Starting phenix.real_space_refine on Mon Aug 25 18:58:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rig_19187/08_2025/8rig_19187.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rig_19187/08_2025/8rig_19187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rig_19187/08_2025/8rig_19187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rig_19187/08_2025/8rig_19187.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rig_19187/08_2025/8rig_19187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rig_19187/08_2025/8rig_19187.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 50 5.49 5 Mg 6 5.21 5 S 137 5.16 5 C 18874 2.51 5 N 5269 2.21 5 O 5867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30208 Number of models: 1 Model: "" Number of chains: 14 Chain: "2" Number of atoms: 4955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4955 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 25, 'TRANS': 600} Chain breaks: 2 Chain: "3" Number of atoms: 4787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4787 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 26, 'TRANS': 584} Chain breaks: 3 Chain: "4" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4985 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 24, 'TRANS': 604} Chain breaks: 4 Chain: "5" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4757 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 25, 'TRANS': 580} Chain breaks: 4 Chain: "6" Number of atoms: 4847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4847 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 22, 'TRANS': 588} Chain breaks: 5 Chain: "7" Number of atoms: 4959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 4959 Classifications: {'peptide': 632} Link IDs: {'PTRANS': 29, 'TRANS': 602} Chain breaks: 3 Chain: "X" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 388 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "Y" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 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: 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: "5" 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: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1302 SG CYS 2 341 20.319 90.801 64.866 1.00148.40 S ATOM 1325 SG CYS 2 344 17.796 91.593 62.025 1.00157.93 S ATOM 1483 SG CYS 2 364 18.827 94.210 65.124 1.00159.84 S ATOM 1504 SG CYS 2 367 16.358 91.091 64.539 1.00163.90 S ATOM 10949 SG CYS 4 349 36.131 98.756 111.988 1.00 92.61 S ATOM 10970 SG CYS 4 352 35.878 100.611 114.526 1.00101.51 S ATOM 11117 SG CYS 4 371 35.027 97.070 115.164 1.00100.08 S ATOM 11159 SG CYS 4 376 32.426 99.738 113.478 1.00108.61 S ATOM 15808 SG CYS 5 183 17.406 65.857 70.276 1.00103.73 S ATOM 15833 SG CYS 5 186 13.964 64.409 69.446 1.00110.80 S ATOM 15955 SG CYS 5 211 15.192 68.395 69.168 1.00113.37 S ATOM 15999 SG CYS 5 236 14.647 67.039 72.432 1.00124.37 S ATOM 20733 SG CYS 6 311 28.080 102.185 92.749 1.00133.81 S ATOM 20755 SG CYS 6 314 25.721 104.275 92.884 1.00139.46 S ATOM 20912 SG CYS 6 333 28.186 104.145 96.588 1.00134.49 S ATOM 20946 SG CYS 6 338 25.389 102.172 94.805 1.00148.81 S ATOM 25738 SG CYS 7 262 35.299 70.743 117.334 1.00105.48 S ATOM 25761 SG CYS 7 265 32.984 68.426 118.768 1.00117.45 S ATOM 25915 SG CYS 7 284 33.070 68.538 115.247 1.00115.84 S ATOM 25952 SG CYS 7 289 31.229 70.973 116.929 1.00137.82 S Time building chain proxies: 5.26, per 1000 atoms: 0.17 Number of scatterers: 30208 At special positions: 0 Unit cell: (136.08, 147.96, 158.76, 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 137 16.00 P 50 15.00 Mg 6 11.99 O 5867 8.00 N 5269 7.00 C 18874 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=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21002 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 341 " pdb=" ZN 41002 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 376 " pdb=" ZN 51002 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 211 " pdb=" ZN 61103 " pdb="ZN ZN 61103 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61103 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61103 " - pdb=" SG CYS 6 333 " pdb="ZN ZN 61103 " - pdb=" SG CYS 6 311 " pdb=" ZN 7 901 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 262 " Number of angles added : 30 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7060 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 43 sheets defined 42.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain '2' and resid 182 through 187 removed outlier: 3.969A pdb=" N SER 2 187 " --> pdb=" O LEU 2 183 " (cutoff:3.500A) Processing helix chain '2' and resid 193 through 200 Processing helix chain '2' and resid 200 through 218 Processing helix chain '2' and resid 225 through 238 Processing helix chain '2' and resid 246 through 252 Processing helix chain '2' and resid 253 through 263 removed outlier: 3.665A pdb=" N ALA 2 257 " --> pdb=" O LYS 2 253 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 283 removed outlier: 3.567A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE 2 270 " --> pdb=" O GLU 2 266 " (cutoff:3.500A) removed outlier: 3.711A 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 310 through 314 Processing helix chain '2' and resid 477 through 489 Processing helix chain '2' and resid 492 through 500 Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 549 through 560 Processing helix chain '2' and resid 594 through 599 Processing helix chain '2' and resid 613 through 627 Processing helix chain '2' and resid 652 through 656 removed outlier: 3.794A pdb=" N ARG 2 656 " --> pdb=" O ASN 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 667 removed outlier: 3.588A pdb=" N ASN 2 666 " --> pdb=" O PRO 2 662 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL 2 667 " --> pdb=" O LEU 2 663 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 662 through 667' Processing helix chain '2' and resid 670 through 675 Processing helix chain '2' and resid 690 through 705 removed outlier: 3.554A pdb=" N ARG 2 694 " --> pdb=" O GLU 2 690 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 774 removed outlier: 3.572A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 779 through 781 No H-bonds generated for 'chain '2' and resid 779 through 781' Processing helix chain '2' and resid 782 through 799 removed outlier: 3.802A pdb=" N ARG 2 788 " --> pdb=" O ASP 2 784 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 removed outlier: 4.026A pdb=" N LEU 2 810 " --> pdb=" O THR 2 806 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 847 Processing helix chain '2' and resid 850 through 862 Processing helix chain '3' and resid 19 through 35 Processing helix chain '3' and resid 36 through 48 removed outlier: 3.683A pdb=" N ARG 3 43 " --> pdb=" O ARG 3 39 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE 3 45 " --> pdb=" O SER 3 41 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN 3 46 " --> pdb=" O VAL 3 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR 3 48 " --> pdb=" O SER 3 44 " (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 118 through 120 No H-bonds generated for 'chain '3' and resid 118 through 120' Processing helix chain '3' and resid 121 through 136 removed outlier: 3.628A pdb=" N ALA 3 125 " --> pdb=" O PHE 3 121 " (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 removed outlier: 3.654A pdb=" N LEU 3 176 " --> pdb=" O ALA 3 173 " (cutoff:3.500A) Processing helix chain '3' and resid 216 through 220 removed outlier: 3.965A pdb=" N THR 3 220 " --> pdb=" O ALA 3 217 " (cutoff:3.500A) Processing helix chain '3' and resid 245 through 248 removed outlier: 3.716A pdb=" N SER 3 248 " --> pdb=" O TYR 3 245 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 245 through 248' Processing helix chain '3' and resid 281 through 283 No H-bonds generated for 'chain '3' and resid 281 through 283' Processing helix chain '3' and resid 343 through 354 