0.43 (0.13), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 74 HIS 0.010 0.001 HIS 3 487 PHE 0.047 0.002 PHE N 78 TYR 0.021 0.001 TYR G 862 ARG 0.006 0.000 ARG F 893 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 4.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8920 (mtp) cc_final: 0.8627 (mtp) REVERT: 3 136 MET cc_start: 0.9271 (tmm) cc_final: 0.8823 (ppp) REVERT: 3 386 MET cc_start: 0.9041 (tpp) cc_final: 0.8836 (tpp) REVERT: 3 407 MET cc_start: 0.9427 (pmm) cc_final: 0.9221 (pmm) REVERT: 3 478 MET cc_start: 0.8792 (tpt) cc_final: 0.8497 (tpp) REVERT: 4 847 MET cc_start: 0.8526 (ppp) cc_final: 0.8064 (mmm) REVERT: 5 65 MET cc_start: 0.9590 (mmp) cc_final: 0.9054 (mmm) REVERT: 5 182 MET cc_start: 0.9556 (tpp) cc_final: 0.9247 (tpp) REVERT: 5 393 MET cc_start: 0.9073 (tpp) cc_final: 0.8063 (tpp) REVERT: 6 143 MET cc_start: 0.9658 (tpt) cc_final: 0.9353 (tpp) REVERT: 6 373 MET cc_start: 0.9231 (ppp) cc_final: 0.8941 (ppp) REVERT: 6 629 MET cc_start: 0.9597 (mmp) cc_final: 0.9373 (mmm) REVERT: 6 709 PHE cc_start: 0.9003 (m-80) cc_final: 0.8277 (m-80) REVERT: 7 64 MET cc_start: 0.9437 (mmp) cc_final: 0.9075 (mmm) REVERT: 7 448 MET cc_start: 0.8814 (tpt) cc_final: 0.8420 (tpt) REVERT: 7 498 MET cc_start: 0.9409 (tpt) cc_final: 0.9158 (tpp) REVERT: 7 529 MET cc_start: 0.8829 (tmm) cc_final: 0.8555 (tmm) REVERT: 7 541 MET cc_start: 0.9286 (ptm) cc_final: 0.8965 (ptm) REVERT: 7 707 MET cc_start: 0.9323 (ppp) cc_final: 0.9110 (ppp) REVERT: A 100 MET cc_start: 0.9282 (mmt) cc_final: 0.8934 (mmm) REVERT: B 21 GLU cc_start: 0.9545 (OUTLIER) cc_final: 0.9292 (mp0) REVERT: B 63 MET cc_start: 0.9468 (mmp) cc_final: 0.9258 (mmm) REVERT: C 16 PHE cc_start: 0.9409 (m-80) cc_final: 0.9084 (m-80) REVERT: C 159 ASN cc_start: 0.8576 (t0) cc_final: 0.8019 (t0) REVERT: D 84 MET cc_start: 0.9419 (mpp) cc_final: 0.9130 (mpp) REVERT: D 103 MET cc_start: 0.9564 (mmp) cc_final: 0.9348 (mmm) REVERT: E 1 MET cc_start: 0.8724 (tmm) cc_final: 0.8382 (tmm) REVERT: E 44 MET cc_start: 0.9389 (mtp) cc_final: 0.8963 (mtp) REVERT: E 362 MET cc_start: 0.9701 (tmm) cc_final: 0.9148 (tmm) REVERT: E 380 MET cc_start: 0.8929 (mmp) cc_final: 0.8631 (mmm) REVERT: E 567 MET cc_start: 0.9340 (tpp) cc_final: 0.9132 (tpp) REVERT: F 477 MET cc_start: 0.9214 (mmm) cc_final: 0.8937 (mmm) REVERT: F 774 MET cc_start: 0.9003 (mpp) cc_final: 0.8715 (mpp) REVERT: F 778 MET cc_start: 0.8797 (mmp) cc_final: 0.8164 (mmm) REVERT: H 477 MET cc_start: 0.8613 (mmm) cc_final: 0.8247 (mmm) REVERT: H 774 MET cc_start: 0.8615 (mpp) cc_final: 0.8360 (mpp) REVERT: H 778 MET cc_start: 0.8665 (mmp) cc_final: 0.8276 (mmm) REVERT: H 821 MET cc_start: 0.9016 (ttt) cc_final: 0.8618 (tpp) REVERT: N 36 ASP cc_start: 0.9583 (p0) cc_final: 0.9087 (p0) REVERT: N 65 GLN cc_start: 0.9078 (tp40) cc_final: 0.8787 (tp-100) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.4706 time to fit residues: 143.6775 Evaluate side-chains 153 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 4.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 508 optimal weight: 10.0000 chunk 346 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 454 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 521 optimal weight: 20.0000 chunk 422 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 311 optimal weight: 10.0000 chunk 548 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 366 ASN ** 2 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 760 GLN ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 29 GLN ** 3 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 349 ASN 3 417 GLN 4 350 ASN ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 676 ASN 4 797 GLN 5 145 GLN 5 196 ASN ** 6 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 357 GLN ** 6 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 518 ASN 7 622 HIS ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS D 160 GLN ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 725 ASN ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 52132 Z= 0.349 Angle : 0.661 12.043 70557 Z= 0.344 Chirality : 0.041 0.186 8065 Planarity : 0.005 0.065 9000 Dihedral : 7.152 177.952 7088 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 6264 helix: 1.22 (0.10), residues: 2818 sheet: -1.27 (0.15), residues: 1065 loop : -0.58 (0.13), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 190 HIS 0.008 0.002 HIS 3 487 PHE 0.029 0.002 PHE N 78 TYR 0.023 0.002 TYR H 862 ARG 0.007 0.001 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 4.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8939 (mtp) cc_final: 0.8603 (mtp) REVERT: 3 136 MET cc_start: 0.9264 (tmm) cc_final: 0.8767 (ppp) REVERT: 3 261 MET cc_start: 0.9053 (tpt) cc_final: 0.8472 (tpp) REVERT: 3 386 MET cc_start: 0.9224 (tpp) cc_final: 0.8872 (tpp) REVERT: 3 407 MET cc_start: 0.9523 (pmm) cc_final: 0.9187 (pmm) REVERT: 4 233 MET cc_start: 0.9497 (ttt) cc_final: 0.9128 (tmm) REVERT: 4 847 MET cc_start: 0.8625 (ppp) cc_final: 0.8132 (mmm) REVERT: 5 65 MET cc_start: 0.9539 (mmp) cc_final: 0.9050 (mmm) REVERT: 5 182 MET cc_start: 0.9548 (tpp) cc_final: 0.9302 (tpp) REVERT: 5 393 MET cc_start: 0.9029 (tpp) cc_final: 0.8044 (tpp) REVERT: 5 404 MET cc_start: 0.9292 (tmm) cc_final: 0.8900 (tmm) REVERT: 6 143 MET cc_start: 0.9634 (tpt) cc_final: 0.9372 (tpp) REVERT: 6 373 MET cc_start: 0.9259 (ppp) cc_final: 0.8992 (ppp) REVERT: 7 64 MET cc_start: 0.9498 (mmp) cc_final: 0.9135 (mmm) REVERT: 7 448 MET cc_start: 0.8963 (tpt) cc_final: 0.8609 (tpt) REVERT: 7 459 MET cc_start: 0.9457 (tpt) cc_final: 0.9171 (tpp) REVERT: 7 498 MET cc_start: 0.9301 (tpt) cc_final: 0.9080 (tpp) REVERT: 7 529 MET cc_start: 0.8813 (tmm) cc_final: 0.8563 (tmm) REVERT: 7 541 MET cc_start: 0.9327 (ptm) cc_final: 0.9000 (ptm) REVERT: A 100 MET cc_start: 0.9259 (mmt) cc_final: 0.8879 (mmm) REVERT: C 159 ASN cc_start: 0.8692 (t0) cc_final: 0.8106 (t0) REVERT: C 191 MET cc_start: 0.9364 (tmm) cc_final: 0.9139 (tmm) REVERT: D 84 MET cc_start: 0.9497 (mpp) cc_final: 0.9092 (mpp) REVERT: E 1 MET cc_start: 0.8753 (tmm) cc_final: 0.8332 (tmm) REVERT: E 44 MET cc_start: 0.9417 (mtp) cc_final: 0.9021 (mtp) REVERT: E 362 MET cc_start: 0.9685 (tmm) cc_final: 0.9173 (tmm) REVERT: E 380 MET cc_start: 0.8981 (mmp) cc_final: 0.8617 (mmm) REVERT: F 778 MET cc_start: 0.8578 (mmp) cc_final: 0.8009 (mmm) REVERT: H 774 MET cc_start: 0.8609 (mpp) cc_final: 0.8367 (mpp) REVERT: H 778 MET cc_start: 0.8480 (mmp) cc_final: 0.8124 (mmm) REVERT: H 821 MET cc_start: 0.9102 (ttt) cc_final: 0.8677 (tpp) REVERT: N 65 GLN cc_start: 0.9158 (tp40) cc_final: 0.8858 (tp-100) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.4750 time to fit residues: 142.1015 Evaluate side-chains 152 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 205 optimal weight: 3.9990 chunk 550 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 358 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 611 optimal weight: 10.0000 chunk 507 optimal weight: 1.9990 chunk 283 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 321 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 349 ASN 4 386 HIS ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 53 ASN ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 