Starting phenix.real_space_refine on Mon Jul 6 03:04:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s0b_19620/07_2026/8s0b_19620.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s0b_19620/07_2026/8s0b_19620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8s0b_19620/07_2026/8s0b_19620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s0b_19620/07_2026/8s0b_19620.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s0b_19620/07_2026/8s0b_19620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s0b_19620/07_2026/8s0b_19620.map" } resolution = 3.6 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= 0.003 sd= 0.027 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 105 5.49 5 Mg 6 5.21 5 S 191 5.16 5 C 20068 2.51 5 N 5750 2.21 5 O 6299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32424 Number of models: 1 Model: "" Number of chains: 15 Chain: "F" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1341 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Chain breaks: 1 Chain: "2" Number of atoms: 5093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5093 Classifications: {'peptide': 643} Link IDs: {'PTRANS': 29, 'TRANS': 613} Chain breaks: 2 Chain: "3" Number of atoms: 4715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4715 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 577} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "4" Number of atoms: 4969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4969 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 28, 'TRANS': 594} Chain breaks: 1 Chain: "5" Number of atoms: 4679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4679 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 25, 'TRANS': 569} Chain breaks: 4 Chain: "6" Number of atoms: 5259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5259 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 21, 'TRANS': 630} Chain breaks: 5 Chain: "7" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4338 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 25, 'TRANS': 522} Chain breaks: 8 Chain: "X" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 921 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "Y" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 924 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2557 SG CYS 2 329 112.947 35.988 67.665 1.00 65.06 S ATOM 2580 SG CYS 2 332 114.338 32.943 66.695 1.00 73.56 S ATOM 2731 SG CYS 2 352 115.830 34.362 70.055 1.00 79.31 S ATOM 2753 SG CYS 2 355 116.625 35.977 66.940 1.00 84.13 S ATOM 12432 SG CYS 4 306 134.093 77.790 90.065 1.00 57.77 S ATOM 12454 SG CYS 4 309 136.428 79.271 92.609 1.00 60.67 S ATOM 12600 SG CYS 4 328 136.874 80.238 88.970 1.00 63.48 S ATOM 12621 SG CYS 4 331 137.551 76.709 89.710 1.00 72.53 S ATOM 17265 SG CYS 5 172 115.482 48.290 47.433 1.00123.88 S ATOM 17288 SG CYS 5 175 116.997 45.833 45.415 1.00127.77 S ATOM 17459 SG CYS 5 197 117.033 45.405 49.177 1.00142.68 S ATOM 21965 SG CYS 6 158 129.206 61.549 85.221 1.00 87.76 S ATOM 21987 SG CYS 6 161 132.916 60.782 86.331 1.00 92.86 S ATOM 22148 SG CYS 6 180 131.347 63.905 86.939 1.00 99.34 S ATOM 22187 SG CYS 6 185 132.385 62.259 83.249 1.00105.97 S ATOM 27397 SG CYS 7 184 132.337 89.444 63.685 1.00137.60 S ATOM 27420 SG CYS 7 187 133.847 91.326 61.010 1.00145.03 S ATOM 27566 SG CYS 7 206 131.342 88.273 60.416 1.00135.17 S ATOM 27603 SG CYS 7 211 134.965 87.669 61.589 1.00136.56 S Time building chain proxies: 6.40, per 1000 atoms: 0.20 Number of scatterers: 32424 At special positions: 0 Unit cell: (179.28, 149.04, 143.64, 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 191 16.00 P 105 15.00 Mg 6 11.99 O 6299 8.00 N 5750 7.00 C 20068 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: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21003 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 355 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 332 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 329 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 352 " pdb=" ZN 4 901 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 306 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 328 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 331 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 309 " pdb=" ZN 5 803 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 172 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 175 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 197 " pdb=" ZN 6 903 " pdb="ZN ZN 6 903 " - pdb=" SG CYS 6 180 " pdb="ZN ZN 6 903 " - pdb=" SG CYS 6 161 " pdb="ZN ZN 6 903 " - pdb=" SG CYS 6 185 " pdb="ZN ZN 6 903 " - pdb=" SG CYS 6 158 " pdb=" ZN 7 804 " pdb="ZN ZN 7 804 " - pdb=" SG CYS 7 184 " pdb="ZN ZN 7 804 " - pdb=" SG CYS 7 187 " pdb="ZN ZN 7 804 " - pdb=" SG CYS 7 206 " pdb="ZN ZN 7 804 " - pdb=" SG CYS 7 211 " Number of angles added : 24 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7304 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 39 sheets defined 48.1% alpha, 14.1% beta 45 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'F' and resid 2 through 14 removed outlier: 3.860A pdb=" N ILE F 6 " --> pdb=" O GLY F 2 " (cutoff:3.500A) Proline residue: F 11 - end of helix Processing helix chain 'F' and resid 17 through 35 removed outlier: 3.570A pdb=" N LEU F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 42 Processing helix chain 'F' and resid 44 through 59 removed outlier: 3.637A pdb=" N ALA F 48 " --> pdb=" O GLU F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 73 Processing helix chain 'F' and resid 75 through 91 Processing helix chain 'F' and resid 97 through 104 removed outlier: 3.661A pdb=" N LEU F 101 " --> pdb=" O GLY F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 123 removed outlier: 4.042A pdb=" N MET F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER F 120 " --> pdb=" O LYS F 116 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER F 123 " --> pdb=" O LYS F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 133 removed outlier: 4.303A pdb=" N ASP F 132 " --> pdb=" O THR F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 151 removed outlier: 3.686A pdb=" N THR F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 166 Processing helix chain 'F' and resid 168 through 182 removed outlier: 3.700A pdb=" N GLN F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain '2' and resid 182 through 188 removed outlier: 3.704A pdb=" N MET 2 188 " --> pdb=" O GLU 2 184 " (cutoff:3.500A) Processing helix chain '2' and resid 188 through 206 Processing helix chain '2' and resid 213 through 225 removed outlier: 3.608A pdb=" N GLU 2 217 " --> pdb=" O ASN 2 213 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU 2 225 " --> pdb=" O ASP 2 221 " (cutoff:3.500A) Processing helix chain '2' and resid 233 through 241 Processing helix chain '2' and resid 242 through 248 Processing helix chain '2' and resid 251 through 271 removed outlier: 3.808A pdb=" N LEU 2 255 " --> pdb=" O ALA 2 251 " (cutoff:3.500A) Processing helix chain '2' and resid 273 through 278 removed outlier: 3.771A pdb=" N ILE 2 277 " --> pdb=" O LYS 2 273 " (cutoff:3.500A) Processing helix chain '2' and resid 293 through 297 removed outlier: 3.802A pdb=" N LEU 2 297 " --> pdb=" O LEU 2 294 " (cutoff:3.500A) Processing helix chain '2' and resid 298 through 302 removed outlier: 3.515A pdb=" N LEU 2 302 " --> pdb=" O GLN 2 299 " (cutoff:3.500A) Processing helix chain '2' and resid 401 through 403 No H-bonds generated for 'chain '2' and resid 401 through 403' Processing helix chain '2' and resid 459 through 469 Processing helix chain '2' and resid 472 through 481 Processing helix chain '2' and resid 488 through 501 Processing helix chain '2' and resid 529 through 540 removed outlier: 3.638A pdb=" N LEU 2 533 " --> pdb=" O LYS 2 529 " (cutoff:3.500A) Processing helix chain '2' and resid 574 through 579 Processing helix chain '2' and resid 588 through 592 removed outlier: 4.142A pdb=" N MET 2 592 " --> pdb=" O PHE 2 589 " (cutoff:3.500A) Processing helix chain '2' and resid 593 through 606 Processing helix chain '2' and resid 642 through 647 Processing helix chain '2' and resid 650 through 657 removed outlier: 3.649A pdb=" N ARG 2 656 " --> pdb=" O PRO 2 652 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE 2 657 " --> pdb=" O ILE 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 668 through 686 Processing helix chain '2' and resid 716 through 730 Processing helix chain '2' and resid 739 through 758 removed outlier: 3.682A pdb=" N VAL 2 743 " --> pdb=" O ASP 2 739 " (cutoff:3.500A) Processing helix chain '2' and resid 763 through 781 removed outlier: 3.988A pdb=" N ILE 2 767 " --> pdb=" O THR 2 763 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS 2 781 " --> pdb=" O HIS 2 777 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 806 removed outlier: 3.610A pdb=" N VAL 2 791 " --> pdb=" O ILE 2 787 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN 2 806 " --> pdb=" O PHE 2 802 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 818 Processing helix chain '2' and resid 818 through 823 Processing helix chain '2' and resid 827 through 851 Processing helix chain '3' and resid 11 through 24 Processing helix chain '3' and resid 25 through 29 removed outlier: 3.516A pdb=" N GLN 3 29 " --> pdb=" O GLU 3 26 