Processing helix chain '3' and resid 358 through 366 removed outlier: 3.657A pdb=" N SER 3 364 " --> pdb=" O PHE 3 360 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER 3 366 " --> pdb=" O ILE 3 362 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 415 through 426 Processing helix chain '3' and resid 438 through 443 removed outlier: 3.766A pdb=" N THR 3 443 " --> pdb=" O GLY 3 439 " (cutoff:3.500A) Processing helix chain '3' and resid 460 through 465 Processing helix chain '3' and resid 474 through 478 Processing helix chain '3' and resid 479 through 484 Processing helix chain '3' and resid 486 through 493 removed outlier: 3.536A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 534 removed outlier: 3.517A pdb=" N ASN 3 532 " --> pdb=" O ASP 3 528 " (cutoff:3.500A) Processing helix chain '3' and resid 536 through 543 removed outlier: 3.794A pdb=" N ARG 3 542 " --> pdb=" O SER 3 538 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE 3 543 " --> pdb=" O LEU 3 539 " (cutoff:3.500A) Processing helix chain '3' and resid 555 through 569 Processing helix chain '3' and resid 652 through 667 Processing helix chain '3' and resid 672 through 688 Processing helix chain '3' and resid 698 through 716 removed outlier: 4.243A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 removed outlier: 3.695A pdb=" N ALA 3 726 " --> pdb=" O ASN 3 722 " (cutoff:3.500A) Processing helix chain '4' and resid 188 through 198 removed outlier: 3.548A pdb=" N ARG 4 195 " --> pdb=" O THR 4 191 " (cutoff:3.500A) Processing helix chain '4' and resid 224 through 237 removed outlier: 3.657A pdb=" N LYS 4 228 " --> pdb=" O LEU 4 224 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN 4 229 " --> pdb=" O TYR 4 225 " (cutoff:3.500A) Processing helix chain '4' and resid 245 through 251 removed outlier: 3.528A pdb=" N TYR 4 251 " --> pdb=" O ASN 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 252 through 254 No H-bonds generated for 'chain '4' and resid 252 through 254' Processing helix chain '4' and resid 255 through 264 removed outlier: 3.922A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 287 removed outlier: 3.812A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN 4 287 " --> pdb=" O LEU 4 283 " (cutoff:3.500A) Processing helix chain '4' and resid 295 through 299 Processing helix chain '4' and resid 318 through 322 Processing helix chain '4' and resid 386 through 389 Processing helix chain '4' and resid 502 through 513 Processing helix chain '4' and resid 517 through 526 removed outlier: 3.669A pdb=" N ALA 4 523 " --> pdb=" O TYR 4 519 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE 4 526 " --> pdb=" O LEU 4 522 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 546 removed outlier: 3.543A pdb=" N PHE 4 545 " --> pdb=" O LEU 4 541 " (cutoff:3.500A) Processing helix chain '4' and resid 573 through 584 removed outlier: 3.593A pdb=" N ILE 4 577 " --> pdb=" O SER 4 573 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) Processing helix chain '4' and resid 597 through 602 removed outlier: 3.579A pdb=" N THR 4 602 " --> pdb=" O ALA 4 598 " (cutoff:3.500A) Processing helix chain '4' and resid 644 through 649 removed outlier: 3.888A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 692 Processing helix chain '4' and resid 695 through 700 Processing helix chain '4' and resid 713 through 726 Processing helix chain '4' and resid 727 through 729 No H-bonds generated for 'chain '4' and resid 727 through 729' Processing helix chain '4' and resid 743 through 758 Processing helix chain '4' and resid 763 through 780 removed outlier: 3.620A pdb=" N THR 4 768 " --> pdb=" O GLU 4 764 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET 4 780 " --> pdb=" O GLY 4 776 " (cutoff:3.500A) Processing helix chain '4' and resid 794 through 812 removed outlier: 4.385A pdb=" N LEU 4 798 " --> pdb=" O THR 4 794 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU 4 799 " --> pdb=" O THR 4 795 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) Processing helix chain '4' and resid 818 through 833 removed outlier: 3.587A pdb=" N GLU 4 824 " --> pdb=" O GLU 4 820 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) Processing helix chain '4' and resid 846 through 850 removed outlier: 3.698A pdb=" N VAL 4 850 " --> pdb=" O MET 4 847 " (cutoff:3.500A) Processing helix chain '5' and resid 26 through 37 Processing helix chain '5' and resid 44 through 54 removed outlier: 4.149A pdb=" N ASP 5 48 " --> pdb=" O PHE 5 44 " (cutoff:3.500A) Processing helix chain '5' and resid 67 through 72 removed outlier: 3.744A pdb=" N TYR 5 71 " --> pdb=" O HIS 5 67 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN 5 72 " --> pdb=" O LEU 5 68 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 67 through 72' Processing helix chain '5' and resid 72 through 81 removed outlier: 3.748A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP 5 81 " --> pdb=" O LYS 5 77 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 105 removed outlier: 3.866A pdb=" N ILE 5 86 " --> pdb=" O GLU 5 82 " (cutoff:3.500A) Proline residue: 5 88 - end of helix removed outlier: 3.552A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 152 through 156 Processing helix chain '5' and resid 245 through 248 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 362 removed outlier: 3.643A pdb=" N ARG 5 362 " --> pdb=" O LEU 5 358 " (cutoff:3.500A) Processing helix chain '5' and resid 365 through 373 removed outlier: 3.591A pdb=" N THR 5 371 " --> pdb=" O TYR 5 367 " (cutoff:3.500A) Processing helix chain '5' and resid 381 through 394 removed outlier: 3.579A pdb=" N LEU 5 392 " --> pdb=" O ILE 5 388 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET 5 393 " --> pdb=" O VAL 5 389 " (cutoff:3.500A) Processing helix chain '5' and resid 423 through 432 Processing helix chain '5' and resid 467 through 472 removed outlier: 3.621A pdb=" N ALA 5 472 " --> pdb=" O ALA 5 468 " (cutoff:3.500A) Processing helix chain '5' and resid 486 through 497 removed outlier: 3.599A pdb=" N GLU 5 495 " --> pdb=" O VAL 5 491 " (cutoff:3.500A) Processing helix chain '5' and resid 535 through 540 removed outlier: 3.859A pdb=" N ILE 5 540 " --> pdb=" O GLY 5 537 " (cutoff:3.500A) Processing helix chain '5' and resid 543 through 547 Processing helix chain '5' and resid 563 through 578 removed outlier: 3.572A pdb=" N HIS 5 576 " --> pdb=" O VAL 5 572 " (cutoff:3.500A) Processing helix chain '5' and resid 586 through 590 removed outlier: 3.712A pdb=" N ASN 5 590 " --> pdb=" O GLN 5 587 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 610 Processing helix chain '5' and resid 615 through 630 removed outlier: 3.786A pdb=" N ASN 5 625 " --> pdb=" O LYS 5 621 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL 5 627 " --> pdb=" O SER 5 623 " (cutoff:3.500A) Processing helix chain '5' and resid 630 through 640 removed outlier: 3.877A pdb=" N ASN 5 636 " --> pdb=" O GLN 5 632 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 665 removed outlier: 3.965A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU 5 654 " --> pdb=" O ILE 5 650 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA 5 664 " --> pdb=" O THR 5 660 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS 5 665 " --> pdb=" O GLU 5 661 " (cutoff:3.500A) Processing helix chain '5' and resid 666 through 668 No H-bonds generated for 'chain '5' and resid 666 through 668' Processing helix chain '5' and resid 673 through 688 removed outlier: 3.841A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER 5 687 " --> pdb=" O LEU 5 683 " (cutoff:3.500A) Processing helix chain '5' and resid 688 through 693 Processing helix chain '6' and resid 105 through 121 removed outlier: 3.845A pdb=" N GLU 6 109 " --> pdb=" O ASP 6 105 " (cutoff:3.500A) Processing helix chain '6' and resid 135 through 147 removed outlier: 3.896A pdb=" N ILE 6 140 " --> pdb=" O TYR 6 136 