730 HIS ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 ASN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 52132 Z= 0.232 Angle : 0.572 10.101 70557 Z= 0.300 Chirality : 0.041 0.184 8065 Planarity : 0.004 0.063 9000 Dihedral : 7.072 176.902 7088 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Rotamer: Outliers : 0.02 % Allowed : 1.66 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.11), residues: 6264 helix: 1.41 (0.10), residues: 2817 sheet: -1.13 (0.16), residues: 1022 loop : -0.50 (0.13), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 6 356 HIS 0.008 0.001 HIS 3 487 PHE 0.032 0.001 PHE N 78 TYR 0.027 0.001 TYR F 749 ARG 0.005 0.000 ARG 7 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 4.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8949 (mtp) cc_final: 0.8575 (mtp) REVERT: 3 136 MET cc_start: 0.9270 (tmm) cc_final: 0.8753 (ppp) REVERT: 3 261 MET cc_start: 0.9071 (tpt) cc_final: 0.8535 (tpp) REVERT: 3 386 MET cc_start: 0.9181 (tpp) cc_final: 0.8798 (tpp) REVERT: 3 407 MET cc_start: 0.9483 (pmm) cc_final: 0.9134 (pmm) REVERT: 3 478 MET cc_start: 0.8764 (tpt) cc_final: 0.8496 (tpp) REVERT: 4 314 MET cc_start: 0.8243 (ppp) cc_final: 0.7763 (ppp) REVERT: 4 847 MET cc_start: 0.8599 (ppp) cc_final: 0.8150 (mmm) REVERT: 5 65 MET cc_start: 0.9512 (mmp) cc_final: 0.9019 (mmm) REVERT: 5 182 MET cc_start: 0.9555 (tpp) cc_final: 0.9281 (tpp) REVERT: 5 393 MET cc_start: 0.9182 (tpp) cc_final: 0.8338 (tpp) REVERT: 5 404 MET cc_start: 0.9242 (tmm) cc_final: 0.8824 (tmm) REVERT: 6 143 MET cc_start: 0.9610 (tpt) cc_final: 0.9349 (tpp) REVERT: 6 373 MET cc_start: 0.9258 (ppp) cc_final: 0.8973 (ppp) REVERT: 7 64 MET cc_start: 0.9498 (mmp) cc_final: 0.9136 (mmm) REVERT: 7 448 MET cc_start: 0.8987 (tpt) cc_final: 0.8615 (tpt) REVERT: 7 498 MET cc_start: 0.9314 (tpt) cc_final: 0.9047 (tpp) REVERT: 7 529 MET cc_start: 0.8901 (tmm) cc_final: 0.8674 (tmm) REVERT: 7 541 MET cc_start: 0.9288 (ptm) cc_final: 0.8956 (ptm) REVERT: A 1 MET cc_start: 0.8541 (tpp) cc_final: 0.8223 (tpp) REVERT: A 100 MET cc_start: 0.9238 (mmt) cc_final: 0.8876 (mmm) REVERT: B 63 MET cc_start: 0.9479 (mmp) cc_final: 0.9255 (mmm) REVERT: C 16 PHE cc_start: 0.9413 (m-80) cc_final: 0.9116 (m-80) REVERT: C 113 MET cc_start: 0.9421 (mmm) cc_final: 0.8992 (mmm) REVERT: C 159 ASN cc_start: 0.8631 (t0) cc_final: 0.8023 (t0) REVERT: D 103 MET cc_start: 0.9577 (mmp) cc_final: 0.9341 (mmm) REVERT: D 277 MET cc_start: 0.9724 (mmm) cc_final: 0.9223 (mmm) REVERT: E 1 MET cc_start: 0.8602 (tmm) cc_final: 0.8187 (tmm) REVERT: E 44 MET cc_start: 0.9398 (mtp) cc_final: 0.8993 (mtp) REVERT: E 362 MET cc_start: 0.9691 (tmm) cc_final: 0.9163 (tmm) REVERT: E 380 MET cc_start: 0.8943 (mmp) cc_final: 0.8578 (mmm) REVERT: F 774 MET cc_start: 0.8938 (mpp) cc_final: 0.8661 (mpp) REVERT: F 778 MET cc_start: 0.8610 (mmp) cc_final: 0.7973 (mmm) REVERT: G 774 MET cc_start: 0.9335 (mpp) cc_final: 0.9105 (mpp) REVERT: H 477 MET cc_start: 0.8619 (mmm) cc_final: 0.8319 (mmm) REVERT: H 778 MET cc_start: 0.8437 (mmp) cc_final: 0.8088 (mmm) REVERT: H 821 MET cc_start: 0.9184 (ttt) cc_final: 0.8776 (tpp) REVERT: N 36 ASP cc_start: 0.9509 (p0) cc_final: 0.9088 (p0) REVERT: N 65 GLN cc_start: 0.9125 (tp40) cc_final: 0.8841 (tp-100) REVERT: N 78 PHE cc_start: 0.9555 (m-10) cc_final: 0.9105 (m-10) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.4690 time to fit residues: 141.6267 Evaluate side-chains 154 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 589 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 348 optimal weight: 2.9990 chunk 446 optimal weight: 4.9990 chunk 