Starting phenix.real_space_refine on Mon Aug 10 09:21:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s0d_19622/08_2026/8s0d_19622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s0d_19622/08_2026/8s0d_19622.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/8s0d_19622/08_2026/8s0d_19622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s0d_19622/08_2026/8s0d_19622.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s0d_19622/08_2026/8s0d_19622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s0d_19622/08_2026/8s0d_19622.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= 0.007 sd= 1.106 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 137 5.49 5 Mg 8 5.21 5 S 261 5.16 5 C 28743 2.51 5 N 8043 2.21 5 O 8827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 46024 Number of models: 1 Model: "" Number of chains: 22 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: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1182 Classifications: {'DNA': 58} Link IDs: {'rna3p': 57} Chain: "Y" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1196 Classifications: {'DNA': 58} Link IDs: {'rna3p': 57} Chain: "A" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1538 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain breaks: 1 Chain: "C" Number of atoms: 4481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4481 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 23, 'TRANS': 522} Chain breaks: 12 Chain: "D" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3029 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 3 Chain: "E" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3065 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 357} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 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} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2557 SG CYS 2 329 112.923 86.652 67.507 1.00 38.92 S ATOM 2580 SG CYS 2 332 114.179 83.873 66.683 1.00 49.71 S ATOM 2731 SG CYS 2 352 115.885 85.158 70.082 1.00 51.99 S ATOM 2753 SG CYS 2 355 116.556 86.680 67.062 1.00 57.31 S ATOM 12432 SG CYS 4 306 134.200 128.510 90.067 1.00 36.38 S ATOM 12454 SG CYS 4 309 136.444 130.108 92.588 1.00 34.02 S ATOM 12600 SG CYS 4 328 136.943 130.964 88.929 1.00 39.80 S ATOM 12621 SG CYS 4 331 137.568 127.594 89.645 1.00 43.37 S ATOM 17265 SG CYS 5 172 115.470 99.085 47.425 1.00 96.73 S ATOM 17288 SG CYS 5 175 116.997 96.560 45.400 1.00 99.70 S ATOM 17459 SG CYS 5 197 117.041 96.089 49.204 1.00111.55 S ATOM 21965 SG CYS 6 158 129.261 112.503 85.063 1.00 56.69 S ATOM 21987 SG CYS 6 161 132.820 111.857 86.108 1.00 65.07 S ATOM 22148 SG CYS 6 180 131.168 114.736 86.781 1.00 73.05 S ATOM 22187 SG CYS 6 185 132.313 113.044 82.944 1.00 77.51 S ATOM 27397 SG CYS 7 184 132.375 140.166 63.618 1.00103.83 S ATOM 27420 SG CYS 7 187 133.869 142.130 61.031 1.00105.99 S ATOM 27566 SG CYS 7 206 131.374 139.056 60.429 1.00110.67 S ATOM 27603 SG CYS 7 211 134.839 138.442 61.265 1.00108.79 S Time building chain proxies: 9.55, per 1000 atoms: 0.21 Number of scatterers: 46024 At special positions: 0 Unit cell: (214.92, 199.8, 156.6, 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 261 16.00 P 137 15.00 Mg 8 11.99 O 8827 8.00 N 8043 7.00 C 28743 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: 3.67 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21003 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 352 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 332 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 355 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 329 " 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 4 309 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 331 " pdb=" ZN 5 803 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 175 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 172 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 197 " pdb=" ZN 6 903 " 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 ZN 6 903 " - pdb=" SG CYS 6 180 " pdb=" ZN 7 804 " pdb="ZN ZN 7 804 " - pdb=" SG CYS 7 206 " pdb="ZN ZN 7 804 " - pdb=" SG CYS 7 187 " pdb="ZN ZN 7 804 " - pdb=" SG CYS 7 184 " pdb="ZN ZN 7 804 " - pdb=" SG CYS 7 211 " Number of angles added : 24 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10406 Finding SS restraints... Secondary structure from input PDB file: 244 helices and 45 sheets defined 53.0% alpha, 11.7% beta 43 base pairs and 102 stacking pairs defined. Time for finding SS restraints: 5.04 Creating SS restraints... Processing helix chain 'F' and resid 2 through 14 removed outlier: 3.767A 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: 3.562A pdb=" N LEU F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 42 removed outlier: 3.525A pdb=" N THR F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 59 removed outlier: 3.537A 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 removed outlier: 3.529A pdb=" N GLY F 91 " --> pdb=" O GLU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 104 removed outlier: 3.664A pdb=" N LEU F 101 " --> pdb=" O GLY F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 123 removed outlier: 3.850A pdb=" N MET F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER F 115 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER F 123 " --> pdb=" O LYS F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 133 removed outlier: 4.124A pdb=" N ASP F 132 " --> pdb=" O THR F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 151 removed outlier: 3.674A 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: 3.652A pdb=" N GLN F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain '2' and resid 182 through 188 removed outlier: 3.723A 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: 3.596A pdb=" N GLU 2 217 " --> pdb=" O ASN 2 213 " (cutoff:3.500A) removed outlier: 3.561A 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: 3.788A pdb=" N LEU 2 255 " --> pdb=" O ALA 2 251 " (cutoff:3.500A) Processing helix chain '2' and resid 273 through 278 removed outlier: 3.768A pdb=" N ILE 2 277 " --> pdb=" O LYS 2 273 " (cutoff:3.500A) Processing helix chain '2' and resid 293 through 297 removed outlier: 3.746A pdb=" N LEU 2 297 " --> pdb=" O LEU 2 294 " (cutoff:3.500A) Processing helix chain '2' and resid 298 through 302 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 removed outlier: 3.546A pdb=" N ILE 2 481 " --> pdb=" O ILE 2 477 " (cutoff:3.500A) Processing helix chain '2' and resid 488 through 501 Processing helix chain '2' and resid 529 through 540 removed outlier: 3.625A 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 593 through 606 Processing helix chain '2' and resid 642 through 647 removed outlier: 3.529A pdb=" N VAL 2 647 " --> pdb=" O PHE 2 643 " (cutoff:3.500A) Processing helix chain '2' and resid 650 through 657 removed outlier: 3.595A pdb=" N ARG 2 656 " --> pdb=" O PRO 2 652 " (cutoff:3.500A) removed outlier: 4.287A 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: 3.710A pdb=" N VAL 2 743 " --> pdb=" O ASP 2 739 " (cutoff:3.500A) Processing helix chain '2' and resid 763 through 781 removed outlier: 3.971A pdb=" N ILE 2 767 " --> pdb=" O THR 2 763 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS 2 781 " --> pdb=" O HIS 2 777 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 806 removed outlier: 3.571A pdb=" N VAL 2 791 " --> pdb=" O ILE 2 787 " (cutoff:3.500A) removed outlier: 3.566A 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: 3.527A 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: 3.856A 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: 4.013A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) removed outlier: 3.878A 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: 4.036A 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: 4.103A pdb=" N ALA 3 587 " --> pdb=" O THR 3 583 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR 3 588 " --> pdb=" O GLN 3 584 " (cutoff:3.500A) Processing helix chain '3' and resid 601 through 604 removed outlier: 3.942A 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: 3.792A pdb=" N GLU 3 619 " --> pdb=" O ALA 3 615 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG 3 632 " --> pdb=" O HIS 3 628 " (cutoff:3.500A) Processing helix chain '3' and resid 638 through 653 removed outlier: 3.576A pdb=" N ALA 3 642 " --> pdb=" O ASP 3 638 " (cutoff:3.500A) Processing