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS 6 144 " --> pdb=" O ILE 6 140 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE 6 145 " --> pdb=" O GLU 6 141 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 159 Processing helix chain '6' and resid 160 through 163 removed outlier: 4.718A pdb=" N ASN 6 163 " --> pdb=" O MET 6 160 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 160 through 163' Processing helix chain '6' and resid 164 through 173 removed outlier: 3.815A pdb=" N MET 6 168 " --> pdb=" O GLY 6 164 " (cutoff:3.500A) Processing helix chain '6' and resid 177 through 193 Processing helix chain '6' and resid 194 through 197 Processing helix chain '6' and resid 275 through 279 removed outlier: 4.095A pdb=" N ILE 6 279 " --> pdb=" O ILE 6 276 " (cutoff:3.500A) Processing helix chain '6' and resid 280 through 284 removed outlier: 3.683A pdb=" N LYS 6 283 " --> pdb=" O ARG 6 280 " (cutoff:3.500A) 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 510 through 521 removed outlier: 3.922A pdb=" N LYS 6 521 " --> pdb=" O LYS 6 517 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 533 Processing helix chain '6' and resid 540 through 552 Processing helix chain '6' and resid 581 through 590 removed outlier: 3.621A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 626 through 631 Processing helix chain '6' and resid 640 through 644 Processing helix chain '6' and resid 645 through 659 Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 707 Processing helix chain '6' and resid 722 through 738 removed outlier: 4.282A pdb=" N GLU 6 726 " --> pdb=" O LYS 6 722 " (cutoff:3.500A) Processing helix chain '6' and resid 739 through 741 No H-bonds generated for 'chain '6' and resid 739 through 741' Processing helix chain '6' and resid 747 through 760 removed outlier: 3.870A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) Processing helix chain '6' and resid 768 through 783 removed outlier: 4.167A pdb=" N TYR 6 772 " --> pdb=" O GLU 6 768 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 815 Processing helix chain '6' and resid 820 through 834 removed outlier: 3.683A pdb=" N SER 6 834 " --> pdb=" O LEU 6 830 " (cutoff:3.500A) Processing helix chain '7' and resid 15 through 28 Processing helix chain '7' and resid 61 through 72 removed outlier: 3.595A pdb=" N MET 7 66 " --> pdb=" O LYS 7 62 " (cutoff:3.500A) Processing helix chain '7' and resid 82 through 96 Processing helix chain '7' and resid 101 through 109 Processing helix chain '7' and resid 112 through 122 removed outlier: 3.794A pdb=" N LEU 7 116 " --> pdb=" O HIS 7 112 " (cutoff:3.500A) Processing helix chain '7' and resid 193 through 197 removed outlier: 3.517A pdb=" N LEU 7 196 " --> pdb=" O PRO 7 193 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 216 removed outlier: 3.680A pdb=" N ALA 7 212 " --> pdb=" O SER 7 208 " (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 387 through 391 Processing helix chain '7' and resid 394 through 406 removed outlier: 3.712A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) Processing helix chain '7' and resid 410 through 417 Processing helix chain '7' and resid 425 through 438 removed outlier: 3.507A pdb=" N LEU 7 436 " --> pdb=" O LEU 7 432 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL 7 437 " --> pdb=" O LEU 7 433 " (cutoff:3.500A) Processing helix chain '7' and resid 466 through 477 removed outlier: 3.758A pdb=" N ALA 7 472 " --> pdb=" O GLN 7 468 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS 7 475 " --> pdb=" O LYS 7 471 " (cutoff:3.500A) Processing helix chain '7' and resid 490 through 494 Processing helix chain '7' and resid 511 through 516 Processing helix chain '7' and resid 525 through 529 removed outlier: 3.802A pdb=" N MET 7 529 " --> pdb=" O PHE 7 526 " (cutoff:3.500A) Processing helix chain '7' and resid 530 through 535 Processing helix chain '7' and resid 536 through 544 removed outlier: 4.360A pdb=" N VAL 7 540 " --> pdb=" O ALA 7 536 " (cutoff:3.500A) Processing helix chain '7' and resid 579 through 584 Processing helix chain '7' and resid 587 through 593 removed outlier: 3.595A pdb=" N ARG 7 593 " --> pdb=" O ALA 7 589 " (cutoff:3.500A) Processing helix chain '7' and resid 607 through 622 removed outlier: 4.226A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 646 Processing helix chain '7' and resid 653 through 678 removed outlier: 4.207A pdb=" N TYR 7 659 " --> pdb=" O ALA 7 655 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS 7 672 " --> pdb=" O ARG 7 668 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG 7 673 " --> pdb=" O GLN 7 669 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU 7 674 " --> pdb=" O ASP 7 670 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 703 removed outlier: 3.776A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG 7 703 " --> pdb=" O LEU 7 699 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 723 removed outlier: 3.989A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 241 through 245 Processing sheet with id=AA2, first strand: chain '2' and resid 331 through 336 removed outlier: 6.625A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU 2 390 " --> pdb=" O ARG 2 406 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N HIS 2 405 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N ILE 2 451 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA 2 453 " --> pdb=" O GLU 2 407 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE 2 409 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N SER 2 455 " --> pdb=" O ILE 2 409 " (cutoff:3.500A) removed outlier: 9.837A pdb=" N LEU 2 411 " --> pdb=" O SER 2 455 " (cutoff:3.500A) removed outlier: 12.501A pdb=" N LYS 2 457 " --> pdb=" O LEU 2 411 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR 2 427 " --> pdb=" O ASN 2 454 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE 2 456 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU 2 425 " --> pdb=" O ILE 2 456 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ARG 2 458 " --> pdb=" O GLU 2 423 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLU 2 423 " --> pdb=" O ARG 2 458 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 347 through 348 Processing sheet with id=AA4, first strand: chain '2' and resid 525 through 526 Processing sheet with id=AA5, first strand: chain '2' and resid 563 through 567 removed outlier: 6.431A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ASP 2 607 " --> pdb=" O VAL 2 564 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA 2 566 " --> pdb=" O ASP 2 607 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL 2 539 " --> pdb=" O ALA 2 648 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA 2 650 " --> pdb=" O VAL 2 539 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU 2 541 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL 2 683 " --> pdb=" O LEU 2 540 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU 2 542 " --> pdb=" O VAL 2 683 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 579 through 582 Processing sheet with id=AA7, first strand: chain '2' and resid 628 through 633 Processing sheet with id=AA8, first strand: chain '3' and resid 95 through 99 Processing sheet with id=AA9, first strand: chain '3' and resid 165 through 166 removed outlier: 3.671A pdb=" N GLU 3 183 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '3' and resid 179 through 188 current: chain '3' and resid 208 through 213 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 208 through 213 current: chain '3' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 273 through 279 current: chain '3' and resid 318 through 330 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 429 through 432 removed outlier: 6.538A pdb=" N ILE 3 405 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ALA 3 516 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N MET 3 407 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU 3 406 " --> pdb=" O PHE 3 547 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL 3 549 " --> pdb=" O LEU 3 406 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL 3 408 " --> pdb=" O VAL 3 549 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 447 through 449 Processing sheet with id=AB4, first strand: chain '3' and resid 494 through 499 Processing sheet with id=AB5, first strand: chain '4' and resid 240 through 244 removed outlier: 6.934A pdb=" N LEU 4 241 " --> pdb=" O ARG 4 304 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TYR 4 306 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 6.380A 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 325 through 335 removed outlier: 6.876A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER 4 335 " --> pdb=" O VAL 4 396 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL 4 396 " --> pdb=" O SER 4 335 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N SER 4 414 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 9.899A pdb=" N VAL 4 461 " --> pdb=" O SER 4 414 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N SER 4 416 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL 4 463 " --> pdb=" O SER 4 416 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS 4 418 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N HIS 4 465 " --> pdb=" O CYS 4 418 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N TYR 4 420 " --> pdb=" O HIS 4 465 " (cutoff:3.500A) removed outlier: 13.411A pdb=" N LYS 4 467 " --> pdb=" O TYR 4 420 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR 4 436 " --> pdb=" O VAL 4 464 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL 4 466 " --> pdb=" O GLU 4 434 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU 4 434 " --> pdb=" O VAL 4 466 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '4' and resid 341 through 349 Processing sheet with id=AB8, first strand: chain '4' and resid 364 through 366 Processing sheet with id=AB9, first strand: chain '4' and resid 453 through 454 Processing sheet with id=AC1, first strand: chain '4' and resid 590 through 591 removed outlier: 6.514A pdb=" N ILE 4 564 " --> pdb=" O ALA 4 673 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA 4 675 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU 4 566 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 603 through 607 removed outlier: 3.551A pdb=" N TYR 4 604 " --> pdb=" O GLU 4 617 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '4' and resid 653 through 658 Processing sheet with id=AC4, first strand: chain '4' and resid 761 through 762 removed outlier: 6.685A pdb=" N ILE 4 761 " --> pdb=" O VAL 4 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain '5' and resid 60 through 64 removed outlier: 6.179A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN 5 140 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL 5 63 " --> pdb=" O ASN 5 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain '5' and resid 159 through 169 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 159 through 169 current: chain '5' and resid 189 through 193 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 189 through 193 current: chain '5' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 273 through 279 current: chain '5' and resid 325 through 337 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain '5' and resid 398 through 399 removed outlier: 3.651A pdb=" N LYS 5 398 " --> pdb=" O LEU 5 406 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '5' and resid 436 through 440 removed outlier: 6.460A pdb=" N VAL 5 412 " --> pdb=" O ALA 5 521 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA 5 523 " --> pdb=" O VAL 5 412 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU 5 414 " --> pdb=" O ALA 5 523 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '5' and resid 453 through 455 Processing sheet with id=AD1, first strand: chain '5' and resid 503 through 505 Processing sheet with id=AD2, first strand: chain '5' and resid 613 through 614 removed outlier: 6.472A pdb=" N ARG 5 613 " --> pdb=" O ALA 5 672 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain '6' and resid 123 through 124 removed outlier: 3.734A pdb=" N VAL 6 124 " --> pdb=" O GLU 6 133 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU 6 133 " --> pdb=" O VAL 6 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain '6' and resid 150 through 154 Processing sheet with id=AD5, first strand: chain '6' and resid 287 through 297 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 287 through 297 current: chain '6' and resid 317 through 322 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 317 through 322 current: chain '6' and resid 376 through 382 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 376 through 382 current: chain '6' and resid 450 through 461 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain '6' and resid 557 through 558 removed outlier: 3.603A pdb=" N LYS 6 557 " --> pdb=" O LEU 6 565 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '6' and resid 595 through 599 removed outlier: 6.480A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS 6 572 " --> pdb=" O PHE 6 713 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE 6 715 " --> pdb=" O CYS 6 572 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL 6 574 " --> pdb=" O ILE 6 715 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '6' and resid 611 through 614 Processing sheet with id=AD9, first strand: chain '6' and resid 660 through 664 Processing sheet with id=AE1, first strand: chain '7' and resid 77 through 81 removed outlier: 6.763A pdb=" N VAL 7 78 " --> pdb=" O TYR 7 203 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LYS 7 205 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE 7 80 " --> pdb=" O LYS 7 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain '7' and resid 224 through 225 removed outlier: 6.039A pdb=" N LEU 7 225 " --> pdb=" O ARG 7 242 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ILE 7 244 " --> pdb=" O LEU 7 225 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '7' and resid 238 through 248 current: chain '7' and resid 307 through 316 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 330 through 336 current: chain '7' and resid 374 through 383 Processing sheet with id=AE3, first strand: chain '7' and resid 268 through 272 Processing sheet with id=AE4, first strand: chain '7' and resid 442 through 443 Processing sheet with id=AE5, first strand: chain '7' and resid 481 through 484 removed outlier: 6.358A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU 7 564 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL 7 456 " --> pdb=" O ALA 7 565 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ALA 7 567 " --> pdb=" O VAL 7 456 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU 7 458 " --> pdb=" O ALA 7 567 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '7' and resid 495 through 499 Processing sheet with id=AE7, first strand: chain '7' and resid 545 through 548 removed outlier: 3.758A pdb=" N ILE 7 546 " --> pdb=" O LEU 7 557 " (cutoff:3.500A) 1073 hydrogen bonds defined for protein. 