345 optimal weight: 20.0000 chunk 514 optimal weight: 20.0000 chunk 341 optimal weight: 20.0000 chunk 609 optimal weight: 20.0000 chunk 381 optimal weight: 0.9980 chunk 371 optimal weight: 10.0000 chunk 281 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 366 ASN ** 2 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 730 HIS ** 7 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 GLN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 52132 Z= 0.249 Angle : 0.582 10.596 70557 Z= 0.305 Chirality : 0.040 0.171 8065 Planarity : 0.004 0.061 9000 Dihedral : 7.054 179.381 7088 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.05 % Favored : 95.91 % Rotamer: Outliers : 0.04 % Allowed : 1.50 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.11), residues: 6264 helix: 1.47 (0.10), residues: 2813 sheet: -1.10 (0.16), residues: 1028 loop : -0.48 (0.13), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 743 HIS 0.010 0.001 HIS 2 621 PHE 0.030 0.001 PHE N 78 TYR 0.020 0.001 TYR F 749 ARG 0.005 0.000 ARG 4 559 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 4.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8948 (mtp) cc_final: 0.8575 (mtp) REVERT: 3 136 MET cc_start: 0.9265 (tmm) cc_final: 0.8726 (ppp) REVERT: 3 261 MET cc_start: 0.9067 (tpt) cc_final: 0.8568 (tpp) REVERT: 3 386 MET cc_start: 0.9221 (tpp) cc_final: 0.8821 (tpp) REVERT: 3 407 MET cc_start: 0.9423 (pmm) cc_final: 0.9091 (pmm) REVERT: 3 478 MET cc_start: 0.8731 (tpt) cc_final: 0.8456 (tpp) REVERT: 4 314 MET cc_start: 0.8267 (ppp) cc_final: 0.7803 (ppp) REVERT: 4 847 MET cc_start: 0.8625 (ppp) cc_final: 0.8236 (mmt) REVERT: 5 65 MET cc_start: 0.9496 (mmp) cc_final: 0.9022 (mmm) REVERT: 5 182 MET cc_start: 0.9545 (tpp) cc_final: 0.9295 (tpp) REVERT: 5 276 MET cc_start: 0.9090 (mpp) cc_final: 0.8886 (mpp) REVERT: 5 393 MET cc_start: 0.9194 (tpp) cc_final: 0.8350 (tpp) REVERT: 6 143 MET cc_start: 0.9607 (tpt) cc_final: 0.9370 (tpp) REVERT: 6 373 MET cc_start: 0.9288 (ppp) cc_final: 0.8997 (ppp) REVERT: 7 64 MET cc_start: 0.9530 (mmp) cc_final: 0.9157 (mmm) REVERT: 7 448 MET cc_start: 0.9081 (tpt) cc_final: 0.8664 (mmm) REVERT: 7 459 MET cc_start: 0.9451 (tpt) cc_final: 0.9166 (tpp) REVERT: 7 498 MET cc_start: 0.9272 (tpt) cc_final: 0.9003 (tpp) REVERT: 7 541 MET cc_start: 0.9258 (ptm) cc_final: 0.8924 (ptm) REVERT: A 100 MET cc_start: 0.9244 (mmt) cc_final: 0.8898 (mmm) REVERT: B 63 MET cc_start: 0.9486 (mmp) cc_final: 0.9273 (mmm) REVERT: C 16 PHE cc_start: 0.9454 (m-80) cc_final: 0.9156 (m-80) REVERT: C 79 MET cc_start: 0.8813 (ptm) cc_final: 0.8456 (ptt) REVERT: D 84 MET cc_start: 0.9483 (mpp) cc_final: 0.9156 (mpp) REVERT: D 103 MET cc_start: 0.9576 (mmp) cc_final: 0.9354 (mmm) REVERT: D 129 MET cc_start: 0.9380 (mmm) cc_final: 0.9123 (mmm) REVERT: E 1 MET cc_start: 0.8765 (tmm) cc_final: 0.8337 (tmm) REVERT: E 44 MET cc_start: 0.9404 (mtp) cc_final: 0.9008 (mtp) REVERT: E 362 MET cc_start: 0.9674 (tmm) cc_final: 0.9154 (tmm) REVERT: E 380 MET cc_start: 0.8969 (mmp) cc_final: 0.8602 (mmm) REVERT: F 477 MET cc_start: 0.9293 (mmm) cc_final: 0.8892 (mmm) REVERT: F 774 MET cc_start: 0.9137 (mpp) cc_final: 0.8815 (mpp) REVERT: F 778 MET cc_start: 0.8646 (mmp) cc_final: 0.8160 (mmm) REVERT: F 821 MET cc_start: 0.9335 (ttt) cc_final: 0.9018 (tmm) REVERT: H 778 MET cc_start: 0.8408 (mmp) cc_final: 0.8064 (mmm) REVERT: N 36 ASP cc_start: 0.9518 (p0) cc_final: 0.9073 (p0) REVERT: N 65 GLN cc_start: 0.9170 (tp40) cc_final: 0.8879 (tp-100) REVERT: N 78 PHE cc_start: 0.9567 (m-10) cc_final: 0.9075 (m-10) outliers start: 2 outliers final: 1 residues processed: 168 average time/residue: 0.4732 time to fit residues: 142.5222 Evaluate side-chains 153 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 4.