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 42 Processing helix chain '3' and resid 51 through 58 Processing helix chain '3' and resid 58 through 68 Processing helix chain '3' and resid 69 through 88 Processing helix chain '3' and resid 88 through 93 Processing helix chain '3' and resid 117 through 121 Processing helix chain '3' and resid 224 through 226 No H-bonds generated for 'chain '3' and resid 224 through 226' Processing helix chain '3' and resid 279 through 291 removed outlier: 4.237A pdb=" N LYS 3 283 " --> pdb=" O GLU 3 279 " (cutoff:3.500A) Processing helix chain '3' and resid 294 through 302 Processing helix chain '3' and resid 310 through 323 Processing helix chain '3' and resid 351 through 362 Processing helix chain '3' and resid 374 through 379 Processing helix chain '3' and resid 396 through 401 Processing helix chain '3' and resid 410 through 414 Processing helix chain '3' and resid 415 through 429 removed outlier: 4.154A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL 3 425 " --> pdb=" O ALA 3 421 " (cutoff:3.500A) Processing helix chain '3' and resid 464 through 470 Processing helix chain '3' and resid 472 through 479 Processing helix chain '3' and resid 490 through 507 Processing helix chain '3' and resid 555 through 559 removed outlier: 3.999A pdb=" N LYS 3 559 " --> pdb=" O LYS 3 556 " (cutoff:3.500A) Processing helix chain '3' and resid 564 through 578 Processing helix chain '3' and resid 583 through 600 removed outlier: 4.100A pdb=" N ALA 3 587 " --> pdb=" O THR 3 583 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR 3 588 " --> pdb=" O GLN 3 584 " (cutoff:3.500A) Processing helix chain '3' and resid 601 through 604 removed outlier: 3.931A pdb=" N SER 3 604 " --> pdb=" O ASP 3 601 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 601 through 604' Processing helix chain '3' and resid 615 through 632 removed outlier: 3.761A pdb=" N GLU 3 619 " --> pdb=" O ALA 3 615 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG 3 632 " --> pdb=" O HIS 3 628 " (cutoff:3.500A) Processing helix chain '3' and resid 638 through 653 removed outlier: 3.528A pdb=" N ALA 3 642 " --> pdb=" O ASP 3 638 " (cutoff:3.500A) Processing helix chain '4' and resid 158 through 173 removed outlier: 3.552A pdb=" N GLN 4 171 " --> pdb=" O GLN 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 191 through 204 Processing helix chain '4' and resid 212 through 219 Processing helix chain '4' and resid 220 through 229 Processing helix chain '4' and resid 229 through 249 Proline residue: 4 235 - end of helix Processing helix chain '4' and resid 270 through 274 Processing helix chain '4' and resid 275 through 279 Processing helix chain '4' and resid 377 through 379 No H-bonds generated for 'chain '4' and resid 377 through 379' Processing helix chain '4' and resid 431 through 436 Processing helix chain '4' and resid 442 through 455 removed outlier: 3.731A pdb=" N LYS 4 455 " --> pdb=" O GLU 4 451 " (cutoff:3.500A) Processing helix chain '4' and resid 457 through 466 Processing helix chain '4' and resid 473 through 486 Processing helix chain '4' and resid 516 through 525 Processing helix chain '4' and resid 536 through 538 No H-bonds generated for 'chain '4' and resid 536 through 538' Processing helix chain '4' and resid 561 through 566 Processing helix chain '4' and resid 580 through 594 removed outlier: 3.905A pdb=" N VAL 4 586 " --> pdb=" O SER 4 582 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU 4 587 " --> pdb=" O THR 4 583 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU 4 589 " --> pdb=" O SER 4 585 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU 4 592 " --> pdb=" O HIS 4 588 " (cutoff:3.500A) Processing helix chain '4' and resid 629 through 635 Processing helix chain '4' and resid 637 through 642 Processing helix chain '4' and resid 655 through 670 removed outlier: 3.790A pdb=" N TYR 4 670 " --> pdb=" O LEU 4 666 " (cutoff:3.500A) Processing helix chain '4' and resid 683 through 698 removed outlier: 3.742A pdb=" N ILE 4 698 " --> pdb=" O ALA 4 694 " (cutoff:3.500A) Processing helix chain '4' and resid 703 through 722 Processing helix chain '4' and resid 730 through 748 removed outlier: 4.073A pdb=" N LEU 4 734 " --> pdb=" O TYR 4 730 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU 4 735 " --> pdb=" O PRO 4 731 " (cutoff:3.500A) Processing helix chain '4' and resid 754 through 769 removed outlier: 3.616A pdb=" N VAL 4 758 " --> pdb=" O GLU 4 754 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU 4 769 " --> pdb=" O HIS 4 765 " (cutoff:3.500A) Processing helix chain '5' and resid 27 through 42 Processing helix chain '5' and resid 53 through 66 Processing helix chain '5' and resid 74 through 81 Processing helix chain '5' and resid 81 through 89 removed outlier: 3.857A pdb=" N ALA 5 85 " --> pdb=" O ASP 5 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR 5 89 " --> pdb=" O ALA 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 111 removed outlier: 3.817A pdb=" N HIS 5 95 " --> pdb=" O GLN 5 91 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) Processing helix chain '5' and resid 136 through 140 removed outlier: 3.955A pdb=" N LEU 5 140 " --> pdb=" O ILE 5 137 " (cutoff:3.500A) Processing helix chain '5' and resid 141 through 145 Processing helix chain '5' and resid 216 through 219 removed outlier: 3.644A pdb=" N CYS 5 219 " --> pdb=" O PRO 5 216 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 216 through 219' Processing helix chain '5' and resid 252 through 254 No H-bonds generated for 'chain '5' and resid 252 through 254' Processing helix chain '5' and resid 317 through 328 removed outlier: 3.616A pdb=" N LEU 5 328 " --> pdb=" O ARG 5 324 " (cutoff:3.500A) Processing helix chain '5' and resid 330 through 339 Processing helix chain '5' and resid 346 through 359 Processing helix chain '5' and resid 387 through 398 Processing helix chain '5' and resid 432 through 437 Processing helix chain '5' and resid 446 through 450 removed outlier: 3.702A pdb=" N LYS 5 449 " --> pdb=" O GLU 5 446 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET 5 450 " --> pdb=" O PHE 5 447 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 446 through 450' Processing helix chain '5' and resid 451 through 464 removed outlier: 3.686A pdb=" N HIS 5 459 " --> pdb=" O ARG 5 455 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU 5 460 " --> pdb=" O VAL 5 456 " (cutoff:3.500A) Processing helix chain '5' and resid 507 through 512 Processing helix chain '5' and resid 525 through 543 removed outlier: 3.569A pdb=" N VAL 5 530 " --> pdb=" O GLU 5 526 " (cutoff:3.500A) Processing helix chain '5' and resid 555 through 570 removed outlier: 3.711A pdb=" N CYS 5 570 " --> pdb=" O CYS 5 566 " (cutoff:3.500A) Processing helix chain '5' and resid 575 through 601 Processing helix chain '5' and resid 609 through 627 removed outlier: 3.631A pdb=" N LEU 5 613 " --> pdb=" O THR 5 609 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS 5 627 " --> pdb=" O LEU 5 623 " (cutoff:3.500A) Processing helix chain '5' and resid 633 through 654 removed outlier: 4.107A pdb=" N ASP 5 650 " --> pdb=" O VAL 5 646 " (cutoff:3.500A) Processing helix chain '6' and resid 20 through 37 Processing helix chain '6' and resid 44 through 52 removed outlier: 3.839A pdb=" N GLN 6 48 " --> pdb=" O ILE 6 44 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 55 No H-bonds generated for 'chain '6' and resid 53 through 55' Processing helix chain '6' and resid 64 through 70 Processing helix chain '6' and resid 72 through 82 Processing helix chain '6' and resid 82 through 102 Proline residue: 6 88 - end of helix Processing helix chain '6' and resid 122 through 126 Processing helix chain '6' and resid 127 through 131 Processing helix chain '6' and resid 195 through 198 Processing helix chain '6' and resid 211 through 215 removed outlier: 3.641A pdb=" N GLU 6 214 " --> pdb=" O THR 6 211 " (cutoff:3.500A) Processing helix chain '6' and resid 231 through 234 Processing helix chain '6' and resid 322 through 329 Processing helix chain '6' and resid 330 through 342 Processing helix chain '6' and resid 345 through 355 removed outlier: 4.216A pdb=" N CYS 6 351 " --> pdb=" O TYR 6 347 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE 6 355 " --> pdb=" O CYS 6 351 " (cutoff:3.500A) Processing helix chain '6' and resid 361 through 374 Processing helix chain '6' and resid 402 through 413 removed outlier: 4.339A pdb=" N LEU 6 406 " --> pdb=" O LYS 6 402 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS 6 407 " --> pdb=" O SER 6 403 " (cutoff:3.500A) Processing helix chain '6' and resid 422 through 424 No H-bonds generated for 'chain '6' and resid 422 through 424' Processing helix chain '6' and resid 447 through 452 Processing helix chain '6' and resid 466 through 480 Processing helix chain '6' and resid 515 through 519 Processing helix chain '6' and resid 523 through 530 removed outlier: 3.671A pdb=" N PHE 6 530 " --> pdb=" O ILE 6 526 " (cutoff:3.500A) Processing helix chain '6' and resid 541 through 558 Processing helix chain '6' and resid 568 through 580 Processing helix chain '6' and resid 587 through 604 removed outlier: 4.085A pdb=" N GLU 6 591 " --> pdb=" O SER 6 587 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP 6 592 " --> pdb=" O LYS 6 588 " (cutoff:3.500A) Processing helix chain '6' and resid 