3069 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: 5.83 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5022 1.31 - 1.44: 7723 1.44 - 1.57: 17701 1.57 - 1.69: 92 1.69 - 1.82: 219 Bond restraints: 30757 Sorted by residual: bond pdb=" CA SER 2 706 " pdb=" CB SER 2 706 " ideal model delta sigma weight residual 1.532 1.454 0.077 1.52e-02 4.33e+03 2.59e+01 bond pdb=" C4 ADP 7 902 " pdb=" C5 ADP 7 902 " ideal model delta sigma weight residual 1.490 1.388 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C4 ADP 31000 " pdb=" C5 ADP 31000 " ideal model delta sigma weight residual 1.490 1.389 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C4 ADP 51000 " pdb=" C5 ADP 51000 " ideal model delta sigma weight residual 1.490 1.391 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C PRO 3 93 " pdb=" O PRO 3 93 " ideal model delta sigma weight residual 1.233 1.184 0.049 9.90e-03 1.02e+04 2.46e+01 ... (remaining 30752 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 39904 1.81 - 3.62: 1522 3.62 - 5.43: 274 5.43 - 7.24: 58 7.24 - 9.05: 11 Bond angle restraints: 41769 Sorted by residual: angle pdb=" N VAL 3 42 " pdb=" CA VAL 3 42 " pdb=" C VAL 3 42 " ideal model delta sigma weight residual 111.45 105.08 6.37 9.30e-01 1.16e+00 4.70e+01 angle pdb=" N ARG 3 39 " pdb=" CA ARG 3 39 " pdb=" C ARG 3 39 " ideal model delta sigma weight residual 111.36 104.68 6.68 1.09e+00 8.42e-01 3.76e+01 angle pdb=" N LYS 5 598 " pdb=" CA LYS 5 598 " pdb=" C LYS 5 598 " ideal model delta sigma weight residual 111.03 104.36 6.67 1.11e+00 8.12e-01 3.61e+01 angle pdb=" C PRO 2 708 " pdb=" CA PRO 2 708 " pdb=" CB PRO 2 708 " ideal model delta sigma weight residual 111.56 102.51 9.05 1.65e+00 3.67e-01 3.01e+01 angle pdb=" C HIS 3 94 " pdb=" CA HIS 3 94 " pdb=" CB HIS 3 94 " ideal model delta sigma weight residual 111.91 104.15 7.76 1.52e+00 4.33e-01 2.60e+01 ... (remaining 41764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.44: 18011 31.44 - 62.87: 788 62.87 - 94.31: 58 94.31 - 125.74: 2 125.74 - 157.18: 4 Dihedral angle restraints: 18863 sinusoidal: 7995 harmonic: 10868 Sorted by residual: dihedral pdb=" O1B ADP 7 902 " pdb=" O3A ADP 7 902 " pdb=" PB ADP 7 902 " pdb=" PA ADP 7 902 " ideal model delta sinusoidal sigma weight residual -60.00 97.17 -157.18 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O2A ADP 7 902 " pdb=" O3A ADP 7 902 " pdb=" PA ADP 7 902 " pdb=" PB ADP 7 902 " ideal model delta sinusoidal sigma weight residual -60.00 84.08 -144.08 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" C5' ADP 31000 " pdb=" O5' ADP 31000 " pdb=" PA ADP 31000 " pdb=" O2A ADP 31000 " ideal model delta sinusoidal sigma weight residual 300.00 157.66 142.35 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 18860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4224 0.074 - 0.148: 566 0.148 - 0.222: 56 0.222 - 0.296: 11 0.296 - 0.371: 3 Chirality restraints: 4860 Sorted by residual: chirality pdb=" CB VAL 4 615 " pdb=" CA VAL 4 615 " pdb=" CG1 VAL 4 615 " pdb=" CG2 VAL 4 615 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CB VAL 5 56 " pdb=" CA VAL 5 56 " pdb=" CG1 VAL 5 56 " pdb=" CG2 VAL 5 56 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA GLU 7 373 " pdb=" N GLU 7 373 " pdb=" C GLU 7 373 " pdb=" CB GLU 7 373 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 4857 not shown) Planarity restraints: 5221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL 7 713 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C VAL 7 713 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL 7 713 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU 7 714 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO 5 266 " -0.018 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C PRO 5 266 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO 5 266 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL 5 267 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG 5 651 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ARG 5 651 " 0.059 2.00e-02 2.50e+03 pdb=" O ARG 5 651 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN 5 652 " -0.020 2.00e-02 2.50e+03 ... (remaining 5218 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 58 2.52 - 3.11: 22331 3.11 - 3.71: 42737 3.71 - 4.30: 62086 4.30 - 4.90: 105185 Nonbonded interactions: 232397 Sorted by model distance: nonbonded pdb=" O3B ADP 51000 " pdb="MG MG 51001 " model vdw 1.922 2.170 nonbonded pdb=" O3B ADP 7 902 " pdb="MG MG 7 903 " model vdw 2.022 2.170 nonbonded pdb=" O3B ADP 41000 " pdb="MG MG 41001 " model vdw 2.024 2.170 nonbonded pdb=" OG SER 6 582 " pdb="MG MG 61102 " model vdw 2.024 2.170 nonbonded pdb=" OG SER 3 416 " pdb="MG MG 31001 " model vdw 2.068 2.170 ... (remaining 232392 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 'X' and resid 19 through 35) selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 25.900 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 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 : 0.006 0.102 30777 Z= 0.367 Angle : 0.915 33.188 41799 Z= 0.511 Chirality : 0.052 0.371 4860 Planarity : 0.005 0.079 5221 Dihedral : 16.508 157.175 11803 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.96 % Favored : 95.88 % Rotamer: Outliers : 0.97 % Allowed : 0.82 % Favored : 98.20 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.14), residues: 3661 helix: -0.16 (0.14), residues: 1355 sheet: -0.39 (0.19), residues: 715 loop : -1.19 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG 6 137 TYR 0.036 0.002 TYR 4 604 PHE 0.026 0.002 PHE 6 343 TRP 0.009 0.002 TRP 6 356 HIS 0.013 0.001 HIS 2 707 Details of bonding type rmsd covalent geometry : bond 0.00627 (30757) covalent geometry : angle 0.82016 (41769) hydrogen bonds : bond 0.18055 ( 1073) hydrogen bonds : angle 6.45043 ( 3069) metal coordination : bond 0.05322 ( 20) metal coordination : angle 15.13740 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.734 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: 4 614 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.7919 (tt) REVERT: 7 499 LYS cc_start: 0.6265 (OUTLIER) cc_final: 0.5839 (tttp) REVERT: 7 506 MET cc_start: 0.4624 (mmm) cc_final: 0.4390 (mmm) outliers start: 32 outliers final: 6 residues processed: 176 average time/residue: 0.1751 time to fit residues: 49.8688 Evaluate side-chains 103 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 154 LYS Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 4 residue 594 LYS Chi-restraints excluded: chain 4 residue 607 ARG Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 7 residue 491 VAL Chi-restraints excluded: chain 7 residue 499 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0050 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.4980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 356 ASN 2 710 ASN 2 779 HIS 4 266 GLN 5 185 ASN 5 359 GLN 7 543 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.045379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.036575 restraints weight = 219653.954| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 4.77 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30777 Z= 0.118 Angle : 0.598 17.556 41799 Z= 0.295 Chirality : 0.043 0.162 4860 Planarity : 0.004 0.063 5221 Dihedral : 13.037 162.124 4580 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 0.52 % Allowed : 4.81 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.14), residues: 3661 helix: 0.55 (0.14), residues: 1393 sheet: -0.23 (0.19), residues: 749 loop : -0.75 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 859 TYR 0.014 0.001 TYR 4 519 PHE 0.015 0.001 PHE 2 259 TRP 0.008 0.001 TRP 3 111 HIS 0.005 0.001 HIS 2 621 Details of bonding type rmsd covalent geometry : bond 0.00247 (30757) covalent geometry : angle 0.57555 (41769) hydrogen bonds : bond 0.04217 ( 1073) hydrogen bonds : angle 4.66968 ( 3069) metal coordination : bond 0.00754 ( 20) metal coordination : angle 6.10296 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 581 ARG cc_start: 0.8171 (mtm110) cc_final: 0.7879 (mtm110) REVERT: 3 462 MET cc_start: 0.9648 (OUTLIER) cc_final: 0.9448 (mtp) REVERT: 3 490 MET cc_start: 0.9546 (mtp) cc_final: 0.9244 (mtm) REVERT: 4 499 ARG cc_start: 0.8105 (mtp180) cc_final: 0.7413 (mtt180) REVERT: 6 143 MET cc_start: 0.8741 (mtt) cc_final: 0.8518 (mtt) REVERT: 7 498 MET cc_start: 0.7826 (ttp) cc_final: 0.7566 (ttp) REVERT: 7 506 MET cc_start: 0.3383 (mmm) cc_final: 0.3140 (mmm) REVERT: 7 529 MET cc_start: 0.9163 (ptm) cc_final: 0.8675 (tmm) REVERT: 7 621 MET cc_start: 0.9430 (ttt) cc_final: 0.8788 (tmm) outliers start: 17 outliers final: 7 residues processed: 110 average time/residue: 