helix chain '4' and resid 158 through 173 removed outlier: 3.545A 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: 3.740A 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: 3.866A pdb=" N VAL 4 586 " --> pdb=" O SER 4 582 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU 4 587 " --> pdb=" O THR 4 583 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU 4 589 " --> pdb=" O SER 4 585 " (cutoff:3.500A) removed outlier: 4.470A 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: 3.741A pdb=" N TYR 4 670 " --> pdb=" O LEU 4 666 " (cutoff:3.500A) Processing helix chain '4' and resid 683 through 698 removed outlier: 3.716A 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: 3.607A pdb=" N GLU 4 735 " --> pdb=" O PRO 4 731 " (cutoff:3.500A) Processing helix chain '4' and resid 754 through 769 removed outlier: 3.637A pdb=" N VAL 4 758 " --> pdb=" O GLU 4 754 " (cutoff:3.500A) removed outlier: 3.837A 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: 3.850A pdb=" N ALA 5 85 " --> pdb=" O ASP 5 81 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR 5 89 " --> pdb=" O ALA 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 111 removed outlier: 3.803A pdb=" N HIS 5 95 " --> pdb=" O GLN 5 91 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) Processing helix chain '5' and resid 136 through 140 removed outlier: 3.924A 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: 3.670A 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 327 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: 3.684A pdb=" N LYS 5 449 " --> pdb=" O GLU 5 446 " (cutoff:3.500A) removed outlier: 4.110A 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: 3.658A pdb=" N HIS 5 459 " --> pdb=" O ARG 5 455 " (cutoff:3.500A) removed outlier: 4.088A 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: 3.618A pdb=" N VAL 5 530 " --> pdb=" O GLU 5 526 " (cutoff:3.500A) Processing helix chain '5' and resid 555 through 570 removed outlier: 3.695A 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: 3.614A pdb=" N LEU 5 613 " --> pdb=" O THR 5 609 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS 5 627 " --> pdb=" O LEU 5 623 " (cutoff:3.500A) Processing helix chain '5' and resid 633 through 654 removed outlier: 4.083A 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: 3.746A pdb=" N GLN 6 48 " --> pdb=" O ILE 6 44 " (cutoff:3.500A) removed outlier: 3.754A 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: 3.606A pdb=" N GLU 6 214 " --> pdb=" O THR 6 211 " (cutoff:3.500A) Processing helix chain '6' and resid 231 through 236 removed outlier: 4.178A pdb=" N SER 6 235 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA 6 236 " --> pdb=" O ALA 6 232 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 231 through 236' 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: 4.353A pdb=" N CYS 6 351 " --> pdb=" O TYR 6 347 " (cutoff:3.500A) removed outlier: 3.711A 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: 4.324A pdb=" N LEU 6 406 " --> pdb=" O LYS 6 402 " (cutoff:3.500A) removed outlier: 3.575A 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: 3.592A 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: 4.076A pdb=" N GLU 6 591 " --> pdb=" O SER 6 587 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP 6 592 " --> pdb=" O LYS 6 588 " (cutoff:3.500A) Processing helix chain '6' and resid 617 through 635 removed outlier: 3.781A 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: 4.097A pdb=" N GLU 7 9 " --> pdb=" O ASP 7 5 " (cutoff:3.500A) removed outlier: 3.676A 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: 4.020A 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: 3.655A 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: 3.579A pdb=" N MET 7 131 " --> pdb=" O PRO 7 127 " (cutoff:3.500A) Processing helix chain '7' and resid 148 through 152 removed outlier: 3.839A 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: 3.716A pdb=" N LYS 7 352 " --> pdb=" O GLU 7 348 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA 7 353 " --> pdb=" O ASP 7 349 " (cutoff:3.500A) removed outlier: 3.557A 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: 3.677A pdb=" N SER 7 410 " --> pdb=" O ARG 7 407 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLY 7 411 " --> pdb=" O GLY 7 408 " (cutoff:3.500A) removed outlier: 6.084A 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: 3.891A 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 569 removed outlier: 3.673A pdb=" N GLU 7 568 " --> pdb=" O ALA 7 564 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS 7 569 " --> pdb=" O MET 7 565 " (cutoff:3.500A) Processing helix chain '7' and resid 576 through 595 removed outlier: 4.021A pdb=" N TYR 7 580 " --> pdb=" O SER 7 576 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA 7 583 " --> pdb=" O ASP 7 579 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET 7 588 " --> pdb=" O ALA 7 584 " (cutoff:3.500A) Processing helix chain '7' and resid 602 through 621 removed outlier: 3.869A pdb=" N LEU 7 606 " --> pdb=" O SER 7 602 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 642 removed outlier: 3.725A pdb=" N VAL 7 630 " --> pdb=" O GLU 7 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 759 Processing helix chain 'A' and resid 762 through 769 Processing helix chain 'A' and resid 771 through 789 Processing helix chain 'A' and resid 794 through 810 removed outlier: 3.687A pdb=" N ILE A 798 " --> pdb=" O THR A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 829 Processing helix chain 'A' and resid 850 through 860 removed outlier: 4.409A pdb=" N ASP A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 283 through 296 removed outlier: 3.978A pdb=" N LEU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.920A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 347 through 358 Processing helix chain 'B' and resid 370 through 383 Processing helix chain 'B' and resid 397 through 401 removed outlier: 3.899A pdb=" N ARG B 401 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 414 Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.644A pdb=" N LEU B 431 " --> pdb=" O ASN B 428 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP B 433 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 441 Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 36 through 85 removed outlier: 4.012A pdb=" N GLY C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 127 removed outlier: 3.683A pdb=" N ASN C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.676A pdb=" N CYS C 141 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 159 removed outlier: 3.516A pdb=" N CYS C 159 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 193 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 226 through 239 removed outlier: 3.595A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 282 through 291 Processing helix chain 'C' and resid 303 through 318 removed outlier: 3.614A pdb=" N LEU C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 339 Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 347 through 357 removed outlier: 3.851A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 368 Processing helix chain 'C' and resid 369 through 375 Processing helix chain 'C' and resid 403 through 426 removed outlier: 4.024A pdb=" N LEU C 414 " --> pdb=" O MET C 410 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 426 " --> pdb=" O PHE C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 445 removed outlier: 4.305A pdb=" N LYS C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 461 removed outlier: 3.607A pdb=" N LEU C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 482 removed outlier: 3.527A pdb=" N TYR C 482 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 500 Processing helix chain 'C' and resid 550 through 567 Processing helix chain 'C' and resid 570 through 574 removed outlier: 3.691A pdb=" N THR C 573 " --> pdb=" O PRO C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 593 Processing helix chain 'C' and resid 595 through 606 Processing helix chain 'C' and resid 607 through 610 Processing helix chain 'C' and resid 628 through 638 removed outlier: 3.593A pdb=" N LEU C 638 " --> pdb=" O TYR C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 661 Processing helix chain 'C' and resid 675 through 691 removed outlier: 3.603A pdb=" N ALA C 679 " --> pdb=" O GLU C 