617 through 635 removed outlier: 3.877A pdb=" N LEU 6 621 " --> pdb=" O THR 6 617 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 655 Processing helix chain '6' and resid 718 through 734 Processing helix chain '6' and resid 744 through 756 Processing helix chain '6' and resid 764 through 783 Processing helix chain '7' and resid 5 through 18 removed outlier: 4.087A pdb=" N GLU 7 9 " --> pdb=" O ASP 7 5 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN 7 18 " --> pdb=" O LYS 7 14 " (cutoff:3.500A) Processing helix chain '7' and resid 31 through 42 Processing helix chain '7' and resid 52 through 56 Processing helix chain '7' and resid 59 through 69 removed outlier: 3.968A pdb=" N VAL 7 63 " --> pdb=" O ASP 7 59 " (cutoff:3.500A) Processing helix chain '7' and resid 69 through 89 Proline residue: 7 86 - end of helix removed outlier: 3.678A pdb=" N LYS 7 89 " --> pdb=" O LEU 7 85 " (cutoff:3.500A) Processing helix chain '7' and resid 97 through 109 Processing helix chain '7' and resid 127 through 132 removed outlier: 3.585A pdb=" N MET 7 131 " --> pdb=" O PRO 7 127 " (cutoff:3.500A) Processing helix chain '7' and resid 148 through 152 removed outlier: 3.840A pdb=" N VAL 7 152 " --> pdb=" O ILE 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 153 through 157 Processing helix chain '7' and resid 208 through 214 Processing helix chain '7' and resid 260 through 262 No H-bonds generated for 'chain '7' and resid 260 through 262' Processing helix chain '7' and resid 347 through 360 removed outlier: 3.647A pdb=" N LYS 7 352 " --> pdb=" O GLU 7 348 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA 7 353 " --> pdb=" O ASP 7 349 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU 7 354 " --> pdb=" O VAL 7 350 " (cutoff:3.500A) Processing helix chain '7' and resid 387 through 398 Processing helix chain '7' and resid 406 through 414 removed outlier: 3.729A pdb=" N SER 7 410 " --> pdb=" O ARG 7 407 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLY 7 411 " --> pdb=" O GLY 7 408 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL 7 412 " --> pdb=" O SER 7 409 " (cutoff:3.500A) Processing helix chain '7' and resid 432 through 437 Processing helix chain '7' and resid 447 through 450 Processing helix chain '7' and resid 451 through 465 Processing helix chain '7' and resid 508 through 515 removed outlier: 3.908A pdb=" N LEU 7 512 " --> pdb=" O PRO 7 508 " (cutoff:3.500A) Processing helix chain '7' and resid 526 through 544 Processing helix chain '7' and resid 555 through 568 removed outlier: 3.713A pdb=" N GLU 7 568 " --> pdb=" O ALA 7 564 " (cutoff:3.500A) Processing helix chain '7' and resid 577 through 595 removed outlier: 4.176A pdb=" N ALA 7 583 " --> pdb=" O ASP 7 579 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET 7 588 " --> pdb=" O ALA 7 584 " (cutoff:3.500A) Processing helix chain '7' and resid 602 through 621 removed outlier: 3.826A pdb=" N LEU 7 606 " --> pdb=" O SER 7 602 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 642 removed outlier: 3.711A pdb=" N VAL 7 630 " --> pdb=" O GLU 7 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 229 through 232 removed outlier: 6.219A pdb=" N LEU 2 230 " --> pdb=" O ARG 2 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '2' and resid 319 through 323 removed outlier: 9.711A pdb=" N ILE 2 439 " --> pdb=" O SER 2 393 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP 2 395 " --> pdb=" O ILE 2 439 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA 2 441 " --> pdb=" O ASP 2 395 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE 2 397 " --> pdb=" O ALA 2 441 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N HIS 2 443 " --> pdb=" O ILE 2 397 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N LEU 2 399 " --> pdb=" O HIS 2 443 " (cutoff:3.500A) removed outlier: 12.594A pdb=" N ALA 2 445 " --> pdb=" O LEU 2 399 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR 2 415 " --> pdb=" O ASN 2 442 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL 2 444 " --> pdb=" O GLU 2 413 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU 2 413 " --> pdb=" O VAL 2 444 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG 2 377 " --> pdb=" O THR 2 313 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N CYS 2 315 " --> pdb=" O ARG 2 375 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ARG 2 375 " --> pdb=" O CYS 2 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 327 through 328 Processing sheet with id=AA4, first strand: chain '2' and resid 543 through 547 removed outlier: 6.665A pdb=" N VAL 2 519 " --> pdb=" O ALA 2 628 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ALA 2 630 " --> pdb=" O VAL 2 519 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU 2 521 " --> pdb=" O ALA 2 630 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU 2 520 " --> pdb=" O CYS 2 661 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL 2 663 " --> pdb=" O LEU 2 520 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N CYS 2 522 " --> pdb=" O VAL 2 663 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 559 through 562 Processing sheet with id=AA6, first strand: chain '2' and resid 608 through 613 Processing sheet with id=AA7, first strand: chain '3' and resid 46 through 50 removed outlier: 3.615A pdb=" N LEU 3 47 " --> pdb=" O TYR 3 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 124 through 133 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 124 through 133 current: chain '3' and resid 153 through 158 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 153 through 158 current: chain '3' and resid 216 through 222 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 216 through 222 current: chain '3' and resid 255 through 267 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 255 through 267 current: chain '5' and resid 178 through 183 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 178 through 183 current: chain '5' and resid 244 through 250 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 244 through 250 current: chain '5' and resid 292 through 301 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain '3' and resid 251 through 252 Processing sheet with id=AB1, first strand: chain '3' and resid 327 through 328 Processing sheet with id=AB2, first strand: chain '3' and resid 365 through 368 removed outlier: 6.928A pdb=" N ILE 3 341 " --> pdb=" O ALA 3 450 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ALA 3 452 " --> pdb=" O ILE 3 341 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU 3 343 " --> pdb=" O ALA 3 452 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU 3 342 " --> pdb=" O PHE 3 483 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET 3 485 " --> pdb=" O LEU 3 342 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE 3 344 " --> pdb=" O MET 3 485 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 381 through 382 Processing sheet with id=AB4, first strand: chain '3' and resid 430 through 435 Processing sheet with id=AB5, first strand: chain '3' and resid 608 through 609 Processing sheet with id=AB6, first strand: chain '4' and resid 207 through 211 Processing sheet with id=AB7, first strand: chain '4' and resid 312 through 316 removed outlier: 7.806A pdb=" N PHE 4 346 " --> pdb=" O PRO 4 297 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N MET 4 299 " --> pdb=" O SER 4 344 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N SER 4 344 " --> pdb=" O MET 4 299 " (cutoff:3.500A) removed outlier: 10.468A pdb=" N GLU 4 301 " --> pdb=" O ASN 4 342 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ASN 4 342 " --> pdb=" O GLU 4 301 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE 4 303 " --> pdb=" O ILE 4 340 " (cutoff:3.500A) removed outlier: 11.187A pdb=" N THR 4 369 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N ILE 4 416 " --> pdb=" O THR 4 369 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE 4 371 " --> pdb=" O ILE 4 416 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL 4 418 " --> pdb=" O ILE 4 371 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE 4 373 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N HIS 4 420 " --> pdb=" O PHE 4 373 " (cutoff:3.500A) removed outlier: 10.957A pdb=" N HIS 4 375 " --> pdb=" O HIS 4 420 " (cutoff:3.500A) removed outlier: 13.733A pdb=" N ARG 4 422 " --> pdb=" O HIS 4 375 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS 4 415 " --> pdb=" O ARG 4 395 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR 4 391 " --> pdb=" O ILE 4 419 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR 4 421 " --> pdb=" O ASN 4 389 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN 4 389 " --> pdb=" O TYR 4 421 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS 4 353 " --> pdb=" O ILE 4 290 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR 4 292 " --> pdb=" O MET 4 351 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET 4 351 " --> pdb=" O THR 4 292 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 400 through 402 removed outlier: 8.105A pdb=" N ASN 4 407 " --> pdb=" O VAL 4 401 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 530 through 534 removed outlier: 6.457A pdb=" N GLN 4 531 " --> pdb=" O CYS 4 572 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASP 4 574 " --> pdb=" O GLN 4 531 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR 4 533 " --> pdb=" O ASP 4 574 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER 4 612 " --> pdb=" O GLY 4 569 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY 4 510 " --> pdb=" O ALA 4 617 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU 4 507 " --> pdb=" O PHE 4 648 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N MET 4 650 " --> pdb=" O LEU 4 507 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYS 4 509 " --> pdb=" O MET 4 650 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 545 through 549 Processing sheet with id=AC2, first strand: chain '4' and resid 595 through 600 Processing sheet with id=AC3, first strand: chain '4' and resid 701 through 702 removed outlier: 6.859A pdb=" N ARG 4 701 " --> pdb=" O VAL 4 753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain '5' and resid 69 through 73 Processing sheet with id=AC5, first strand: chain '5' and resid 363 through 364 removed outlier: 3.640A pdb=" N LYS 5 363 " --> pdb=" O ARG 5 371 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 401 through 403 removed outlier: 6.281A pdb=" N VAL 5 402 " --> pdb=" O CYS 5 443 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU 5 378 " --> pdb=" O PHE 5 518 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL 5 520 " --> pdb=" O LEU 5 378 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU 5 380 " --> pdb=" O VAL 5 520 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 417 through 420 Processing sheet with id=AC8, first strand: chain '5' and resid 466 through 471 Processing sheet with id=AC9, first strand: chain '6' and resid 60 through 63 Processing sheet with id=AD1, first strand: chain '6' and resid 134 through 143 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 134 through 143 current: chain '6' and resid 199 through 209 removed outlier: 3.613A pdb=" N GLN 6 204 " --> pdb=" O LEU 6 228 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '6' and resid 223 through 229 current: chain '6' and resid 294 through 299 Processing sheet with id=AD2, first strand: chain '6' and resid 164 through 165 Processing sheet with id=AD3, first strand: chain '6' and resid 378 through 379 removed outlier: 3.702A pdb=" N LYS 6 378 " --> pdb=" O LEU 6 386 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '6' and resid 416 through 420 removed outlier: 6.091A pdb=" N VAL 6 417 " --> pdb=" O CYS 6 458 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASP 6 460 " --> pdb=" O VAL 6 417 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR 6 419 " --> pdb=" O ASP 6 460 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N CYS 6 457 " --> pdb=" O LEU 6 500 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ALA 6 502 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE 6 459 " --> pdb=" O ALA 6 502 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL 6 392 " --> pdb=" O ALA 6 501 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ALA 6 503 " --> pdb=" O VAL 6 392 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE 6 394 " --> pdb=" O ALA 6 503 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '6' and resid 431 through 435 Processing sheet with id=AD6, first strand: chain '6' and resid 481 through 486 Processing sheet with id=AD7, first strand: chain '6' and resid 585 through 586 removed outlier: 7.164A pdb=" N LYS 6 585 " --> pdb=" O VAL 6 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain '7' and resid 48 through 51 removed outlier: 6.171A pdb=" N LEU 7 48 " --> pdb=" O TYR 7 137 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN 7 139 " --> pdb=" O LEU 7 48 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL 7 50 " --> pdb=" O GLN 7 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain '7' and resid 160 through 170 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 160 through 170 current: chain '7' and resid 190 through 194 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 190 through 194 current: chain '7' and resid 252 through 258 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 252 through 258 current: chain '7' and resid 295 through 305 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain '7' and resid 401 through 404 removed outlier: 6.683A pdb=" N GLN 7 402 " --> pdb=" O CYS 7 443 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASP 7 445 " --> pdb=" O GLN 7 402 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR 7 404 " --> pdb=" O ASP 7 445 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER 7 483 " --> pdb=" O GLY 7 440 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE 7 377 " --> pdb=" O ALA 7 486 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ALA 7 488 " --> pdb=" O ILE 7 377 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU 7 379 " --> pdb=" O ALA 7 488 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '7' and resid 416 through 418 Processing sheet with id=AE3, first strand: chain '7' and resid 466 through 471 1309 hydrogen bonds defined for protein. 3771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 226 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 10811 1.36 - 1.51: 8708 1.51 - 1.65: 13322 1.65 - 1.80: 205 1.80 - 1.95: 92 Bond restraints: 33138 Sorted by residual: bond pdb=" O3B AGS 6 901 " pdb=" PB AGS 6 901 " ideal model delta sigma weight residual 1.673 1.576 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" O3B AGS 7 802 " pdb=" PB AGS 7 802 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" O3B AGS 21001 " pdb=" PB AGS 21001 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" O3A AGS 6 901 " pdb=" PA AGS 6 901 " ideal model delta sigma weight residual 1.664 1.580 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" O3A AGS 7 802 " pdb=" PA AGS 7 802 " ideal model delta sigma weight residual 1.664 1.580 0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 33133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 44544 2.01 - 4.03: 514 4.03 - 6.04: 52 6.04 - 8.06: 12 8.06 - 10.07: 11 Bond angle restraints: 45133 Sorted by residual: angle pdb=" N3 DT Y 42 " pdb=" C4 DT Y 42 " pdb=" O4 DT Y 42 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT X 28 " pdb=" C4 DT X 28 " pdb=" O4 DT X 28 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT Y 8 " pdb=" C4 DT Y 8 " pdb=" O4 DT Y 8 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT X 52 " pdb=" C4 DT X 52 " pdb=" O4 DT X 52 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT Y 30 " pdb=" C4 DT Y 30 " pdb=" O4 DT Y 30 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 ... (remaining 45128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.96: 19320 32.96 - 65.93: 858 65.93 - 98.89: 60 98.89 - 131.85: 6 131.85 - 164.82: 3 Dihedral angle restraints: 20247 sinusoidal: 9019 harmonic: 11228 Sorted by residual: dihedral pdb=" C5' ADP 3 901 " pdb=" O5' ADP 3 901 " pdb=" PA ADP 3 901 " pdb=" O2A ADP 3 901 " ideal model delta sinusoidal sigma weight residual 300.00 176.34 123.66 1 2.00e+01 2.50e-03 3.73e+01 dihedral pdb=" O1B AGS 7 802 " pdb=" O3B AGS 7 802 " pdb=" PB AGS 7 802 " pdb=" PG AGS 7 802 " ideal model delta sinusoidal sigma weight residual 138.55 -12.20 150.75 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" O1B AGS 21001 " pdb=" O3B AGS 21001 " pdb=" PB AGS 21001 " pdb=" PG AGS 21001 " ideal model delta sinusoidal sigma weight residual 138.55 -7.14 145.69 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 20244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4409 0.058 - 0.117: 670 0.117 - 0.175: 55 0.175 - 0.233: 0 0.233 - 0.292: 4 Chirality restraints: 5138 Sorted by residual: chirality pdb=" P DA X 26 " pdb=" OP1 DA X 26 " pdb=" OP2 DA X 26 " pdb=" O5' DA X 26 " both_signs ideal model delta sigma weight residual True 2.34 -2.63 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C3' AGS 6 901 " pdb=" C2' AGS 6 901 " pdb=" C4' AGS 6 901 " pdb=" O3' AGS 6 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3' AGS 21001 " pdb=" C2' AGS 21001 " pdb=" C4' AGS 21001 " pdb=" O3' AGS 21001 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 5135 not shown) Planarity restraints: 5476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL 4 590 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" C VAL 4 590 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL 4 590 " 0.020 2.00e-02 2.50e+03 pdb=" N MET 4 591 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU 6 346 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" C LEU 6 346 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU 6 346 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR 6 347 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO 4 191 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C PRO 4 191 " -0.045 2.00e-02 2.50e+03 pdb=" O PRO 4 191 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU 4 192 " 0.015 2.00e-02 2.50e+03 ... (remaining 5473 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 95 2.46 - 3.07: 20321 3.07 - 3.68: 45830 3.68 - 4.29: 65129 4.29 - 4.90: 110632 Nonbonded interactions: 242007 Sorted by model distance: nonbonded pdb=" O2G AGS 21001 " pdb="MG MG 21002 " model vdw 1.851 2.170 nonbonded pdb=" OG SER 2 530 " pdb="MG MG 21002 " model vdw 1.884 2.170 nonbonded pdb=" O1B AGS 21001 " pdb="MG MG 21002 " model vdw 1.938 2.170 nonbonded pdb=" O2G AGS 6 901 " pdb="MG MG 6 902 " model vdw 1.942 2.170 nonbonded pdb=" OG SER 6 403 " pdb="MG MG 6 902 " model vdw 2.060 2.170 ... (remaining 242002 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 31.930 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 33157 Z= 0.228 Angle : 0.591 19.935 45157 Z= 0.342 Chirality : 0.042 0.292 5138 Planarity : 0.004 0.060 5476 Dihedral : 17.088 164.816 12943 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % 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 are not related in a simple way. whole: 1.23 (0.14), residues: 3768 helix: 1.99 (0.13), residues: 1609 sheet: 0.29 (0.20), residues: 698 loop : -0.17 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 5 138 TYR 0.015 0.001 TYR 7 182 PHE 0.034 0.001 PHE F 86 TRP 0.024 0.001 TRP 6 614 HIS 0.012 0.001 HIS 5 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.23 (33138) covalent geometry : angle 0.56124 / 0.34 (45133) hydrogen bonds : bond 0.10316 / 6.70 ( 1422) hydrogen bonds : angle 4.75864 / 3.44 ( 3997) metal coordination : bond 0.01279 / 0.92 ( 19) metal coordination : angle 8.01855 / 5.