0.2023 time to fit residues: 36.2952 Evaluate side-chains 103 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 337 VAL Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 612 MET Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 4 residue 607 ARG Chi-restraints excluded: chain 6 residue 519 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 357 optimal weight: 5.9990 chunk 310 optimal weight: 8.9990 chunk 339 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 322 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 353 GLN 2 615 GLN ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 682 ASN 4 500 GLN ** 6 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 514 ASN 7 543 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.042213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.033711 restraints weight = 233622.888| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 4.66 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 30777 Z= 0.260 Angle : 0.666 10.553 41799 Z= 0.331 Chirality : 0.043 0.166 4860 Planarity : 0.005 0.061 5221 Dihedral : 12.629 171.252 4564 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.31 % Rotamer: Outliers : 0.79 % Allowed : 7.22 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.14), residues: 3661 helix: 0.81 (0.14), residues: 1395 sheet: -0.40 (0.18), residues: 787 loop : -0.62 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 676 TYR 0.014 0.002 TYR 7 260 PHE 0.015 0.002 PHE 3 655 TRP 0.008 0.001 TRP 6 356 HIS 0.012 0.001 HIS 4 413 Details of bonding type rmsd covalent geometry : bond 0.00577 (30757) covalent geometry : angle 0.65501 (41769) hydrogen bonds : bond 0.04561 ( 1073) hydrogen bonds : angle 4.75913 ( 3069) metal coordination : bond 0.01020 ( 20) metal coordination : angle 4.62539 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 386 MET cc_start: 0.9031 (ttm) cc_final: 0.8722 (ttm) REVERT: 3 462 MET cc_start: 0.9618 (OUTLIER) cc_final: 0.9295 (tpp) REVERT: 4 499 ARG cc_start: 0.8283 (mtp180) cc_final: 0.7619 (mtt180) REVERT: 4 749 MET cc_start: 0.9366 (ptt) cc_final: 0.9126 (ppp) REVERT: 5 583 MET cc_start: 0.8048 (ppp) cc_final: 0.7718 (pmm) REVERT: 6 143 MET cc_start: 0.8733 (mtt) cc_final: 0.8515 (mtt) REVERT: 7 125 MET cc_start: 0.9117 (ttp) cc_final: 0.8712 (tpp) REVERT: 7 498 MET cc_start: 0.8149 (ttp) cc_final: 0.7865 (ttp) outliers start: 26 outliers final: 10 residues processed: 109 average time/residue: 0.1825 time to fit residues: 33.4609 Evaluate side-chains 102 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 337 VAL Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 6 residue 331 THR Chi-restraints excluded: chain 7 residue 121 ILE Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 652 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 296 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 370 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 224 optimal weight: 0.6980 chunk 263 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 219 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 615 GLN ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 125 GLN 6 323 GLN 7 543 GLN 7 583 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.043192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.034596 restraints weight = 225912.536| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 4.67 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30777 Z= 0.096 Angle : 0.521 9.912 41799 Z= 0.258 Chirality : 0.041 0.146 4860 Planarity : 0.004 0.062 5221 Dihedral : 12.268 174.552 4560 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.30 % Rotamer: Outliers : 0.73 % Allowed : 8.13 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.14), residues: 3661 helix: 1.24 (0.15), residues: 1391 sheet: -0.09 (0.18), residues: 763 loop : -0.43 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 676 TYR 0.015 0.001 TYR 2 555 PHE 0.014 0.001 PHE 6 142 TRP 0.008 0.001 TRP 6 356 HIS 0.006 0.001 HIS 4 413 Details of bonding type rmsd covalent geometry : bond 0.00210 (30757) covalent geometry : angle 0.51206 (41769) hydrogen bonds : bond 0.03216 ( 1073) hydrogen bonds : angle 4.28197 ( 3069) metal coordination : bond 0.00466 ( 20) metal coordination : angle 3.59400 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 386 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8633 (ttm) REVERT: 3 462 MET cc_start: 0.9569 (OUTLIER) cc_final: 0.9287 (tpp) REVERT: 3 483 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8828 (ptp90) REVERT: 6 143 MET cc_start: 0.8569 (mtt) cc_final: 0.8281 (mtt) REVERT: 6 736 MET cc_start: 0.8552 (ttm) cc_final: 0.8325 (ttm) REVERT: 7 498 MET cc_start: 0.8109 (ttp) cc_final: 0.7814 (ttp) REVERT: 7 621 MET cc_start: 0.9330 (ttt) cc_final: 0.8941 (tmm) outliers start: 24 outliers final: 9 residues processed: 111 average time/residue: 0.1896 time to fit residues: 35.7570 Evaluate side-chains 104 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 337 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 446 VAL Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 3 residue 483 ARG Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 6 residue 331 THR Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 541 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 106 optimal weight: 0.0870 chunk 209 optimal weight: 0.4980 chunk 6 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 314 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 chunk 367 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 overall best weight: 2.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 531 GLN 7 583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.042449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.033898 restraints weight = 232766.307| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 4.69 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30777 Z= 0.154 Angle : 0.540 8.833 41799 Z= 0.267 Chirality : 0.041 0.149 4860 Planarity : 0.004 0.062 5221 Dihedral : 12.087 176.489 4560 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 0.97 % Allowed : 8.96 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.14), residues: 3661 helix: 1.38 (0.15), residues: 1397 sheet: 0.01 (0.19), residues: 759 loop : -0.30 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 716 TYR 0.011 0.001 TYR 4 580 PHE 0.009 0.001 PHE 3 655 TRP 0.007 0.001 TRP 6 356 HIS 0.004 0.001 HIS 7 615 Details of bonding type rmsd covalent geometry : bond 0.00347 (30757) covalent geometry : angle 0.53381 (41769) hydrogen bonds : bond 0.03341 ( 1073) hydrogen bonds : angle 4.26696 ( 3069) metal coordination : bond 0.00625 ( 20) metal coordination : angle 3.14193 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 276 MET cc_start: 0.9232 (tpp) cc_final: 0.8979 (tpp) REVERT: 3 386 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8695 (ttm) REVERT: 3 483 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8688 (ptp90) REVERT: 6 143 MET cc_start: 0.8579 (mtt) cc_final: 0.8272 (mtt) REVERT: 7 125 MET cc_start: 0.9126 (ttp) cc_final: 0.8716 (tpp) REVERT: 7 402 MET cc_start: 0.9126 (ppp) cc_final: 0.8916 (ppp) REVERT: 7 498 MET cc_start: 0.8246 (ttp) cc_final: 0.7930 (ttp) REVERT: 7 529 MET cc_start: 0.9125 (ptm) cc_final: 0.8449 (tmm) REVERT: 7 621 MET cc_start: 0.9326 (ttt) cc_final: 0.8902 (tmm) outliers start: 32 outliers final: 18 residues processed: 113 average time/residue: 0.1797 time to fit residues: 35.0345 Evaluate side-chains 109 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 337 VAL Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 709 GLU Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 3 residue 446 VAL Chi-restraints excluded: chain 3 residue 483 ARG Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 5 residue 265 VAL Chi-restraints excluded: chain 5 residue 267 VAL Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 556 VAL