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 40 through 57 Processing helix chain 'D' and resid 72 through 84 removed outlier: 4.079A pdb=" N LEU D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 161 through 167 removed outlier: 3.818A pdb=" N HIS D 167 " --> pdb=" O PHE D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'D' and resid 203 through 210 Processing helix chain 'D' and resid 222 through 234 removed outlier: 3.566A pdb=" N LEU D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 258 removed outlier: 3.956A pdb=" N GLU D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.673A pdb=" N LEU D 279 " --> pdb=" O ASN D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 310 Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.635A pdb=" N ASN D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 339 Processing helix chain 'D' and resid 345 through 360 removed outlier: 3.725A pdb=" N VAL D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 382 removed outlier: 3.829A pdb=" N VAL D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 Processing helix chain 'D' and resid 422 through 431 removed outlier: 3.734A pdb=" N ARG D 426 " --> pdb=" O PRO D 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 23 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 68 through 85 Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.690A pdb=" N TYR E 129 " --> pdb=" O LYS E 126 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG E 131 " --> pdb=" O GLU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 143 Processing helix chain 'E' and resid 143 through 149 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 200 through 216 Processing helix chain 'E' and resid 221 through 243 Proline residue: E 234 - end of helix removed outlier: 3.648A pdb=" N CYS E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU E 238 " --> pdb=" O PRO E 234 " (cutoff:3.500A) Proline residue: E 239 - end of helix Processing helix chain 'E' and resid 249 through 268 Proline residue: E 259 - end of helix Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 305 through 318 Processing helix chain 'E' and resid 358 through 370 removed outlier: 3.519A pdb=" N LEU E 362 " --> pdb=" O PRO E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 386 removed outlier: 3.703A pdb=" N PHE E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 412 through 424 Processing helix chain 'E' and resid 427 through 431 Processing sheet with id=AA1, first strand: chain '2' and resid 229 through 232 removed outlier: 6.239A 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: 9.769A pdb=" N ILE 2 439 " --> pdb=" O SER 2 393 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP 2 395 " --> pdb=" O ILE 2 439 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ALA 2 441 " --> pdb=" O ASP 2 395 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE 2 397 " --> pdb=" O ALA 2 441 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N HIS 2 443 " --> pdb=" O ILE 2 397 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N LEU 2 399 " --> pdb=" O HIS 2 443 " (cutoff:3.500A) removed outlier: 12.488A pdb=" N ALA 2 445 " --> pdb=" O LEU 2 399 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN 2 442 " --> pdb=" O THR 2 415 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR 2 415 " --> pdb=" O ASN 2 442 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL 2 444 " --> pdb=" O GLU 2 413 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU 2 413 " --> pdb=" O VAL 2 444 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG 2 377 " --> pdb=" O THR 2 313 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N CYS 2 315 " --> pdb=" O ARG 2 375 " (cutoff:3.500A) removed outlier: 7.141A 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: 3.501A pdb=" N ILE 2 627 " --> pdb=" O CYS 2 584 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE 2 586 " --> pdb=" O ILE 2 627 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU 2 520 " --> pdb=" O CYS 2 661 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL 2 663 " --> pdb=" O LEU 2 520 " (cutoff:3.500A) removed outlier: 6.657A 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: 3.641A 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 removed outlier: 3.569A pdb=" N ARG 3 327 " --> pdb=" O ILE 3 335 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 365 through 368 removed outlier: 3.636A pdb=" N SER 3 447 " --> pdb=" O GLY 3 404 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE 3 341 " --> pdb=" O ALA 3 450 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ALA 3 452 " --> pdb=" O ILE 3 341 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU 3 343 " --> pdb=" O ALA 3 452 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU 3 342 " --> pdb=" O PHE 3 483 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N MET 3 485 " --> pdb=" O LEU 3 342 " (cutoff:3.500A) removed outlier: 6.585A 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 removed outlier: 3.524A pdb=" N LYS 3 655 " --> pdb=" O ALA 3 608 " (cutoff:3.500A) 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: 7.711A pdb=" N PHE 4 346 " --> pdb=" O PRO 4 297 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N MET 4 299 " --> pdb=" O SER 4 344 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N SER 4 344 " --> pdb=" O MET 4 299 " (cutoff:3.500A) removed outlier: 10.471A pdb=" N GLU 4 301 " --> pdb=" O ASN 4 342 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ASN 4 342 " --> pdb=" O GLU 4 301 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE 4 303 " --> pdb=" O ILE 4 340 " (cutoff:3.500A) removed outlier: 11.299A pdb=" N THR 4 369 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N ILE 4 416 " --> pdb=" O THR 4 369 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE 4 371 " --> pdb=" O ILE 4 416 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL 4 418 " --> pdb=" O ILE 4 371 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE 4 373 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N HIS 4 420 " --> pdb=" O PHE 4 373 " (cutoff:3.500A) removed outlier: 10.956A pdb=" N HIS 4 375 " --> pdb=" O HIS 4 420 " (cutoff:3.500A) removed outlier: 13.696A pdb=" N ARG 4 422 " --> pdb=" O HIS 4 375 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS 4 415 " --> pdb=" O ARG 4 395 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR 4 391 " --> pdb=" O ILE 4 419 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR 4 421 " --> pdb=" O ASN 4 389 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASN 4 389 " --> pdb=" O TYR 4 421 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS 4 353 " --> pdb=" O ILE 4 290 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR 4 292 " --> pdb=" O MET 4 351 " (cutoff:3.500A) removed outlier: 7.095A 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: 8.213A 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: 6.537A pdb=" N GLN 4 531 " --> pdb=" O CYS 4 572 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP 4 574 " --> pdb=" O GLN 4 531 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR 4 533 " --> pdb=" O ASP 4 574 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER 4 612 " --> pdb=" O GLY 4 569 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY 4 510 " --> pdb=" O ALA 4 617 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU 4 507 " --> pdb=" O PHE 4 648 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N MET 4 650 " --> pdb=" O LEU 4 507 " (cutoff:3.500A) removed outlier: 6.498A 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: 6.803A 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: 3.685A 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: 6.241A pdb=" N VAL 5 402 " --> pdb=" O CYS 5 443 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU 5 378 " --> pdb=" O PHE 5 518 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL 5 520 " --> pdb=" O LEU 5 378 " (cutoff:3.500A) removed outlier: 6.705A 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: 3.608A 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: 3.728A 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: 6.232A pdb=" N VAL 6 417 " --> pdb=" O CYS 6 458 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASP 6 460 " --> pdb=" O VAL 6 417 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR 6 419 " --> pdb=" O ASP 6 460 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N