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 709 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 50 MET cc_start: 0.6469 (mtt) cc_final: 0.6108 (mtp) REVERT: F 59 MET cc_start: 0.7004 (mmm) cc_final: 0.6767 (mmm) REVERT: F 82 CYS cc_start: 0.8448 (m) cc_final: 0.8168 (t) REVERT: F 159 ASN cc_start: 0.7684 (m-40) cc_final: 0.7448 (m-40) REVERT: 2 222 MET cc_start: 0.7297 (tmm) cc_final: 0.7046 (tmm) REVERT: 2 328 ASN cc_start: 0.8268 (t0) cc_final: 0.7988 (t0) REVERT: 3 547 LYS cc_start: 0.7485 (mptt) cc_final: 0.7267 (tmtt) REVERT: 4 186 ILE cc_start: 0.8544 (mm) cc_final: 0.8340 (mm) REVERT: 4 192 LEU cc_start: 0.7355 (tp) cc_final: 0.6758 (tp) REVERT: 4 207 PHE cc_start: 0.6889 (m-80) cc_final: 0.6626 (m-80) REVERT: 4 403 PRO cc_start: 0.8162 (Cg_exo) cc_final: 0.7589 (Cg_endo) REVERT: 4 650 MET cc_start: 0.8617 (mtp) cc_final: 0.8323 (mtt) REVERT: 5 184 MET cc_start: 0.8039 (mmm) cc_final: 0.7756 (mmt) REVERT: 6 527 MET cc_start: 0.7710 (mmm) cc_final: 0.7340 (ttp) REVERT: 6 769 LYS cc_start: 0.8829 (tptt) cc_final: 0.8451 (ptpp) REVERT: 7 306 MET cc_start: 0.5686 (mmm) cc_final: 0.5340 (mmt) REVERT: 7 540 VAL cc_start: 0.7321 (t) cc_final: 0.7069 (t) outliers start: 0 outliers final: 0 residues processed: 709 average time/residue: 0.2300 time to fit residues: 248.4065 Evaluate side-chains 313 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.0060 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.6980 overall best weight: 1.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 531 GLN 2 606 GLN 2 671 GLN ** 2 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 781 HIS 3 236 GLN 3 298 GLN 3 573 HIS 4 225 GLN 4 342 ASN 4 521 GLN ** 4 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 32 GLN 7 212 GLN ** 7 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.146168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.113654 restraints weight = 64970.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.116145 restraints weight = 39210.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.117103 restraints weight = 28178.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.117596 restraints weight = 25015.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.117814 restraints weight = 23026.161| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33157 Z= 0.187 Angle : 0.646 13.272 45157 Z= 0.330 Chirality : 0.043 0.188 5138 Planarity : 0.005 0.070 5476 Dihedral : 17.108 175.982 5328 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.37 % Allowed : 9.15 % Favored : 89.48 % 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 are not related in a simple way. whole: 0.94 (0.14), residues: 3768 helix: 1.77 (0.13), residues: 1623 sheet: 0.08 (0.19), residues: 709 loop : -0.34 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 6 435 TYR 0.024 0.002 TYR 4 249 PHE 0.017 0.002 PHE F 86 TRP 0.012 0.002 TRP 6 614 HIS 0.012 0.001 HIS 4 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (33138) covalent geometry : angle 0.62899 / 0.33 (45133) hydrogen bonds : bond 0.04513 / 2.92 ( 1422) hydrogen bonds : angle 4.36563 / 3.14 ( 3997) metal coordination : bond 0.01113 / 0.72 ( 19) metal coordination : angle 6.47213 / 3.97 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 318 time to evaluate : 1.226 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: F 20 MET cc_start: 0.7042 (tpp) cc_final: 0.6488 (ttm) REVERT: F 35 CYS cc_start: 0.7970 (m) cc_final: 0.7295 (t) REVERT: F 50 MET cc_start: 0.6606 (mtt) cc_final: 0.6286 (mtp) REVERT: F 59 MET cc_start: 0.7141 (mmm) cc_final: 0.6678 (mmm) REVERT: F 82 CYS cc_start: 0.8615 (m) cc_final: 0.8346 (t) REVERT: F 86 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: 2 328 ASN cc_start: 0.8284 (t0) cc_final: 0.7939 (t0) REVERT: 2 683 HIS cc_start: 0.8698 (OUTLIER) cc_final: 0.8441 (t-90) REVERT: 3 64 ARG cc_start: 0.8484 (mmp80) cc_final: 0.8177 (mpt-90) REVERT: 3 485 MET cc_start: 0.7755 (mtt) cc_final: 0.7506 (mtt) REVERT: 3 547 LYS cc_start: 0.7526 (mptt) cc_final: 0.7255 (tmtt) REVERT: 4 220 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7276 (tppt) REVERT: 4 650 MET cc_start: 0.8655 (mtp) cc_final: 0.8379 (mtt) REVERT: 4 699 MET cc_start: 0.6079 (mmm) cc_final: 0.5604 (mmm) REVERT: 5 87 TYR cc_start: 0.7811 (m-80) cc_final: 0.7605 (m-10) REVERT: 6 179 ILE cc_start: 0.7979 (tp) cc_final: 0.7651 (mp) REVERT: 6 521 ASN cc_start: 0.8014 (t0) cc_final: 0.7805 (t0) REVERT: 6 527 MET cc_start: 0.7725 (mmm) cc_final: 0.7214 (ttp) REVERT: 7 108 MET cc_start: 0.5200 (ppp) cc_final: 0.4235 (ppp) REVERT: 7 269 ASP cc_start: 0.7223 (t0) cc_final: 0.6982 (t0) REVERT: 7 306 MET cc_start: 0.5992 (mmm) cc_final: 0.5459 (mmt) outliers start: 46 outliers final: 28 residues processed: 343 average time/residue: 0.2120 time to fit residues: 116.7540 Evaluate side-chains 294 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 421 ASN Chi-restraints excluded: chain 2 residue 606 GLN Chi-restraints excluded: chain 2 residue 683 HIS Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 4 residue 157 VAL Chi-restraints excluded: chain 4 residue 220 LYS Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 255 ASP Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 346 LEU Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 177 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 273 optimal weight: 0.8980 chunk 344 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 354 optimal weight: 0.9990 chunk 270 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 284 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 606 GLN ** 2 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 187 ASN ** 6 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 541 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.147437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.114646 restraints weight = 64645.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.117670 restraints weight = 38612.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.119124 restraints weight = 26046.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.119459 restraints weight = 22797.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.119522 restraints weight = 21358.658| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33157 Z= 0.116 Angle : 0.560 10.483 45157 Z= 0.286 Chirality : 0.041 0.210 5138 Planarity : 0.004 0.060 5476 Dihedral : 17.017 178.363 5328 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.49 % Allowed : 10.46 % Favored : 88.05 % 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 are not related in a simple way. whole: 1.02 (0.14), residues: 3768 helix: 1.85 (0.13), residues: 1614 sheet: 0.18 (0.19), residues: 694 loop : -0.34 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.000 ARG 4 319 TYR 0.025 0.001 TYR 4 249 PHE 0.023 0.001 PHE 4 207 TRP 0.010 0.001 TRP 6 614 HIS 0.008 0.001 HIS 7 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (33138) covalent geometry : angle 0.54833 / 0.29 (45133) hydrogen bonds : bond 0.03629 / 2.36 ( 1422) hydrogen bonds : angle 4.05869 / 2.93 ( 3997) metal coordination : bond 0.00862 / 0.53 ( 19) metal coordination : angle 4.90233 / 3.14 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 299 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 20 MET cc_start: 0.6893 (tpp) cc_final: 0.6468 (ttm) REVERT: F 50 MET cc_start: 0.6701 (mtt) cc_final: 0.6327 (mtp) REVERT: F 59 MET cc_start: 0.7086 (mmm) cc_final: 0.6519 (mmm) REVERT: F 82 CYS cc_start: 0.8595 (m) cc_final: 0.8252 (t) REVERT: 3 70 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6682 (m-80) REVERT: 3 547 LYS cc_start: 0.7453 (mptt) cc_final: 0.7211 (tmtt) REVERT: 4 650 MET cc_start: 0.8658 (mtp) cc_final: 0.8396 (mtt) REVERT: 4 699 MET cc_start: 0.5944 (mmm) cc_final: 0.5510 (mmm) REVERT: 6 450 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7878 (mtm) REVERT: 6 527 MET cc_start: 0.7698 (mmm) cc_final: 0.7257 (ttp) REVERT: 7 108 MET cc_start: 0.5477 (ppp) cc_final: 0.4633 (ppp) REVERT: 7 306 MET cc_start: 0.5847 (mmm) cc_final: 0.5401 (mmt) REVERT: 7 450 MET cc_start: 0.6823 (mmp) cc_final: 0.6471 (mmt) REVERT: 7 531 LEU cc_start: 0.8156 (mt) cc_final: 0.7953 (mt) outliers start: 50 outliers final: 32 residues processed: 331 average time/residue: 0.1876 time to fit residues: 101.6503 Evaluate side-chains 300 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 421 ASN Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 780 ILE Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 594 ILE Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 651 LEU Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 177 MET Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 640 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 77 optimal weight: 7.9990 chunk 252 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 323 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 549 GLN 2 683 HIS 2 687 HIS 3 29 GLN 3 461 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 542 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.147201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.114135 restraints weight = 64595.