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 376 optimal weight: 0.6980 chunk 243 optimal weight: 0.4980 chunk 363 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 119 optimal weight: 0.4980 chunk 118 optimal weight: 10.0000 chunk 387 optimal weight: 2.9990 chunk 415 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 478 optimal weight: 8.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 730 HIS 7 271 GLN 7 320 GLN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN D 160 GLN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 52132 Z= 0.174 Angle : 0.550 10.637 70557 Z= 0.287 Chirality : 0.041 0.178 8065 Planarity : 0.004 0.058 9000 Dihedral : 6.956 178.697 7088 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.11), residues: 6264 helix: 1.57 (0.10), residues: 2824 sheet: -1.00 (0.16), residues: 1048 loop : -0.34 (0.13), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 3 111 HIS 0.011 0.001 HIS 2 621 PHE 0.028 0.001 PHE N 78 TYR 0.019 0.001 TYR 4 580 ARG 0.005 0.000 ARG 2 705 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 4.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8959 (mtp) cc_final: 0.8628 (mtp) REVERT: 3 136 MET cc_start: 0.9285 (tmm) cc_final: 0.8974 (tmm) REVERT: 3 261 MET cc_start: 0.9044 (tpt) cc_final: 0.8579 (tpp) REVERT: 3 386 MET cc_start: 0.9139 (tpp) cc_final: 0.8801 (tpp) REVERT: 3 478 MET cc_start: 0.8793 (tpt) cc_final: 0.8384 (tpp) REVERT: 4 233 MET cc_start: 0.9519 (ttt) cc_final: 0.9204 (tmm) REVERT: 4 314 MET cc_start: 0.8204 (ppp) cc_final: 0.7762 (ppp) REVERT: 4 847 MET cc_start: 0.8598 (ppp) cc_final: 0.8209 (mmt) REVERT: 5 65 MET cc_start: 0.9476 (mmp) cc_final: 0.9008 (mmm) REVERT: 5 182 MET cc_start: 0.9547 (tpp) cc_final: 0.9267 (tpp) REVERT: 5 276 MET cc_start: 0.9044 (mpp) cc_final: 0.8807 (mpp) REVERT: 5 393 MET cc_start: 0.9162 (tpp) cc_final: 0.8290 (tpp) REVERT: 6 143 MET cc_start: 0.9605 (tpp) cc_final: 0.9357 (tpp) REVERT: 6 313 MET cc_start: 0.9611 (ptm) cc_final: 0.9306 (ptt) REVERT: 6 373 MET cc_start: 0.9302 (ppp) cc_final: 0.8993 (ppp) REVERT: 7 64 MET cc_start: 0.9553 (mmp) cc_final: 0.9182 (mmm) REVERT: 7 448 MET cc_start: 0.8711 (tpt) cc_final: 0.8322 (tpt) REVERT: 7 459 MET cc_start: 0.9452 (tpt) cc_final: 0.9078 (tpp) REVERT: 7 498 MET cc_start: 0.9220 (tpt) cc_final: 0.8911 (tpp) REVERT: 7 529 MET cc_start: 0.8862 (tmm) cc_final: 0.8613 (tmm) REVERT: 7 541 MET cc_start: 0.9290 (ptm) cc_final: 0.8960 (ptm) REVERT: A 1 MET cc_start: 0.8691 (tpp) cc_final: 0.8362 (tpp) REVERT: A 79 MET cc_start: 0.9689 (mtm) cc_final: 0.9393 (ptp) REVERT: A 100 MET cc_start: 0.9228 (mmt) cc_final: 0.8937 (mmm) REVERT: B 63 MET cc_start: 0.9490 (mmp) cc_final: 0.9222 (mmm) REVERT: C 16 PHE cc_start: 0.9430 (m-80) cc_final: 0.9100 (m-80) REVERT: C 79 MET cc_start: 0.8827 (ptm) cc_final: 0.8465 (ptt) REVERT: D 84 MET cc_start: 0.9507 (mpp) cc_final: 0.9186 (mpp) REVERT: D 103 MET cc_start: 0.9572 (mmp) cc_final: 0.9339 (mmm) REVERT: D 129 MET cc_start: 0.9312 (mmm) cc_final: 0.9022 (mmm) REVERT: D 277 MET cc_start: 0.9613 (mmm) cc_final: 0.9117 (mmm) REVERT: E 1 MET cc_start: 0.8681 (tmm) cc_final: 0.8180 (tmm) REVERT: E 44 MET cc_start: 0.9474 (mtp) cc_final: 0.9051 (mtp) REVERT: E 362 MET cc_start: 0.9681 (tmm) cc_final: 0.9070 (tmm) REVERT: E 380 MET cc_start: 0.8953 (mmp) cc_final: 0.8664 (mmm) REVERT: E 567 MET cc_start: 0.9386 (tpp) cc_final: 0.9153 (tpp) REVERT: F 477 MET cc_start: 0.9286 (mmm) cc_final: 0.8734 (mmm) REVERT: F 774 MET cc_start: 0.9202 (mpp) cc_final: 0.8890 (mpp) REVERT: F 778 MET cc_start: 0.8645 (mmp) cc_final: 0.8127 (mmm) REVERT: F 821 MET cc_start: 0.9319 (ttt) cc_final: 0.9030 (tmm) REVERT: H 477 MET cc_start: 0.8599 (mmm) cc_final: 0.8303 (mmm) REVERT: H 778 MET cc_start: 0.8307 (mmp) cc_final: 0.7969 (mmm) REVERT: N 36 ASP cc_start: 0.9528 (p0) cc_final: 0.9131 (p0) REVERT: N 65 GLN cc_start: 0.9171 (tp40) cc_final: 0.8918 (tp-100) REVERT: N 78 PHE cc_start: 0.9592 (m-10) cc_final: 0.9135 (m-10) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.4969 time to fit residues: 147.9217 Evaluate side-chains 153 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 4.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 554 optimal weight: 40.0000 chunk 583 optimal weight: 10.0000 chunk 532 optimal weight: 3.9990 chunk 567 optimal weight: 30.0000 chunk 341 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 chunk 445 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 512 optimal weight: 7.9990 chunk 536 optimal weight: 7.9990 chunk 565 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 366 ASN ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 349 ASN ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 625 GLN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS D 160 GLN ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 555 GLN ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 753 ASN ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 52132 Z= 0.347 Angle : 0.658 12.293 70557 Z= 0.342 Chirality : 0.041 0.172 8065 Planarity : 0.004 0.063 9000 Dihedral : 7.034 168.257 7088 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.50 % Rotamer: Outliers : 0.02 % Allowed : 0.55 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.11), residues: 6264 helix: 1.35 (0.10), residues: 2814 sheet: -1.07 (0.16), residues: 1050 loop : -0.50 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 3 111 HIS 0.012 0.002 HIS 2 621 PHE 0.024 0.002 PHE 5 550 TYR 0.020 0.002 TYR F 749 ARG 0.006 0.001 ARG 4 559 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 4.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8968 (mtp) cc_final: 0.8622 (mtp) REVERT: 3 136 MET cc_start: 0.9256 (tmm) cc_final: 0.8946 (tmm) REVERT: 3 261 MET cc_start: 0.9098 (tpt) cc_final: 0.8641 (tpp) REVERT: 3 386 MET cc_start: 0.9273 (tpp) cc_final: 0.8884 (tpp) REVERT: 3 478 MET cc_start: 0.8594 (tpt) cc_final: 0.8388 (tpp) REVERT: 4 233 MET cc_start: 0.9543 (ttt) cc_final: 0.9234 (tmm) REVERT: 4 314 MET cc_start: 0.8132 (ppp) cc_final: 0.7833 (ppp) REVERT: 4 847 MET cc_start: 0.8646 (ppp) cc_final: 0.8224 (mmm) REVERT: 5 65 MET cc_start: 0.9454 (mmp) cc_final: 0.9013 (mmm) REVERT: 5 182 MET cc_start: 0.9534 (tpp) cc_final: 0.9294 (tpp) REVERT: 5 393 MET cc_start: 0.9168 (tpp) cc_final: 0.8224 (tpp) REVERT: 5 404 MET cc_start: 0.8968 (tmm) cc_final: 0.8609 (tmm) REVERT: 5 552 MET cc_start: 0.9698 (tpp) cc_final: 0.9358 (tpp) REVERT: 6 143 MET cc_start: 0.9614 (tpp) cc_final: 0.9381 (tpp) REVERT: 6 313 MET cc_start: 0.9626 (ptm) cc_final: 0.9345 (ptt) REVERT: 6 373 MET cc_start: 0.9292 (ppp) cc_final: 0.9010 (ppp) REVERT: 7 64 MET cc_start: 0.9568 (mmp) cc_final: 0.9202 (mmm) REVERT: 7 448 MET cc_start: 0.8910 (tpt) cc_final: 0.8492 (tpt) REVERT: 7 459 MET cc_start: 0.9444 (tpt) cc_final: 0.9109 (tpp) REVERT: 7 498 MET cc_start: 0.9209 (tpt) cc_final: 0.8903 (tpp) REVERT: 7 529 MET cc_start: 0.8817 (tmm) cc_final: 0.8517 (tmm) REVERT: 7 541 MET cc_start: 0.9286 (ptm) cc_final: 0.9022 (ptm) REVERT: A 100 MET cc_start: 0.9280 (mmt) cc_final: 