CYS 6 457 " --> pdb=" O LEU 6 500 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ALA 6 502 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE 6 459 " --> pdb=" O ALA 6 502 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY 6 396 " --> 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: 7.224A 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: 6.219A pdb=" N LEU 7 48 " --> pdb=" O TYR 7 137 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLN 7 139 " --> pdb=" O LEU 7 48 " (cutoff:3.500A) removed outlier: 6.678A 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: 3.530A pdb=" N SER 7 483 " --> pdb=" O GLY 7 440 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE 7 377 " --> pdb=" O ALA 7 486 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA 7 488 " --> pdb=" O ILE 7 377 " (cutoff:3.500A) removed outlier: 6.224A 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 Processing sheet with id=AE4, first strand: chain 'A' and resid 832 through 833 removed outlier: 3.586A pdb=" N ARG A 846 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 336 through 339 removed outlier: 6.431A pdb=" N VAL B 337 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 423 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE B 311 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE B 424 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU B 313 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 446 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR B 314 " --> pdb=" O TYR B 446 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 133 through 136 removed outlier: 7.838A pdb=" N PHE C 250 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA C 103 " --> pdb=" O PHE C 250 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 95 through 100 removed outlier: 6.571A pdb=" N LEU D 95 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE D 157 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL D 97 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ASP D 159 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU D 99 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA D 188 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.044A pdb=" N VAL E 120 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU E 155 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE E 122 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE E 33 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER E 32 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N LEU E 177 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE E 34 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 393 through 395 2010 hydrogen bonds defined for protein. 5793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 102 stacking parallelities Total time for adding SS restraints: 11.23 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 15174 1.36 - 1.51: 12459 1.51 - 1.66: 19044 1.66 - 1.80: 224 1.80 - 1.95: 179 Bond restraints: 47080 Sorted by residual: bond pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" O3B AGS 6 901 " pdb=" PB AGS 6 901 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" O3B AGS 7 802 " pdb=" PB AGS 7 802 " ideal model delta sigma weight residual 1.673 1.587 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" O3B AGS D 901 " pdb=" PB AGS D 901 " ideal model delta sigma weight residual 1.673 1.587 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" O3B AGS 21001 " pdb=" PB AGS 21001 " ideal model delta sigma weight residual 1.673 1.588 0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 47075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 63370 2.04 - 4.07: 639 4.07 - 6.11: 70 6.11 - 8.15: 22 8.15 - 10.19: 14 Bond angle restraints: 64115 Sorted by residual: angle pdb=" N3 DT X 10 " pdb=" C4 DT X 10 " pdb=" O4 DT X 10 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT X 5 " pdb=" C4 DT X 5 " pdb=" O4 DT X 5 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT Y 8 " pdb=" C4 DT Y 8 " pdb=" O4 DT Y 8 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT X 4 " pdb=" C4 DT X 4 " pdb=" O4 DT X 4 " 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 Y 38 " pdb=" C4 DT Y 38 " pdb=" O4 DT Y 38 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 64110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.00: 27392 33.00 - 66.00: 1159 66.00 - 99.01: 80 99.01 - 132.01: 10 132.01 - 165.01: 3 Dihedral angle restraints: 28644 sinusoidal: 12688 harmonic: 15956 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 300.00 176.37 123.63 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 -12.15 150.70 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 -7.07 145.62 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 28641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 6203 0.053 - 0.105: 917 0.105 - 0.158: 180 0.158 - 0.211: 3 0.211 - 0.263: 5 Chirality restraints: 7308 Sorted by residual: 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 chirality pdb=" C3' AGS 7 802 " pdb=" C2' AGS 7 802 " pdb=" C4' AGS 7 802 " pdb=" O3' AGS 7 802 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C3' AGS D 901 " pdb=" C2' AGS D 901 " pdb=" C4' AGS D 901 " pdb=" O3' AGS D 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 7305 not shown) Planarity restraints: 7758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP 4 457 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.04e+00 pdb=" C ASP 4 457 " 0.049 2.00e-02 2.50e+03 pdb=" O ASP 4 457 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE 4 458 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU 3 279 " 0.014 2.00e-02 2.50e+03 2.71e-02 7.35e+00 pdb=" C GLU 3 279 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU 3 279 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP 3 280 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 41 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.15e+00 pdb=" C LYS C 41 " -0.046 2.00e-02 2.50e+03 pdb=" O LYS C 41 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU C 42 " 0.016 2.00e-02 2.50e+03 ... (remaining 7755 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 68 2.38 - 3.01: 23858 3.01 - 3.64: 65647 3.64 - 4.27: 94770 4.27 - 4.90: 160769 Nonbonded interactions: 345112 Sorted by model distance: nonbonded pdb=" O3G AGS 7 802 " pdb="MG MG 7 803 " model vdw 1.751 2.170 nonbonded pdb=" O1B AGS 7 802 " pdb="MG MG 7 803 " model vdw 1.911 2.170 nonbonded pdb=" O1B AGS 21001 " pdb="MG MG 21002 " model vdw 1.946 2.170 nonbonded pdb=" O1B AGS E 501 " pdb="MG MG E 502 " model vdw 1.948 2.170 nonbonded pdb=" O1B AGS 6 901 " pdb="MG MG 6 902 " model vdw 1.985 2.170 ... (remaining 345107 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: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 50.570 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.110 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 47099 Z= 0.202 Angle : 0.569 30.733 64139 Z= 0.320 Chirality : 0.039 0.263 7308 Planarity : 0.003 0.057 7758 Dihedral : 16.923 165.009 18238 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.12), residues: 5310 helix: 1.89 (0.11), residues: 2505 sheet: 0.31 (0.18), residues: 826 loop : -0.40 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 417 TYR 0.018 0.001 TYR C 47 PHE 0.015 0.001 PHE C 76 TRP 0.026 0.001 TRP 6 614 HIS 0.003 0.000 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.20 (47080) covalent geometry : angle 0.51710 / 0.32 (64115) hydrogen bonds : bond 0.14102 / 9.22 ( 2115) hydrogen bonds : angle 5.17654 / 3.63 ( 5999) metal coordination : bond 0.06213 / 3.76 ( 19) metal coordination : angle 12.33831 / 8.65 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1192 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 20 MET cc_start: 0.7033 (tpp) cc_final: 0.6810 (tpp) REVERT: F 50 MET cc_start: 0.5995 (mtt) cc_final: 0.5717 (mtp) REVERT: F 146 LEU cc_start: 0.8525 (tp) cc_final: 0.8006 (pp) REVERT: 4 192 LEU cc_start: 0.7377 (tp) cc_final: 0.6943 (tp) REVERT: 6 527 MET cc_start: 0.7482 (mmm) cc_final: 0.7159 (ttp) REVERT: 7 540 VAL cc_start: 0.7266 (t) cc_final: 0.7005 (t) REVERT: A 756 ASP cc_start: 0.7889 (p0) cc_final: 0.7428 (t0) REVERT: A 816 MET cc_start: 0.5915 (ttm) cc_final: 0.5639 (ttp) REVERT: C 222 MET cc_start: 0.7878 (tmm) cc_final: 0.7596 (tmm) REVERT: C 685 VAL cc_start: 0.8437 (t) cc_final: 0.8237 (t) REVERT: D 218 MET cc_start: 0.4834 (mpp) cc_final: 0.3343 (mtm) REVERT: D 402 MET cc_start: 0.5666 (mmp) cc_final: 0.4755 (mmt) REVERT: E 130 LEU cc_start: 0.8699 (mt) cc_final: 0.8416 (tt) REVERT: E 234 PRO cc_start: 0.5860 (Cg_exo) cc_final: 0.5469 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 1192 average time/residue: 0.3008 time to fit residues: 573.0552 Evaluate side-chains 566 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 566 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 6.9990 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 9.9990 chunk 366 optimal weight: 0.7980 chunk 223 optimal weight: 0.3980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 104 GLN 2 606 GLN ** 2 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 781 HIS 3 298 GLN 3 308 HIS 3 353 GLN 4 225 GLN 4 521 GLN 5 32 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 479 ASN 7 541 HIS A 769 ASN B 291 ASN C 154 GLN ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN D 267 GLN D 307 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS E 193 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.143516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.113207 restraints weight = 117210.