Chi-restraints excluded: chain 6 residue 331 THR Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 394 THR Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 652 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 99 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 286 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 202 optimal weight: 0.6980 chunk 295 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 chunk 340 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 290 HIS ** 2 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 307 ASN 3 308 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.042314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.033818 restraints weight = 232877.343| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 4.66 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30777 Z= 0.142 Angle : 0.536 10.005 41799 Z= 0.263 Chirality : 0.041 0.144 4860 Planarity : 0.004 0.062 5221 Dihedral : 11.919 166.606 4560 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.24 % Rotamer: Outliers : 0.70 % Allowed : 9.75 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.14), residues: 3661 helix: 1.50 (0.15), residues: 1398 sheet: 0.10 (0.19), residues: 755 loop : -0.22 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 716 TYR 0.011 0.001 TYR 2 555 PHE 0.009 0.001 PHE 6 142 TRP 0.008 0.001 TRP 6 356 HIS 0.003 0.001 HIS 7 615 Details of bonding type rmsd covalent geometry : bond 0.00320 (30757) covalent geometry : angle 0.52998 (41769) hydrogen bonds : bond 0.03170 ( 1073) hydrogen bonds : angle 4.17543 ( 3069) metal coordination : bond 0.00570 ( 20) metal coordination : angle 2.97283 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 267 MET cc_start: 0.8883 (mtp) cc_final: 0.8672 (ptp) REVERT: 2 276 MET cc_start: 0.9274 (tpp) cc_final: 0.9052 (tpp) REVERT: 3 386 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8760 (ttm) REVERT: 3 462 MET cc_start: 0.9626 (tpp) cc_final: 0.9251 (tpp) REVERT: 3 483 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8487 (mtm-85) REVERT: 3 490 MET cc_start: 0.9274 (mtm) cc_final: 0.8387 (mpp) REVERT: 4 314 MET cc_start: 0.8367 (ppp) cc_final: 0.7922 (ppp) REVERT: 6 143 MET cc_start: 0.8576 (mtt) cc_final: 0.8309 (mtt) REVERT: 7 125 MET cc_start: 0.9162 (ttp) cc_final: 0.8737 (tpp) REVERT: 7 498 MET cc_start: 0.8297 (ttp) cc_final: 0.7994 (ttp) REVERT: 7 621 MET cc_start: 0.9334 (ttt) cc_final: 0.9101 (ttt) outliers start: 23 outliers final: 18 residues processed: 106 average time/residue: 0.1656 time to fit residues: 30.5820 Evaluate side-chains 108 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 337 VAL Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 3 residue 446 VAL Chi-restraints excluded: chain 3 residue 483 ARG Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 768 THR Chi-restraints excluded: chain 5 residue 267 VAL Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 556 VAL Chi-restraints excluded: chain 6 residue 331 THR Chi-restraints excluded: chain 6 residue 695 LEU Chi-restraints excluded: chain 7 residue 121 ILE Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 394 THR Chi-restraints excluded: chain 7 residue 652 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 312 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 316 optimal weight: 0.8980 chunk 341 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.041026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.032637 restraints weight = 240202.892| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 4.67 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 30777 Z= 0.290 Angle : 0.655 11.144 41799 Z= 0.325 Chirality : 0.043 0.145 4860 Planarity : 0.004 0.060 5221 Dihedral : 11.957 155.247 4560 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 0.85 % Allowed : 10.63 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.14), residues: 3661 helix: 1.28 (0.14), residues: 1406 sheet: -0.14 (0.18), residues: 766 loop : -0.30 (0.16), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 7 400 TYR 0.015 0.002 TYR 2 227 PHE 0.013 0.002 PHE 3 28 TRP 0.009 0.001 TRP 6 356 HIS 0.007 0.001 HIS 7 615 Details of bonding type rmsd covalent geometry : bond 0.00648 (30757) covalent geometry : angle 0.64832 (41769) hydrogen bonds : bond 0.04008 ( 1073) hydrogen bonds : angle 4.54070 ( 3069) metal coordination : bond 0.01127 ( 20) metal coordination : angle 3.55745 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: 3 386 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8817 (ttm) REVERT: 3 462 MET cc_start: 0.9613 (tpp) cc_final: 0.9244 (tpp) REVERT: 3 483 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8447 (mtm-85) REVERT: 4 314 MET cc_start: 0.8188 (ppp) cc_final: 0.7814 (ppp) REVERT: 5 182 MET cc_start: 0.8918 (ttp) cc_final: 0.8112 (ppp) REVERT: 6 143 MET cc_start: 0.8686 (mtt) cc_final: 0.8431 (mtt) REVERT: 7 125 MET cc_start: 0.9125 (ttp) cc_final: 0.8782 (tpp) REVERT: 7 498 MET cc_start: 0.8269 (ttp) cc_final: 0.7933 (ttp) REVERT: 7 529 MET cc_start: 0.9206 (ptm) cc_final: 0.8514 (tmm) REVERT: 7 600 MET cc_start: 0.8972 (mtm) cc_final: 0.8770 (mtm) REVERT: 7 621 MET cc_start: 0.9332 (ttt) cc_final: 0.9107 (ttt) outliers start: 28 outliers final: 19 residues processed: 105 average time/residue: 0.1603 time to fit residues: 29.4839 Evaluate side-chains 105 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 337 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 3 residue 483 ARG Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 4 residue 768 THR Chi-restraints excluded: chain 5 residue 267 VAL Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 556 VAL Chi-restraints excluded: chain 6 residue 331 THR Chi-restraints excluded: chain 6 residue 519 MET Chi-restraints excluded: chain 6 residue 695 LEU Chi-restraints excluded: chain 7 residue 66 MET Chi-restraints excluded: chain 7 residue 121 ILE Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 394 THR Chi-restraints excluded: chain 7 residue 652 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 229 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 350 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 369 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 90 ASN 7 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.041757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.033305 restraints weight = 237089.686| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 4.70 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30777 Z= 0.135 Angle : 0.544 11.485 41799 Z= 0.269 Chirality : 0.041 0.146 4860 Planarity : 0.004 0.061 5221 Dihedral : 11.714 141.054 4560 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.24 % Rotamer: Outliers : 0.76 % Allowed : 11.24 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.14), residues: 3661 helix: 1.57 (0.14), residues: 1397 sheet: -0.02 (0.19), residues: 747 loop : -0.16 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 716 TYR 0.015 0.001 TYR 2 555 PHE 0.011 0.001 PHE 6 397 TRP 0.010 0.001 TRP 3 111 HIS 0.003 0.001 HIS 6 157 Details of bonding type rmsd covalent geometry : bond 0.00307 (30757) covalent geometry : angle 0.53856 (41769) hydrogen bonds : bond 0.03256 ( 1073) hydrogen bonds : angle 4.21675 ( 3069) metal coordination : bond 0.00615 ( 20) metal coordination : angle 3.02220 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 501 MET cc_start: 0.8885 (mmm) cc_final: 0.8658 (mmm) REVERT: 3 386 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8839 (ttm) REVERT: 3 462 MET cc_start: 0.9621 (tpp) cc_final: 0.9240 (tpp) REVERT: 3 483 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8467 (mtm-85) REVERT: 4 314 MET cc_start: 0.8316 (ppp) cc_final: 0.7786 (ppp) REVERT: 6 143 MET cc_start: 0.8662 (mtt) cc_final: 0.8423 (mtt) REVERT: 7 125 MET cc_start: 0.9129 (ttp) cc_final: 0.8761 (tpp) REVERT: 7 498 MET cc_start: 0.8451 (ttp) cc_final: 