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.118026 restraints weight = 38501.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.118705 restraints weight = 25291.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.119174 restraints weight = 22723.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.119317 restraints weight = 21767.372| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 33157 Z= 0.111 Angle : 0.542 11.958 45157 Z= 0.275 Chirality : 0.041 0.234 5138 Planarity : 0.004 0.062 5476 Dihedral : 16.902 178.575 5328 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.85 % Allowed : 11.89 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.14), residues: 3768 helix: 1.93 (0.13), residues: 1614 sheet: 0.22 (0.20), residues: 695 loop : -0.33 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 812 TYR 0.025 0.001 TYR F 121 PHE 0.015 0.001 PHE 7 77 TRP 0.009 0.001 TRP 2 569 HIS 0.030 0.001 HIS 2 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (33138) covalent geometry : angle 0.53261 / 0.27 (45133) hydrogen bonds : bond 0.03421 / 2.24 ( 1422) hydrogen bonds : angle 3.94240 / 2.84 ( 3997) metal coordination : bond 0.00699 / 0.42 ( 19) metal coordination : angle 4.38514 / 2.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 277 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 20 MET cc_start: 0.6831 (tpp) cc_final: 0.6355 (ttm) REVERT: F 50 MET cc_start: 0.6691 (mtt) cc_final: 0.6311 (mtp) REVERT: F 59 MET cc_start: 0.7285 (mmm) cc_final: 0.6759 (mmm) REVERT: F 82 CYS cc_start: 0.8590 (m) cc_final: 0.8252 (t) REVERT: F 121 TYR cc_start: 0.6788 (t80) cc_final: 0.6514 (t80) REVERT: 2 481 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8387 (tt) REVERT: 2 683 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.7971 (t70) REVERT: 3 70 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6758 (m-80) REVERT: 3 547 LYS cc_start: 0.7421 (mptt) cc_final: 0.7194 (tmtt) REVERT: 4 650 MET cc_start: 0.8666 (mtp) cc_final: 0.8374 (mtt) REVERT: 4 699 MET cc_start: 0.5936 (mmm) cc_final: 0.5505 (mmm) REVERT: 6 450 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7821 (mtt) REVERT: 6 527 MET cc_start: 0.7639 (mmm) cc_final: 0.7165 (ttp) REVERT: 7 269 ASP cc_start: 0.7278 (t0) cc_final: 0.6968 (t0) REVERT: 7 450 MET cc_start: 0.6934 (mmp) cc_final: 0.6472 (mmt) outliers start: 62 outliers final: 44 residues processed: 313 average time/residue: 0.1911 time to fit residues: 99.6013 Evaluate side-chains 304 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 421 ASN Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 683 HIS Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 780 ILE Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 486 LEU Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 127 MET Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 353 ILE Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 594 ILE Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 651 LEU Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 640 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 356 optimal weight: 0.9980 chunk 258 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 34 optimal weight: 0.0030 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 chunk 162 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 235 optimal weight: 0.0030 chunk 30 optimal weight: 0.4980 chunk 303 optimal weight: 0.6980 overall best weight: 0.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 606 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 542 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 = 0.4263 r_free = 0.4263 target = 0.148462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.115456 restraints weight = 64499.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.119554 restraints weight = 38391.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.120282 restraints weight = 24893.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.121187 restraints weight = 22235.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.121212 restraints weight = 20839.221| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33157 Z= 0.093 Angle : 0.516 9.979 45157 Z= 0.264 Chirality : 0.040 0.229 5138 Planarity : 0.003 0.062 5476 Dihedral : 16.763 179.059 5328 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.73 % Allowed : 12.16 % Favored : 86.11 % 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 are not related in a simple way. whole: 1.20 (0.14), residues: 3768 helix: 1.97 (0.13), residues: 1620 sheet: 0.34 (0.20), residues: 695 loop : -0.26 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 812 TYR 0.016 0.001 TYR F 121 PHE 0.014 0.001 PHE 7 77 TRP 0.008 0.001 TRP 6 614 HIS 0.022 0.001 HIS 2 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (33138) covalent geometry : angle 0.50885 / 0.26 (45133) hydrogen bonds : bond 0.03105 / 2.02 ( 1422) hydrogen bonds : angle 3.81058 / 2.76 ( 3997) metal coordination : bond 0.00580 / 0.35 ( 19) metal coordination : angle 3.71257 / 2.37 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 289 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 35 CYS cc_start: 0.7779 (m) cc_final: 0.7318 (t) REVERT: F 50 MET cc_start: 0.6684 (mtt) cc_final: 0.6441 (mtp) REVERT: F 59 MET cc_start: 0.7305 (mmm) cc_final: 0.6772 (mmm) REVERT: F 179 LEU cc_start: 0.6367 (tp) cc_final: 0.5921 (tp) REVERT: 2 481 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8345 (tt) REVERT: 2 683 HIS cc_start: 0.8387 (OUTLIER) cc_final: 0.6864 (t-90) REVERT: 3 47 LEU cc_start: 0.7863 (tp) cc_final: 0.7540 (mt) REVERT: 3 70 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6749 (m-80) REVERT: 3 547 LYS cc_start: 0.7470 (mptt) cc_final: 0.7221 (tmtt) REVERT: 4 650 MET cc_start: 0.8656 (mtp) cc_final: 0.8344 (mtt) REVERT: 4 699 MET cc_start: 0.5903 (mmm) cc_final: 0.5470 (mmm) REVERT: 6 450 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7809 (mtt) REVERT: 6 527 MET cc_start: 0.7560 (mmm) cc_final: 0.7093 (ttp) REVERT: 7 108 MET cc_start: 0.5570 (ppp) cc_final: 0.4579 (ppp) REVERT: 7 269 ASP cc_start: 0.7262 (t0) cc_final: 0.6957 (t0) REVERT: 7 450 MET cc_start: 0.6830 (mmp) cc_final: 0.6158 (mmt) outliers start: 58 outliers final: 40 residues processed: 320 average time/residue: 0.1924 time to fit residues: 103.3379 Evaluate side-chains 304 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 421 ASN Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 606 GLN Chi-restraints excluded: chain 2 residue 653 ILE Chi-restraints excluded: chain 2 residue 683 HIS Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 322 LEU Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 3 residue 486 LEU Chi-restraints excluded: chain 4 residue 207 PHE Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 127 MET Chi-restraints excluded: chain 5 residue 353 ILE Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 594 ILE Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 651 LEU Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 102 TYR Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 640 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 279 optimal weight: 0.9980 chunk 382 optimal weight: 40.0000 chunk 311 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 329 optimal weight: 2.9990 chunk 105 optimal weight: 0.0370 chunk 92 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 328 optimal weight: 0.9980 chunk 93 optimal weight: 0.0670 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 129 GLN 2 606 GLN 2 683 HIS 3 353 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.147839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.115198 restraints weight = 64374.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.118232 restraints weight = 38904.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.119296 restraints weight = 26712.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.120385 restraints weight = 22752.