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.117418 restraints weight = 65434.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.117952 restraints weight = 40109.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.118427 restraints weight = 35046.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.118754 restraints weight = 32872.624| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 47099 Z= 0.237 Angle : 0.715 14.902 64139 Z= 0.365 Chirality : 0.045 0.217 7308 Planarity : 0.005 0.077 7758 Dihedral : 16.523 175.420 7396 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.13 % Allowed : 10.69 % Favored : 87.18 % 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: 0.69 (0.11), residues: 5310 helix: 1.55 (0.10), residues: 2547 sheet: -0.07 (0.18), residues: 833 loop : -0.71 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 3 13 TYR 0.025 0.002 TYR 5 565 PHE 0.027 0.002 PHE E 156 TRP 0.024 0.002 TRP E 278 HIS 0.010 0.001 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (47080) covalent geometry : angle 0.70224 / 0.36 (64115) hydrogen bonds : bond 0.04846 / 3.21 ( 2115) hydrogen bonds : angle 4.56695 / 3.23 ( 5999) metal coordination : bond 0.01383 / 0.92 ( 19) metal coordination : angle 6.96940 / 4.19 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 577 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 117 ILE cc_start: 0.6294 (OUTLIER) cc_final: 0.6084 (mm) REVERT: F 122 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7391 (tm-30) REVERT: 2 185 TRP cc_start: 0.8499 (t-100) cc_final: 0.8231 (t-100) REVERT: 3 398 MET cc_start: 0.8740 (ttm) cc_final: 0.8490 (mtp) REVERT: 4 216 LYS cc_start: 0.7822 (tttt) cc_final: 0.7505 (tppt) REVERT: 5 450 MET cc_start: 0.8557 (mtp) cc_final: 0.8355 (ttm) REVERT: 6 32 ASP cc_start: 0.7704 (t0) cc_final: 0.6206 (t0) REVERT: 6 47 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7120 (pp) REVERT: 6 450 MET cc_start: 0.8488 (mtm) cc_final: 0.8149 (mtt) REVERT: 6 527 MET cc_start: 0.7939 (mmm) cc_final: 0.7338 (ttp) REVERT: 6 779 ARG cc_start: 0.8475 (ttt90) cc_final: 0.8270 (ttt90) REVERT: 7 18 GLN cc_start: 0.8712 (pt0) cc_final: 0.8299 (pm20) REVERT: 7 108 MET cc_start: 0.5200 (ppp) cc_final: 0.4562 (ppp) REVERT: A 756 ASP cc_start: 0.8825 (p0) cc_final: 0.8610 (t0) REVERT: A 808 MET cc_start: 0.8481 (mtp) cc_final: 0.8234 (tmm) REVERT: B 278 LYS cc_start: 0.7496 (ptpt) cc_final: 0.6938 (tmtt) REVERT: C 222 MET cc_start: 0.8498 (tmm) cc_final: 0.8164 (tmm) REVERT: C 354 ARG cc_start: 0.2847 (mtt180) cc_final: 0.1398 (tpp80) REVERT: D 210 PHE cc_start: 0.7010 (t80) cc_final: 0.6718 (t80) REVERT: D 281 MET cc_start: 0.7817 (mmm) cc_final: 0.7518 (mmm) REVERT: E 94 ILE cc_start: 0.8516 (mm) cc_final: 0.8235 (mm) REVERT: E 130 LEU cc_start: 0.8430 (mt) cc_final: 0.8064 (tt) REVERT: E 133 MET cc_start: 0.6437 (mmt) cc_final: 0.5662 (mmt) REVERT: E 189 LYS cc_start: 0.6632 (mtmt) cc_final: 0.6357 (ptpt) outliers start: 103 outliers final: 69 residues processed: 636 average time/residue: 0.2724 time to fit residues: 289.1414 Evaluate side-chains 538 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 467 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 606 GLN Chi-restraints excluded: chain 2 residue 679 VAL 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 2 residue 805 THR Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 4 residue 157 VAL Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 300 GLN Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 127 MET Chi-restraints excluded: chain 5 residue 255 ASP Chi-restraints excluded: chain 5 residue 296 VAL Chi-restraints excluded: chain 5 residue 382 ASP Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 5 residue 637 VAL Chi-restraints excluded: chain 6 residue 47 LEU Chi-restraints excluded: chain 6 residue 112 VAL Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 346 LEU Chi-restraints excluded: chain 6 residue 358 ILE Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 7 residue 16 PHE 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 464 GLN Chi-restraints excluded: chain 7 residue 616 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 419 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 538 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 316 optimal weight: 3.9990 chunk 375 optimal weight: 7.9990 chunk 392 optimal weight: 0.4980 chunk 293 optimal weight: 0.6980 chunk 188 optimal weight: 0.3980 chunk 273 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 chunk 517 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 687 HIS 6 187 ASN ** 6 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 212 GLN B 340 ASN B 416 HIS ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.145737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.115851 restraints weight = 116915.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.120135 restraints weight = 62957.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.120995 restraints weight = 37542.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.121457 restraints weight = 31919.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.121664 restraints weight = 31772.848| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 47099 Z= 0.121 Angle : 0.596 16.276 64139 Z= 0.301 Chirality : 0.041 0.254 7308 Planarity : 0.004 0.061 7758 Dihedral : 16.393 178.604 7396 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.34 % Allowed : 11.89 % Favored : 85.77 % 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: 0.92 (0.12), residues: 5310 helix: 1.73 (0.10), residues: 2535 sheet: 0.06 (0.18), residues: 823 loop : -0.58 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 401 TYR 0.025 0.001 TYR B 294 PHE 0.022 0.001 PHE 4 263 TRP 0.038 0.002 TRP B 433 HIS 0.008 0.001 HIS 7 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (47080) covalent geometry : angle 0.58758 / 0.30 (64115) hydrogen bonds : bond 0.03994 / 2.63 ( 2115) hydrogen bonds : angle 4.20118 / 2.96 ( 5999) metal coordination : bond 0.00714 / 0.42 ( 19) metal coordination : angle 5.29476 / 3.36 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 525 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 121 TYR cc_start: 0.6904 (t80) cc_final: 0.6670 (t80) REVERT: F 146 LEU cc_start: 0.8248 (tp) cc_final: 0.7678 (pp) REVERT: 2 185 TRP cc_start: 0.8435 (t-100) cc_final: 0.8193 (t-100) REVERT: 2 193 LEU cc_start: 0.8796 (tt) cc_final: 0.8542 (tp) REVERT: 3 47 LEU cc_start: 0.7843 (tp) cc_final: 0.7550 (mt) REVERT: 3 322 LEU cc_start: 0.7183 (mp) cc_final: 0.6964 (mp) REVERT: 3 398 MET cc_start: 0.8723 (ttm) cc_final: 0.8462 (mtp) REVERT: 3 449 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6820 (mp) REVERT: 4 684 MET cc_start: 0.7287 (tpp) cc_final: 0.7064 (tpp) REVERT: 6 47 LEU cc_start: 0.7263 (tp) cc_final: 0.6962 (pp) REVERT: 6 450 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7956 (mtt) REVERT: 6 527 MET cc_start: 0.7865 (mmm) cc_final: 0.7230 (ttp) REVERT: 7 18 GLN cc_start: 0.8618 (pt0) cc_final: 0.8331 (pm20) REVERT: 7 108 MET cc_start: 0.5406 (ppp) cc_final: 0.4698 (ppp) REVERT: 7 430 GLU cc_start: 0.6599 (mt-10) cc_final: 0.6384 (mt-10) REVERT: A 756 ASP cc_start: 