0.8088 (ttp) REVERT: 7 529 MET cc_start: 0.9197 (ptm) cc_final: 0.8481 (tmm) REVERT: 7 600 MET cc_start: 0.8956 (mtm) cc_final: 0.8713 (mtm) REVERT: 7 621 MET cc_start: 0.9349 (ttt) cc_final: 0.9142 (ttt) outliers start: 25 outliers final: 16 residues processed: 106 average time/residue: 0.1759 time to fit residues: 32.6519 Evaluate side-chains 103 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 337 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 3 residue 483 ARG Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 5 residue 267 VAL Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 556 VAL Chi-restraints excluded: chain 6 residue 331 THR Chi-restraints excluded: chain 6 residue 695 LEU Chi-restraints excluded: chain 7 residue 121 ILE Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 394 THR Chi-restraints excluded: chain 7 residue 652 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 307 optimal weight: 0.9990 chunk 253 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 368 optimal weight: 5.9990 chunk 181 optimal weight: 0.0270 chunk 369 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 246 optimal weight: 3.9990 chunk 342 optimal weight: 0.9980 chunk 131 optimal weight: 0.0670 chunk 102 optimal weight: 5.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 707 HIS ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.042524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.034028 restraints weight = 231859.970| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 4.70 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30777 Z= 0.089 Angle : 0.529 12.999 41799 Z= 0.257 Chirality : 0.040 0.136 4860 Planarity : 0.003 0.066 5221 Dihedral : 11.337 115.962 4560 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 0.52 % Allowed : 11.54 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.14), residues: 3661 helix: 1.66 (0.15), residues: 1411 sheet: 0.26 (0.19), residues: 756 loop : -0.09 (0.17), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 694 TYR 0.009 0.001 TYR 3 659 PHE 0.010 0.001 PHE 6 142 TRP 0.009 0.001 TRP 6 356 HIS 0.003 0.000 HIS 6 157 Details of bonding type rmsd covalent geometry : bond 0.00197 (30757) covalent geometry : angle 0.52378 (41769) hydrogen bonds : bond 0.02811 ( 1073) hydrogen bonds : angle 4.00736 ( 3069) metal coordination : bond 0.00346 ( 20) metal coordination : angle 2.77098 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: 3 386 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8846 (ttm) REVERT: 3 462 MET cc_start: 0.9617 (tpp) cc_final: 0.9267 (tpp) REVERT: 3 483 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8504 (mtm-85) REVERT: 4 314 MET cc_start: 0.8295 (ppp) cc_final: 0.7806 (ppp) REVERT: 4 382 MET cc_start: 0.8499 (mmp) cc_final: 0.8256 (mmp) REVERT: 5 182 MET cc_start: 0.8842 (ttp) cc_final: 0.8112 (ppp) REVERT: 5 583 MET cc_start: 0.8196 (ppp) cc_final: 0.7849 (ppp) REVERT: 6 143 MET cc_start: 0.8574 (mtt) cc_final: 0.8342 (mtt) REVERT: 7 125 MET cc_start: 0.9124 (ttp) cc_final: 0.8753 (tpp) REVERT: 7 498 MET cc_start: 0.8383 (ttp) cc_final: 0.8030 (ttp) REVERT: 7 529 MET cc_start: 0.9169 (ptm) cc_final: 0.8459 (tmm) REVERT: 7 621 MET cc_start: 0.9348 (ttt) cc_final: 0.9127 (ttt) outliers start: 17 outliers final: 10 residues processed: 100 average time/residue: 0.1750 time to fit residues: 30.7759 Evaluate side-chains 96 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 337 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 3 residue 483 ARG Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 4 residue 768 THR Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 556 VAL Chi-restraints excluded: chain 7 residue 121 ILE Chi-restraints excluded: chain 7 residue 244 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 16 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 189 optimal weight: 0.0980 chunk 107 optimal weight: 0.5980 chunk 254 optimal weight: 8.9990 chunk 311 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 316 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.042079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.033631 restraints weight = 234216.467| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 4.68 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30777 Z= 0.127 Angle : 0.542 13.356 41799 Z= 0.264 Chirality : 0.040 0.149 4860 Planarity : 0.004 0.066 5221 Dihedral : 11.220 108.940 4560 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.81 % Favored : 97.16 % Rotamer: Outliers : 0.40 % Allowed : 11.91 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.14), residues: 3661 helix: 1.76 (0.15), residues: 1402 sheet: 0.27 (0.19), residues: 756 loop : -0.06 (0.17), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 491 TYR 0.008 0.001 TYR 3 659 PHE 0.009 0.001 PHE 2 259 TRP 0.008 0.001 TRP 6 356 HIS 0.002 0.001 HIS 7 615 Details of bonding type rmsd covalent geometry : bond 0.00289 (30757) covalent geometry : angle 0.53757 (41769) hydrogen bonds : bond 0.02968 ( 1073) hydrogen bonds : angle 4.05845 ( 3069) metal coordination : bond 0.00509 ( 20) metal coordination : angle 2.64426 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.070 Fit side-chains REVERT: 3 386 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8901 (ttm) REVERT: 3 462 MET cc_start: 0.9599 (tpp) cc_final: 0.9247 (tpp) REVERT: 4 314 MET cc_start: 0.8291 (ppp) cc_final: 0.7713 (ppp) REVERT: 4 382 MET cc_start: 0.8563 (mmp) cc_final: 0.8321 (mmp) REVERT: 5 182 MET cc_start: 0.8921 (ttp) cc_final: 0.8213 (ppp) REVERT: 5 583 MET cc_start: 0.8222 (ppp) cc_final: 0.7867 (ppp) REVERT: 6 143 MET cc_start: 0.8623 (mtt) cc_final: 0.8384 (mtt) REVERT: 7 125 MET cc_start: 0.9139 (ttp) cc_final: 0.8755 (tpp) REVERT: 7 498 MET cc_start: 0.8407 (ttp) cc_final: 0.8051 (ttp) REVERT: 7 529 MET cc_start: 0.9148 (ptm) cc_final: 0.8933 (tmm) REVERT: 7 600 MET cc_start: 0.9002 (mtm) cc_final: 0.8690 (mtm) REVERT: 7 621 MET cc_start: 0.9359 (ttt) cc_final: 0.9133 (ttt) REVERT: 7 707 MET cc_start: 0.8430 (mmm) cc_final: 0.8189 (mmp) outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 0.1482 time to fit residues: 24.4934 Evaluate side-chains 94 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 337 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 4 residue 768 THR Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 556 VAL Chi-restraints excluded: chain 7 residue 121 ILE Chi-restraints excluded: chain 7 residue 244 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 231 optimal weight: 0.9980 chunk 364 optimal weight: 7.9990 chunk 200 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 262 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 301 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.041794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.033351 restraints weight = 237740.210| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 4.70 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30777 Z= 0.141 Angle : 0.548 13.172 41799 Z= 0.268 Chirality : 0.040 0.146 4860 Planarity : 0.004 0.066 5221 Dihedral : 11.102 101.813 4560 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.94 % Rotamer: Outliers : 0.43 % Allowed : 11.82 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.14), residues: 3661 helix: 1.76 (0.15), residues: 1406 sheet: 0.27 (0.19), residues: 747 loop : -0.04 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 489 TYR 0.010 0.001 TYR 7 63 PHE 0.008 0.001 PHE 6 180 TRP 0.008 0.001 TRP 6 356 HIS 0.003 0.001 HIS 7 615 Details of bonding type rmsd covalent geometry : bond 0.00319 (30757) covalent geometry : angle 0.54390 (41769) hydrogen bonds : bond 0.03070 ( 1073) hydrogen bonds : angle 4.07677 ( 3069) metal coordination : bond 0.00602 ( 20) metal coordination : angle 2.65875 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3971.89 seconds wall clock time: 69 minutes 49.03 seconds (4189.03 seconds total)