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.120302 restraints weight = 20771.312| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 33157 Z= 0.099 Angle : 0.513 8.946 45157 Z= 0.262 Chirality : 0.040 0.226 5138 Planarity : 0.003 0.064 5476 Dihedral : 16.666 178.678 5328 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.88 % Allowed : 12.49 % Favored : 85.64 % 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 are not related in a simple way. whole: 1.28 (0.14), residues: 3768 helix: 2.02 (0.13), residues: 1608 sheet: 0.43 (0.20), residues: 715 loop : -0.22 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 812 TYR 0.029 0.001 TYR F 121 PHE 0.015 0.001 PHE 5 514 TRP 0.008 0.001 TRP 6 751 HIS 0.018 0.001 HIS 2 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (33138) covalent geometry : angle 0.50765 / 0.26 (45133) hydrogen bonds : bond 0.03091 / 2.03 ( 1422) hydrogen bonds : angle 3.76421 / 2.72 ( 3997) metal coordination : bond 0.00560 / 0.35 ( 19) metal coordination : angle 3.35390 / 2.18 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 271 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 35 CYS cc_start: 0.7761 (m) cc_final: 0.7290 (t) REVERT: F 59 MET cc_start: 0.7298 (mmm) cc_final: 0.6954 (mmm) REVERT: 2 481 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8329 (tt) REVERT: 2 683 HIS cc_start: 0.8494 (OUTLIER) cc_final: 0.7846 (t70) REVERT: 3 70 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6782 (m-80) REVERT: 3 547 LYS cc_start: 0.7488 (mptt) cc_final: 0.7232 (tmtt) REVERT: 3 607 THR cc_start: 0.3315 (OUTLIER) cc_final: 0.3058 (p) REVERT: 4 699 MET cc_start: 0.5886 (mmm) cc_final: 0.5437 (mmm) REVERT: 6 220 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8607 (pt) REVERT: 6 450 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7820 (mtt) REVERT: 6 527 MET cc_start: 0.7566 (mmm) cc_final: 0.7100 (ttp) REVERT: 7 108 MET cc_start: 0.5783 (ppp) cc_final: 0.4861 (ppp) REVERT: 7 177 MET cc_start: 0.7213 (mmm) cc_final: 0.6871 (mmm) REVERT: 7 269 ASP cc_start: 0.7314 (t0) cc_final: 0.7002 (t0) outliers start: 63 outliers final: 47 residues processed: 307 average time/residue: 0.1772 time to fit residues: 91.8334 Evaluate side-chains 307 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 254 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 419 HIS Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 653 ILE Chi-restraints excluded: chain 2 residue 683 HIS Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 780 ILE Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 3 residue 486 LEU Chi-restraints excluded: chain 3 residue 607 THR Chi-restraints excluded: chain 4 residue 195 GLN Chi-restraints excluded: chain 4 residue 207 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 127 MET Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 353 ILE Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 5 residue 619 ILE Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 651 LEU Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 102 TYR Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 385 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 109 optimal weight: 1.9990 chunk 315 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 103 optimal weight: 0.2980 chunk 171 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 214 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 328 ASN 2 683 HIS 4 638 HIS ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.147515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.114456 restraints weight = 64833.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.118671 restraints weight = 38380.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.119456 restraints weight = 24726.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.120088 restraints weight = 21486.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.120168 restraints weight = 20619.827| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33157 Z= 0.100 Angle : 0.513 9.533 45157 Z= 0.261 Chirality : 0.040 0.223 5138 Planarity : 0.003 0.062 5476 Dihedral : 16.577 177.698 5328 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.82 % Allowed : 13.50 % Favored : 84.68 % 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 are not related in a simple way. whole: 1.29 (0.14), residues: 3768 helix: 2.05 (0.13), residues: 1602 sheet: 0.41 (0.20), residues: 717 loop : -0.20 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 2 812 TYR 0.036 0.001 TYR 2 821 PHE 0.018 0.001 PHE 7 77 TRP 0.010 0.001 TRP 6 751 HIS 0.016 0.001 HIS 2 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (33138) covalent geometry : angle 0.50811 / 0.26 (45133) hydrogen bonds : bond 0.03084 / 2.01 ( 1422) hydrogen bonds : angle 3.73823 / 2.70 ( 3997) metal coordination : bond 0.00544 / 0.34 ( 19) metal coordination : angle 3.07194 / 2.02 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 263 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 35 CYS cc_start: 0.7755 (m) cc_final: 0.7309 (t) REVERT: F 59 MET cc_start: 0.7301 (mmm) cc_final: 0.6945 (mmm) REVERT: 2 328 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7883 (t0) REVERT: 2 481 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8350 (tt) REVERT: 3 70 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6880 (m-80) REVERT: 3 547 LYS cc_start: 0.7539 (mptt) cc_final: 0.7303 (tmtt) REVERT: 4 699 MET cc_start: 0.5871 (mmm) cc_final: 0.5447 (mmt) REVERT: 6 450 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7866 (mtt) REVERT: 6 527 MET cc_start: 0.7656 (mmm) cc_final: 0.7165 (ttp) REVERT: 7 108 MET cc_start: 0.5975 (ppp) cc_final: 0.5128 (ppp) REVERT: 7 177 MET cc_start: 0.7237 (mmm) cc_final: 0.6868 (mmm) REVERT: 7 269 ASP cc_start: 0.7331 (t0) cc_final: 0.7065 (t0) outliers start: 61 outliers final: 45 residues processed: 301 average time/residue: 0.1842 time to fit residues: 94.0021 Evaluate side-chains 306 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 328 ASN Chi-restraints excluded: chain 2 residue 367 GLU Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 419 HIS Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 653 ILE Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 3 residue 486 LEU Chi-restraints excluded: chain 4 residue 195 GLN Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 353 ILE Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 594 ILE Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 651 LEU Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 640 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 363 optimal weight: 0.5980 chunk 314 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 249 optimal weight: 10.0000 chunk 273 optimal weight: 0.7980 chunk 272 optimal weight: 0.9980 chunk 284 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 287 optimal weight: 0.7980 chunk 105 optimal weight: 0.0980 chunk 318 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 129 GLN 2 328 ASN 3 553 HIS 4 593 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.147548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.114636 restraints weight = 64646.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.118439 restraints weight = 38364.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.119424 restraints weight = 25382.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.120480 restraints weight = 21512.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.120316 restraints weight = 20065.814| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33157 Z= 0.097 Angle : 0.512 10.014 45157 Z= 0.260 Chirality : 0.040 0.223 5138 Planarity : 0.003 0.057 5476 Dihedral : 16.511 177.475 5328 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.06 % Allowed : 13.26 % Favored : 84.68 % 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 are not related in a simple way. whole: 1.33 (0.14), residues: 3768 helix: 2.08 (0.13), residues: 1606 sheet: 0.42 (0.20), residues: 719 loop : -0.19 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 2 812 TYR 0.020 0.001 TYR F 121 PHE 0.019 0.001 PHE 4 207 TRP 0.010 0.001 TRP 6 751 HIS 0.020 0.001 HIS 2 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (33138) covalent geometry : angle 0.50655 / 0.26 (45133) hydrogen bonds : bond 0.03012 / 1.97 ( 1422) hydrogen bonds : angle 3.71676 / 2.69 ( 3997) metal coordination : bond 0.00593 / 0.36 ( 19) metal coordination : angle 3.35970 / 2.31 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 267 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 35 CYS cc_start: 0.7735 (m) cc_final: 0.7299 (t) REVERT: F 59 MET cc_start: 0.7297 (mmm) cc_final: 0.6935 (mmm) REVERT: 3 70 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: 3 547 LYS cc_start: 0.7604 (mptt) cc_final: 0.7370 (tmtt) REVERT: 4 699 MET cc_start: 0.5880 (mmm) cc_final: 0.5441 (mmt) REVERT: 6 450 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7889 (mtt) REVERT: 6 527 MET cc_start: 0.7662 (mmm) cc_final: 0.7158 (ttp) REVERT: 6 775 LYS cc_start: 0.8871 (mttt) cc_final: 0.8136 (tmtt) REVERT: 7 108 MET cc_start: 0.6102 (ppp) cc_final: 0.5257 (ppp) REVERT: 7 177 MET cc_start: 0.7265 (mmm) cc_final: 0.6882 (mmm) REVERT: 7 269 ASP cc_start: 0.7343 (t0) cc_final: 0.7069 (t0) REVERT: 7 306 MET cc_start: 0.5608 (mmm) cc_final: 0.5055 (mmt) outliers start: 69 outliers final: 50 residues processed: 311 average time/residue: 0.1775 time to fit residues: 93.4967 Evaluate side-chains 307 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 255 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 367 GLU Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 419 HIS Chi-restraints excluded: chain 2 residue 653 ILE Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 3 residue 486 LEU Chi-restraints excluded: chain 4 residue 195 GLN Chi-restraints excluded: chain 4 residue 207 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 353 ILE Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 594 ILE Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 631 MET Chi-restraints excluded: chain 6 residue 651 LEU Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 640 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 279 optimal weight: 0.9980 chunk 358 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 241 optimal weight: 4.9990 chunk 300 optimal weight: 3.9990 chunk 336 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 129 GLN 4 350 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 597 GLN ** 7 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.144056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.111049 restraints weight = 64880.