0.8901 (p0) cc_final: 0.8505 (t0) REVERT: B 278 LYS cc_start: 0.7509 (ptpt) cc_final: 0.6907 (tmtt) REVERT: C 189 MET cc_start: 0.8510 (ppp) cc_final: 0.8253 (ppp) REVERT: C 222 MET cc_start: 0.8518 (tmm) cc_final: 0.8200 (tmm) REVERT: C 231 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8183 (mp10) REVERT: C 354 ARG cc_start: 0.2911 (mtt180) cc_final: 0.1357 (tpp80) REVERT: C 556 VAL cc_start: 0.7237 (t) cc_final: 0.6945 (m) REVERT: C 680 ARG cc_start: 0.8265 (ttm110) cc_final: 0.8015 (ttm110) REVERT: D 189 VAL cc_start: 0.7837 (t) cc_final: 0.7350 (p) REVERT: D 218 MET cc_start: 0.5154 (mpp) cc_final: 0.3816 (mtm) REVERT: D 281 MET cc_start: 0.7759 (mmm) cc_final: 0.7542 (mmm) REVERT: D 303 MET cc_start: 0.5700 (mmp) cc_final: 0.5491 (mmt) REVERT: D 351 ASN cc_start: 0.8743 (t0) cc_final: 0.8499 (t0) REVERT: E 94 ILE cc_start: 0.8462 (mm) cc_final: 0.8185 (mm) REVERT: E 130 LEU cc_start: 0.8419 (mt) cc_final: 0.8016 (tt) REVERT: E 133 MET cc_start: 0.6177 (mmt) cc_final: 0.5528 (mmt) REVERT: E 189 LYS cc_start: 0.6344 (mtmt) cc_final: 0.6014 (ptpt) REVERT: E 429 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7429 (ptpt) outliers start: 113 outliers final: 62 residues processed: 595 average time/residue: 0.2711 time to fit residues: 272.6747 Evaluate side-chains 541 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 475 time to evaluate : 1.756 ------------------------------------------------------------------------------- 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 406 CYS Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 805 THR Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 449 LEU Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 300 GLN Chi-restraints excluded: chain 4 residue 585 SER Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 127 MET Chi-restraints excluded: chain 5 residue 255 ASP 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 637 VAL Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 217 ARG Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 346 LEU Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 177 MET 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 464 GLN Chi-restraints excluded: chain 7 residue 616 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 278 TRP Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 429 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 215 optimal weight: 4.9990 chunk 462 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 461 optimal weight: 20.0000 chunk 229 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 442 optimal weight: 7.9990 chunk 496 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 515 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 461 GLN 4 494 HIS 4 608 ASN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 597 GLN 7 542 GLN A 769 ASN C 265 HIS ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 HIS C 500 GLN D 61 ASN D 381 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.140509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.109695 restraints weight = 116003.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.113805 restraints weight = 62690.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.114738 restraints weight = 38459.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.115305 restraints weight = 31944.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.115492 restraints weight = 31261.152| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 47099 Z= 0.202 Angle : 0.658 15.639 64139 Z= 0.334 Chirality : 0.043 0.220 7308 Planarity : 0.005 0.075 7758 Dihedral : 16.417 175.107 7396 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.78 % Allowed : 14.25 % Favored : 82.97 % 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: 0.59 (0.11), residues: 5310 helix: 1.47 (0.10), residues: 2538 sheet: -0.17 (0.18), residues: 827 loop : -0.74 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 273 TYR 0.026 0.002 TYR D 399 PHE 0.040 0.002 PHE 7 77 TRP 0.019 0.002 TRP B 433 HIS 0.008 0.001 HIS C 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (47080) covalent geometry : angle 0.65110 / 0.33 (64115) hydrogen bonds : bond 0.04405 / 2.92 ( 2115) hydrogen bonds : angle 4.37237 / 3.09 ( 5999) metal coordination : bond 0.01033 / 0.67 ( 19) metal coordination : angle 5.02471 / 3.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 504 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 26 GLU cc_start: 0.6904 (tp30) cc_final: 0.6612 (tp30) REVERT: 2 188 MET cc_start: 0.7768 (mmm) cc_final: 0.7534 (mmm) REVERT: 2 193 LEU cc_start: 0.8800 (tt) cc_final: 0.8559 (tp) REVERT: 4 216 LYS cc_start: 0.7958 (tttt) cc_final: 0.7554 (tppt) REVERT: 4 684 MET cc_start: 0.7474 (tpp) cc_final: 0.7219 (tpp) REVERT: 5 429 MET cc_start: 0.7455 (mmt) cc_final: 0.7154 (mmt) REVERT: 6 47 LEU cc_start: 0.7332 (tp) cc_final: 0.7006 (pp) REVERT: 6 450 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8323 (mtm) REVERT: 6 527 MET cc_start: 0.7796 (mmm) cc_final: 0.7315 (ttp) REVERT: 7 18 GLN cc_start: 0.8707 (pt0) cc_final: 0.8330 (pm20) REVERT: 7 108 MET cc_start: 0.5808 (ppp) cc_final: 0.5034 (ppp) REVERT: 7 269 ASP cc_start: 0.7359 (t0) cc_final: 0.6973 (t0) REVERT: 7 430 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6562 (mt-10) REVERT: 7 565 MET cc_start: 0.5954 (tmm) cc_final: 0.5749 (tmm) REVERT: 7 622 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.7935 (p) REVERT: A 756 ASP cc_start: 0.8934 (p0) cc_final: 0.8588 (t0) REVERT: B 390 LEU cc_start: 0.7516 (mp) cc_final: 0.7296 (tp) REVERT: C 189 MET cc_start: 0.8587 (ppp) cc_final: 0.8290 (ppp) REVERT: C 354 ARG cc_start: 0.2820 (mtt180) cc_final: 0.1631 (tpp80) REVERT: D 189 VAL cc_start: 0.7912 (t) cc_final: 0.7445 (p) REVERT: D 218 MET cc_start: 0.5115 (mpp) cc_final: 0.3858 (mtm) REVERT: D 281 MET cc_start: 0.8117 (mmm) cc_final: 0.7774 (mmm) REVERT: D 351 ASN cc_start: 0.8852 (t0) cc_final: 0.8588 (t0) REVERT: E 94 ILE cc_start: 0.8577 (mm) cc_final: 0.8277 (mm) REVERT: E 130 LEU cc_start: 0.8305 (mt) cc_final: 0.7958 (tt) REVERT: E 189 LYS cc_start: 0.6531 (mtmt) cc_final: 0.6071 (ptpt) outliers start: 134 outliers final: 93 residues processed: 590 average time/residue: 0.2614 time to fit residues: 264.2486 Evaluate side-chains 550 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 455 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 68 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 379 GLN Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 419 HIS Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 684 VAL Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 805 THR Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 4 residue 157 VAL Chi-restraints excluded: chain 4 residue 195 GLN Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 300 GLN Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 5 residue 96 LEU 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 382 ASP Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 507 MET Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 5 residue 637 VAL Chi-restraints excluded: chain 5 residue 641 LEU Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 217 ARG Chi-restraints excluded: chain 6 residue 234 GLU Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 293 SER 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 562 SER Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 628 SER Chi-restraints excluded: chain 7 residue 13 VAL Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain 7 residue 177 MET 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 298 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 464 GLN Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 622 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 419 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 167 optimal weight: 0.0030 chunk 183 optimal weight: 0.7980 chunk 335 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 512 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 444 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 489 optimal weight: 2.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 549 GLN 4 608 ASN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 479 ASN B 340 ASN ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 ASN ** 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 = 0.4304 r_free = 0.4304 target = 0.142767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.112796 restraints weight = 115465.