0.8951 (mmm) REVERT: B 63 MET cc_start: 0.9499 (mmp) cc_final: 0.9287 (mmm) REVERT: D 202 MET cc_start: 0.9693 (tpp) cc_final: 0.9468 (tpp) REVERT: D 277 MET cc_start: 0.9726 (mmm) cc_final: 0.9249 (mmm) REVERT: E 1 MET cc_start: 0.8784 (tmm) cc_final: 0.8346 (tmm) REVERT: E 44 MET cc_start: 0.9461 (mtp) cc_final: 0.9055 (mtp) REVERT: E 362 MET cc_start: 0.9689 (tmm) cc_final: 0.9164 (tmm) REVERT: E 366 MET cc_start: 0.9156 (mmp) cc_final: 0.8908 (mmm) REVERT: E 380 MET cc_start: 0.9036 (mmp) cc_final: 0.8667 (mmm) REVERT: E 567 MET cc_start: 0.9369 (tpp) cc_final: 0.9151 (tpp) REVERT: F 774 MET cc_start: 0.9167 (mpp) cc_final: 0.8860 (mpp) REVERT: F 778 MET cc_start: 0.8497 (mmp) cc_final: 0.8037 (mmm) REVERT: F 821 MET cc_start: 0.9330 (ttt) cc_final: 0.9008 (tmm) REVERT: G 496 MET cc_start: 0.8001 (mpp) cc_final: 0.7781 (mpp) REVERT: H 778 MET cc_start: 0.8144 (mmp) cc_final: 0.7823 (mmm) REVERT: N 36 ASP cc_start: 0.9516 (p0) cc_final: 0.9101 (p0) REVERT: N 65 GLN cc_start: 0.9202 (tp40) cc_final: 0.8956 (tp-100) REVERT: N 78 PHE cc_start: 0.9605 (m-10) cc_final: 0.9167 (m-10) outliers start: 1 outliers final: 1 residues processed: 162 average time/residue: 0.4806 time to fit residues: 140.0495 Evaluate side-chains 153 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 372 optimal weight: 3.9990 chunk 600 optimal weight: 6.9990 chunk 366 optimal weight: 5.9990 chunk 284 optimal weight: 9.9990 chunk 417 optimal weight: 0.9990 chunk 629 optimal weight: 20.0000 chunk 579 optimal weight: 10.0000 chunk 501 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 387 optimal weight: 1.9990 chunk 307 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: ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 349 ASN ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 730 HIS 7 292 ASN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 555 GLN ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 52132 Z= 0.212 Angle : 0.574 12.553 70557 Z= 0.300 Chirality : 0.041 0.177 8065 Planarity : 0.004 0.057 9000 Dihedral : 6.940 159.516 7088 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.11), residues: 6264 helix: 1.52 (0.10), residues: 2818 sheet: -0.97 (0.16), residues: 1035 loop : -0.42 (0.13), residues: 2411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 74 HIS 0.012 0.001 HIS 2 621 PHE 0.019 0.001 PHE 2 677 TYR 0.018 0.001 TYR H 862 ARG 0.008 0.000 ARG H 524 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12528 Ramachandran restraints generated. 6264 Oldfield, 0 Emsley, 6264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 4.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8942 (mtp) cc_final: 0.8592 (mtp) REVERT: 3 136 MET cc_start: 0.9263 (tmm) cc_final: 0.8953 (tmm) REVERT: 3 261 MET cc_start: 0.9065 (tpt) cc_final: 0.8627 (tpp) REVERT: 3 386 MET cc_start: 0.9157 (tpp) cc_final: 0.8751 (tpp) REVERT: 3 478 MET cc_start: 0.8615 (tpt) cc_final: 0.8363 (tpp) REVERT: 4 233 MET cc_start: 0.9511 (ttt) cc_final: 0.9238 (tmm) REVERT: 4 314 MET cc_start: 0.8223 (ppp) cc_final: 0.7783 (ppp) REVERT: 4 847 MET cc_start: 0.8635 (ppp) cc_final: 0.8252 (mmt) REVERT: 5 65 MET cc_start: 0.9443 (mmp) cc_final: 0.9007 (mmm) REVERT: 5 182 MET cc_start: 0.9563 (tpp) cc_final: 0.9302 (tpp) REVERT: 5 276 MET cc_start: 0.9045 (mpp) cc_final: 0.8825 (mpp) REVERT: 5 393 MET cc_start: 0.9134 (tpp) cc_final: 0.8219 (tpp) REVERT: 5 404 MET cc_start: 0.8953 (tmm) cc_final: 0.8644 (tmm) REVERT: 5 552 MET cc_start: 0.9717 (tpp) cc_final: 0.9400 (tpp) REVERT: 6 143 MET cc_start: 0.9611 (tpp) cc_final: 0.9372 (tpp) REVERT: 6 313 MET cc_start: 0.9630 (ptm) cc_final: 0.9360 (ptt) REVERT: 6 373 MET cc_start: 0.9314 (ppp) cc_final: 0.9014 (ppp) REVERT: 7 64 MET cc_start: 0.9552 (mmp) cc_final: 0.9168 (mmm) REVERT: 7 448 MET cc_start: 0.8828 (tpt) cc_final: 0.8445 (tpt) REVERT: 7 459 MET cc_start: 0.9430 (tpt) cc_final: 0.9144 (tpp) REVERT: 7 498 MET cc_start: 0.9210 (tpt) cc_final: 0.8899 (tpp) REVERT: 7 529 MET cc_start: 0.8832 (tmm) cc_final: 0.8563 (tmm) REVERT: 7 541 MET cc_start: 0.9334 (ptm) cc_final: 0.8987 (ptm) REVERT: 7 638 MET cc_start: 0.9674 (mpp) cc_final: 0.9350 (mpp) REVERT: A 1 MET cc_start: 0.8701 (tpp) cc_final: 0.8403 (tpp) REVERT: A 100 MET cc_start: 0.9253 (mmt) cc_final: 0.8980 (mmm) REVERT: B 63 MET cc_start: 0.9518 (mmp) cc_final: 0.9245 (mmm) REVERT: D 103 MET cc_start: 0.9582 (mmp) cc_final: 0.9339 (mmm) REVERT: D 129 MET cc_start: 0.9319 (mmm) cc_final: 0.8773 (mmm) REVERT: D 277 MET cc_start: 0.9681 (mmm) cc_final: 0.9162 (mmm) REVERT: E 1 MET cc_start: 0.8679 (tmm) cc_final: 0.8295 (tmm) REVERT: E 44 MET cc_start: 0.9471 (mtp) cc_final: 0.9071 (mtp) REVERT: E 362 MET cc_start: 0.9677 (tmm) cc_final: 0.9145 (tmm) REVERT: E 366 MET cc_start: 0.9129 (mmp) cc_final: 0.8890 (mmm) REVERT: E 380 MET cc_start: 0.8982 (mmp) cc_final: 0.8619 (mmm) REVERT: E 567 MET cc_start: 0.9372 (tpp) cc_final: 0.9139 (tpp) REVERT: F 774 MET cc_start: 0.9198 (mpp) cc_final: 0.8893 (mpp) REVERT: F 778 MET cc_start: 0.8560 (mmp) cc_final: 0.8088 (mmm) REVERT: F 821 MET cc_start: 0.9312 (ttt) cc_final: 0.9008 (tmm) REVERT: H 774 MET cc_start: 0.8759 (mpp) cc_final: 0.8553 (mpp) REVERT: H 778 MET cc_start: 0.8142 (mmp) cc_final: 0.7822 (mmm) REVERT: H 821 MET cc_start: 0.8927 (ttt) cc_final: 0.8440 (tpp) REVERT: N 36 ASP cc_start: 0.9449 (p0) cc_final: 0.8893 (p0) REVERT: N 65 GLN cc_start: 0.9202 (tp40) cc_final: 0.8966 (tp-100) REVERT: N 78 PHE cc_start: 0.9632 (m-10) cc_final: 0.9289 (m-10) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.4906 time to fit residues: 144.0608 Evaluate side-chains 152 residues out of total 5711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 398 optimal weight: 5.9990 chunk 534 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 462 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 502 optimal weight: 0.0370 chunk 210 optimal weight: 0.4980 chunk 515 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 569 GLN ** 2 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 151 HIS ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 357 GLN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 HIS ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 436 ASN F 741 HIS G 563 HIS ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.026652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.019623 restraints weight = 735653.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.020224 restraints weight = 452695.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.020638 restraints weight = 322562.637| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 52132 Z= 0.150 Angle : 0.559 14.342 70557 Z= 0.288 Chirality : 0.041 0.203 8065 Planarity : 0.004 0.057 9000 Dihedral : 6.747 153.025 7088 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.11), residues: 6264 helix: 1.60 (0.10), residues: 2839 sheet: -0.80 (0.16), residues: 1065 loop : -0.32 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 74 HIS 0.012 0.001 HIS 2 621 PHE 0.026 0.001 PHE 2 677 TYR 0.016 0.001 TYR H 862 ARG 0.008 0.000 ARG H 524 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5951.76 seconds wall clock time: 108 minutes 24.83 seconds (6504.83 seconds total)