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.114097 restraints weight = 39580.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.115036 restraints weight = 27271.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.115499 restraints weight = 24694.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.115566 restraints weight = 23035.110| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33157 Z= 0.175 Angle : 0.591 15.331 45157 Z= 0.301 Chirality : 0.043 0.202 5138 Planarity : 0.004 0.060 5476 Dihedral : 16.551 174.336 5328 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.82 % Allowed : 13.74 % Favored : 84.45 % 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 are not related in a simple way. whole: 1.05 (0.14), residues: 3768 helix: 1.92 (0.13), residues: 1612 sheet: 0.13 (0.20), residues: 709 loop : -0.33 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 2 812 TYR 0.034 0.002 TYR F 121 PHE 0.048 0.002 PHE 6 649 TRP 0.013 0.001 TRP 6 751 HIS 0.016 0.001 HIS 2 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (33138) covalent geometry : angle 0.58726 / 0.30 (45133) hydrogen bonds : bond 0.03674 / 2.40 ( 1422) hydrogen bonds : angle 3.91391 / 2.81 ( 3997) metal coordination : bond 0.00676 / 0.42 ( 19) metal coordination : angle 2.76538 / 1.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 265 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 MET cc_start: 0.7386 (mmm) cc_final: 0.7042 (mmm) REVERT: 2 746 MET cc_start: 0.8595 (mmm) cc_final: 0.8282 (tpp) REVERT: 2 821 TYR cc_start: 0.6575 (m-80) cc_final: 0.5708 (m-10) REVERT: 3 29 GLN cc_start: 0.8492 (tm130) cc_final: 0.8103 (tm-30) REVERT: 3 547 LYS cc_start: 0.7611 (mptt) cc_final: 0.7362 (tmtt) REVERT: 4 699 MET cc_start: 0.6001 (mmm) cc_final: 0.5529 (mmt) REVERT: 6 450 MET cc_start: 0.8288 (mtm) cc_final: 0.7918 (mtt) REVERT: 6 527 MET cc_start: 0.7479 (mmm) cc_final: 0.7193 (ttp) REVERT: 7 108 MET cc_start: 0.6180 (ppp) cc_final: 0.5321 (ppp) REVERT: 7 269 ASP cc_start: 0.7459 (t0) cc_final: 0.7192 (t0) REVERT: 7 450 MET cc_start: 0.6759 (mmt) cc_final: 0.6488 (mmt) outliers start: 61 outliers final: 49 residues processed: 301 average time/residue: 0.1824 time to fit residues: 91.6937 Evaluate side-chains 307 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 258 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 367 GLU Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 419 HIS Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 653 ILE Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 486 LEU Chi-restraints excluded: chain 4 residue 207 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 317 MET Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 124 ILE Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 353 ILE Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 5 residue 619 ILE Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 594 ILE Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 631 MET Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 640 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 263 optimal weight: 8.9990 chunk 350 optimal weight: 0.0030 chunk 312 optimal weight: 0.3980 chunk 152 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 375 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 275 optimal weight: 0.5980 chunk 386 optimal weight: 30.0000 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 212 HIS ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 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 = 0.4240 r_free = 0.4240 target = 0.146389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.113494 restraints weight = 65353.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.117185 restraints weight = 38938.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.118152 restraints weight = 26172.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.118800 restraints weight = 22446.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.118938 restraints weight = 21005.186| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33157 Z= 0.098 Angle : 0.540 11.777 45157 Z= 0.272 Chirality : 0.040 0.217 5138 Planarity : 0.003 0.055 5476 Dihedral : 16.466 178.188 5328 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.34 % Allowed : 14.39 % Favored : 84.27 % 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 are not related in a simple way. whole: 1.22 (0.14), residues: 3768 helix: 2.06 (0.13), residues: 1605 sheet: 0.22 (0.20), residues: 711 loop : -0.25 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 2 812 TYR 0.034 0.001 TYR F 121 PHE 0.043 0.001 PHE 6 649 TRP 0.013 0.001 TRP 6 751 HIS 0.015 0.001 HIS 2 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (33138) covalent geometry : angle 0.53328 / 0.27 (45133) hydrogen bonds : bond 0.03035 / 1.98 ( 1422) hydrogen bonds : angle 3.74938 / 2.70 ( 3997) metal coordination : bond 0.00565 / 0.38 ( 19) metal coordination : angle 3.75197 / 2.19 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 260 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 MET cc_start: 0.7277 (mmm) cc_final: 0.6906 (mmm) REVERT: 3 29 GLN cc_start: 0.8480 (tm130) cc_final: 0.8114 (tm-30) REVERT: 3 47 LEU cc_start: 0.7857 (tp) cc_final: 0.7649 (mt) REVERT: 3 547 LYS cc_start: 0.7549 (mptt) cc_final: 0.7308 (tmtt) REVERT: 4 699 MET cc_start: 0.5886 (mmm) cc_final: 0.5456 (mmt) REVERT: 6 450 MET cc_start: 0.8159 (mtm) cc_final: 0.7846 (mtt) REVERT: 6 527 MET cc_start: 0.7617 (mmm) cc_final: 0.7277 (ttp) REVERT: 7 177 MET cc_start: 0.7276 (mmm) cc_final: 0.6934 (mmm) REVERT: 7 269 ASP cc_start: 0.7343 (t0) cc_final: 0.7090 (t0) REVERT: 7 306 MET cc_start: 0.5528 (mmm) cc_final: 0.5180 (mmt) REVERT: 7 438 ASP cc_start: 0.7444 (t0) cc_final: 0.7231 (m-30) REVERT: 7 450 MET cc_start: 0.6661 (mmt) cc_final: 0.6415 (mmt) outliers start: 45 outliers final: 39 residues processed: 286 average time/residue: 0.1706 time to fit residues: 82.3528 Evaluate side-chains 295 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain 2 residue 260 ASP Chi-restraints excluded: chain 2 residue 419 HIS Chi-restraints excluded: chain 2 residue 653 ILE Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 750 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 486 LEU Chi-restraints excluded: chain 4 residue 195 GLN Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 317 MET Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 127 MET Chi-restraints excluded: chain 5 residue 353 ILE Chi-restraints excluded: chain 5 residue 400 ILE Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 234 GLU Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 299 LEU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 443 VAL Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 640 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 201 optimal weight: 0.0000 chunk 139 optimal weight: 2.9990 chunk 361 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 335 optimal weight: 4.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 838 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 22 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 = 0.4217 r_free = 0.4217 target = 0.144411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.111384 restraints weight = 65263.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.114784 restraints weight = 39226.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.115520 restraints weight = 26530.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.116415 restraints weight = 23594.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.116351 restraints weight = 22103.094| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33157 Z= 0.137 Angle : 0.562 12.057 45157 Z= 0.283 Chirality : 0.041 0.227 5138 Planarity : 0.004 0.059 5476 Dihedral : 16.439 177.180 5328 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.40 % Allowed : 14.54 % Favored : 84.06 % 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 are not related in a simple way. whole: 1.11 (0.14), residues: 3768 helix: 1.98 (0.13), residues: 1611 sheet: 0.09 (0.20), residues: 713 loop : -0.29 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 2 812 TYR 0.035 0.001 TYR F 121 PHE 0.043 0.001 PHE 6 649 TRP 0.038 0.002 TRP 6 751 HIS 0.014 0.001 HIS 2 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (33138) covalent geometry : angle 0.55527 / 0.28 (45133) hydrogen bonds : bond 0.03374 / 2.20 ( 1422) hydrogen bonds : angle 3.82894 / 2.75 ( 3997) metal coordination : bond 0.00628 / 0.41 ( 19) metal coordination : angle 3.68541 / 2.15 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5127.53 seconds wall clock time: 89 minutes 29.88 seconds (5369.88 seconds total)