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.116738 restraints weight = 62682.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.116946 restraints weight = 38364.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.117324 restraints weight = 37825.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.117377 restraints weight = 35068.086| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 47099 Z= 0.114 Angle : 0.575 18.358 64139 Z= 0.290 Chirality : 0.041 0.338 7308 Planarity : 0.004 0.060 7758 Dihedral : 16.235 173.154 7396 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.28 % Allowed : 15.50 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.81 (0.12), residues: 5310 helix: 1.66 (0.10), residues: 2542 sheet: -0.08 (0.18), residues: 817 loop : -0.64 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 7 302 TYR 0.026 0.001 TYR F 121 PHE 0.050 0.001 PHE 7 77 TRP 0.034 0.002 TRP E 278 HIS 0.007 0.001 HIS 7 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (47080) covalent geometry : angle 0.56916 / 0.29 (64115) hydrogen bonds : bond 0.03756 / 2.50 ( 2115) hydrogen bonds : angle 4.12785 / 2.90 ( 5999) metal coordination : bond 0.00678 / 0.42 ( 19) metal coordination : angle 4.33286 / 2.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 497 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 122 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7587 (tm-30) REVERT: F 130 GLN cc_start: 0.7794 (tm-30) cc_final: 0.6803 (mp10) REVERT: F 146 LEU cc_start: 0.8228 (tp) cc_final: 0.7669 (pp) REVERT: 2 185 TRP cc_start: 0.8338 (t-100) cc_final: 0.8091 (t-100) REVERT: 2 193 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8542 (tp) REVERT: 3 47 LEU cc_start: 0.7933 (tp) cc_final: 0.7545 (mt) REVERT: 4 684 MET cc_start: 0.7534 (tpp) cc_final: 0.7285 (tpp) REVERT: 5 429 MET cc_start: 0.7334 (mmt) cc_final: 0.7002 (mmt) REVERT: 6 47 LEU cc_start: 0.7346 (tp) cc_final: 0.7025 (pp) REVERT: 6 450 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8041 (mtt) REVERT: 6 527 MET cc_start: 0.7720 (mmm) cc_final: 0.7249 (ttp) REVERT: 7 18 GLN cc_start: 0.8645 (pt0) cc_final: 0.8272 (pm20) REVERT: 7 108 MET cc_start: 0.6023 (ppp) cc_final: 0.5275 (ppp) REVERT: 7 430 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6408 (mt-10) REVERT: 7 565 MET cc_start: 0.6050 (tmm) cc_final: 0.5830 (tmm) REVERT: A 756 ASP cc_start: 0.8923 (p0) cc_final: 0.8564 (t0) REVERT: A 769 ASN cc_start: 0.7642 (t160) cc_final: 0.7332 (p0) REVERT: B 278 LYS cc_start: 0.7619 (ptpt) cc_final: 0.6905 (tmtt) REVERT: B 446 TYR cc_start: 0.7199 (m-80) cc_final: 0.6957 (m-80) REVERT: C 189 MET cc_start: 0.8612 (ppp) cc_final: 0.8344 (ppp) REVERT: C 318 ASP cc_start: 0.7242 (p0) cc_final: 0.7010 (p0) REVERT: C 354 ARG cc_start: 0.2691 (mtt180) cc_final: 0.1180 (tpp80) REVERT: C 562 CYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7560 (p) REVERT: D 218 MET cc_start: 0.5053 (mpp) cc_final: 0.3951 (mtm) REVERT: D 281 MET cc_start: 0.7951 (mmm) cc_final: 0.7672 (mmp) REVERT: D 351 ASN cc_start: 0.8819 (t0) cc_final: 0.8584 (t0) REVERT: E 94 ILE cc_start: 0.8646 (mm) cc_final: 0.8344 (mm) REVERT: E 130 LEU cc_start: 0.8414 (mt) cc_final: 0.8026 (tt) outliers start: 110 outliers final: 71 residues processed: 564 average time/residue: 0.2620 time to fit residues: 253.8057 Evaluate side-chains 545 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 471 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 149 CYS Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 379 GLN Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 805 THR 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 195 GLN Chi-restraints excluded: chain 4 residue 207 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 300 GLN 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 353 ILE Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 458 ILE Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 5 residue 619 ILE Chi-restraints excluded: chain 5 residue 637 VAL Chi-restraints excluded: chain 6 residue 112 VAL Chi-restraints excluded: chain 6 residue 152 VAL Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 217 ARG Chi-restraints excluded: chain 6 residue 234 GLU Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 346 LEU Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 520 ILE 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 177 MET 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 464 GLN Chi-restraints excluded: chain 7 residue 479 ASN Chi-restraints excluded: chain 7 residue 616 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 260 HIS Chi-restraints excluded: chain E residue 414 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 207 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 325 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 340 optimal weight: 3.9990 chunk 417 optimal weight: 3.9990 chunk 476 optimal weight: 9.9990 chunk 494 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 419 HIS 2 549 GLN 2 838 GLN 4 350 GLN 4 608 ASN 5 300 GLN 6 187 ASN ** 7 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.140163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.109468 restraints weight = 116118.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.113459 restraints weight = 63251.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.114406 restraints weight = 38634.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.114716 restraints weight = 32508.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.115066 restraints weight = 31301.125| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 47099 Z= 0.185 Angle : 0.616 16.826 64139 Z= 0.313 Chirality : 0.042 0.259 7308 Planarity : 0.004 0.067 7758 Dihedral : 16.211 177.720 7396 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.86 % Allowed : 16.06 % Favored : 81.09 % 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: 0.63 (0.12), residues: 5310 helix: 1.53 (0.10), residues: 2540 sheet: -0.26 (0.18), residues: 834 loop : -0.70 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 2 812 TYR 0.032 0.002 TYR F 121 PHE 0.048 0.002 PHE 7 77 TRP 0.039 0.002 TRP E 278 HIS 0.005 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (47080) covalent geometry : angle 0.61073 / 0.31 (64115) hydrogen bonds : bond 0.04096 / 2.72 ( 2115) hydrogen bonds : angle 4.27374 / 3.01 ( 5999) metal coordination : bond 0.00889 / 0.57 ( 19) metal coordination : angle 4.08156 / 2.52 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 481 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 LEU cc_start: 0.8364 (mt) cc_final: 0.8046 (mp) REVERT: F 122 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7564 (tm-30) REVERT: F 129 GLN cc_start: 0.7183 (mm110) cc_final: 0.6977 (mt0) REVERT: F 130 GLN cc_start: 0.7965 (tm-30) cc_final: 0.6853 (mp10) REVERT: 2 193 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8560 (tp) REVERT: 4 216 LYS cc_start: 0.7965 (tttt) cc_final: 0.7547 (tppt) REVERT: 4 284 THR cc_start: 0.6130 (OUTLIER) cc_final: 0.5818 (p) REVERT: 4 684 MET cc_start: 0.7499 (tpp) cc_final: 0.7238 (tpp) REVERT: 5 429 MET cc_start: 0.7405 (mmt) cc_final: 0.7091 (mmt) REVERT: 6 450 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8268 (mtm) REVERT: 6 527 MET cc_start: 0.7842 (mmm) cc_final: 0.7289 (ttp) REVERT: 7 18 GLN cc_start: 0.8667 (pt0) cc_final: 0.8299 (pm20) REVERT: 7 108 MET cc_start: 0.6086 (ppp) cc_final: 0.5307 (ppp) REVERT: 7 269 ASP cc_start: 0.7450 (t0) cc_final: 0.7098 (t0) REVERT: 7 430 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6507 (mt-10) REVERT: 7 565 MET cc_start: 0.6169 (tmm) cc_final: 0.5936 (tmm) REVERT: A 756 ASP cc_start: 0.8934 (p0) cc_final: 0.8555 (t0) REVERT: B 393 HIS cc_start: 0.7989 (OUTLIER) cc_final: 0.7345 (m90) REVERT: C 189 MET cc_start: 0.8626 (ppp) cc_final: 0.8350 (ppp) REVERT: C 354 ARG cc_start: 0.2757 (mtt180) cc_final: 0.1618 (tpp80) REVERT: C 358 LEU cc_start: 0.7743 (tp) cc_final: 0.7469 (tp) REVERT: D 218 MET cc_start: 0.4808 (mpp) cc_final: 0.3741 (mtm) REVERT: D 281 MET cc_start: 0.8211 (mmm) cc_final: 0.7802 (mmm) REVERT: D 351 ASN cc_start: 0.8862 (t0) cc_final: 0.8606 (t0) REVERT: E 94 ILE cc_start: 0.8674 (mm) cc_final: 0.8225 (mm) REVERT: E 130 LEU cc_start: 0.8291 (mt) cc_final: 0.7949 (tt) outliers start: 138 outliers final: 104 residues processed: 571 average time/residue: 0.2484 time to fit residues: 244.1847 Evaluate side-chains 563 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 455 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 68 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 2 residue 288 LEU Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 335 VAL Chi-restraints excluded: chain 2 residue 379 GLN Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 534 LYS Chi-restraints excluded: chain 2 residue 546 THR Chi-restraints excluded: chain 2 residue 549 GLN Chi-restraints excluded: chain 2 residue 679 VAL Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 805 THR Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 260 LEU Chi-restraints excluded: chain 3 residue 268 MET Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 4 residue 157 VAL Chi-restraints excluded: chain 4 residue 195 GLN Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 284 THR Chi-restraints excluded: chain 4 residue 300 GLN Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 5 residue 96 LEU 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 382 ASP Chi-restraints excluded: chain 5 residue 400 ILE Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 458 ILE Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 5 residue 637 VAL Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 6 residue 112 VAL Chi-restraints excluded: chain 6 residue 152 VAL Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 217 ARG Chi-restraints excluded: chain 6 residue 234 GLU Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 346 LEU Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 562 SER Chi-restraints excluded: chain 6 residue 618 VAL 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 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 298 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 464 GLN Chi-restraints excluded: chain 7 residue 616 LEU Chi-restraints excluded: chain 7 residue 621 MET Chi-restraints excluded: chain 7 residue 639 MET Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 255 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 345 optimal weight: 8.9990 chunk 386 optimal weight: 30.0000 chunk 64 optimal weight: 2.9990 chunk 417 optimal weight: 2.9990 chunk 363 optimal weight: 0.8980 chunk 402 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 473 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 549 GLN 2 838 GLN 4 608 ASN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 479 ASN A 796 GLN ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 HIS ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN E 193 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.139669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.109218 restraints weight = 115081.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.113000 restraints weight = 60824.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.113584 restraints weight = 36762.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.114568 restraints weight = 34591.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.114579 restraints weight = 32429.794| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 47099 Z= 0.170 Angle : 0.617 15.164 64139 Z= 0.313 Chirality : 0.042 0.374 7308 Planarity : 0.004 0.068 7758 Dihedral : 16.161 176.407 7396 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.86 % Allowed : 16.82 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.52 (0.12), residues: 5310 helix: 1.46 (0.10), residues: 2541 sheet: -0.33 (0.18), residues: 841 loop : -0.77 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 325 TYR 0.023 0.002 TYR E 204 PHE 0.048 0.002 PHE 7 77 TRP 0.032 0.002 TRP E 278 HIS 0.016 0.001 HIS C 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (47080) covalent geometry : angle 0.61236 / 0.31 (64115) hydrogen bonds : bond 0.04055 / 2.69 ( 2115) hydrogen bonds : angle 4.27911 / 3.02 ( 5999) metal coordination : bond 0.00840 / 0.53 ( 19) metal coordination : angle 3.83396 / 2.38 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 475 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 LEU cc_start: 0.8371 (mt) cc_final: 0.8035 (mp) REVERT: F 122 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7870 (tm-30) REVERT: F 130 GLN cc_start: 0.8016 (tm-30) cc_final: 0.6813 (mp10) REVERT: 2 193 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8578 (tp) REVERT: 2 773 MET cc_start: 0.7697 (tpp) cc_final: 0.7473 (tpp) REVERT: 2 811 MET cc_start: 0.7822 (tmm) cc_final: 0.7341 (tmm) REVERT: 4 216 LYS cc_start: 0.7984 (tttt) cc_final: 0.7534 (tppt) REVERT: 4 284 THR cc_start: 0.6130 (OUTLIER) cc_final: 0.5795 (p) REVERT: 4 474 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6582 (mm-30) REVERT: 4 684 MET cc_start: 0.7591 (tpp) cc_final: 0.7332 (tpp) REVERT: 5 429 MET cc_start: 0.7429 (mmt) cc_final: 0.7153 (mmt) REVERT: 6 47 LEU cc_start: 0.7370 (tp) cc_final: 0.7065 (pp) REVERT: 6 450 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8252 (mtm) REVERT: 6 527 MET cc_start: 0.7931 (mmm) cc_final: 0.7366 (ttp) REVERT: 7 18 GLN cc_start: 0.8679 (pt0) cc_final: 0.8292 (pm20) REVERT: 7 108 MET cc_start: 0.6084 (ppp) cc_final: 0.5314 (ppp) REVERT: 7 223 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6537 (tt0) REVERT: 7 269 ASP cc_start: 0.7477 (t0) cc_final: 0.7130 (t0) REVERT: 7 430 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6462 (mt-10) REVERT: 7 565 MET cc_start: 0.6389 (tmm) cc_final: 0.6170 (tmm) REVERT: A 756 ASP cc_start: 0.8876 (p0) cc_final: 0.8451 (t0) REVERT: B 278 LYS cc_start: 0.7591 (ptpt) cc_final: 0.7245 (ptpp) REVERT: B 390 LEU cc_start: 0.7544 (mp) cc_final: 0.7247 (tp) REVERT: B 393 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7324 (m90) REVERT: C 189 MET cc_start: 0.8605 (ppp) cc_final: 0.8400 (ppp) REVERT: C 354 ARG cc_start: 0.2616 (mtt180) cc_final: 0.1634 (tpp80) REVERT: C 358 LEU cc_start: 0.7869 (tp) cc_final: 0.7540 (tp) REVERT: C 410 MET cc_start: 0.7076 (tmm) cc_final: 0.6846 (tmm) REVERT: C 562 CYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7347 (p) REVERT: D 218 MET cc_start: 0.4783 (mpp) cc_final: 0.3731 (mtm) REVERT: D 281 MET cc_start: 0.8199 (mmm) cc_final: 0.7832 (mmp) REVERT: D 351 ASN cc_start: 0.8852 (t0) cc_final: 0.8604 (t0) REVERT: E 94 ILE cc_start: 0.8779 (mm) cc_final: 0.8314 (mm) REVERT: E 130 LEU cc_start: 0.8251 (mt) cc_final: 0.7934 (tt) REVERT: E 219 CYS cc_start: 0.5703 (t) cc_final: 0.5339 (p) outliers start: 138 outliers final: 105 residues processed: 567 average time/residue: 0.2367 time to fit residues: 231.0734 Evaluate side-chains 567 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 455 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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 68 LEU Chi-restraints excluded: chain F residue 111 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 2 residue 193 LEU Chi-restraints excluded: chain 2 residue 288 LEU Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 379 GLN Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 2 residue 534 LYS Chi-restraints excluded: chain 2 residue 546 THR Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 805 THR Chi-restraints excluded: chain 2 residue 834 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 240 THR Chi-restraints excluded: chain 3 residue 268 MET Chi-restraints excluded: chain 3 residue 307 ILE Chi-restraints excluded: chain 3 residue 393 LEU Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 4 residue 157 VAL Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 284 THR Chi-restraints excluded: chain 4 residue 300 GLN Chi-restraints excluded: chain 4 residue 474 GLU Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 4 residue 580 ASN Chi-restraints excluded: chain 5 residue 96 LEU 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 382 ASP Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 458 ILE Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 5 residue 619 ILE Chi-restraints excluded: chain 5 residue 637 VAL Chi-restraints excluded: chain 6 residue 112 VAL Chi-restraints excluded: chain 6 residue 152 VAL Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 217 ARG Chi-restraints excluded: chain 6 residue 234 GLU Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 346 LEU Chi-restraints excluded: chain 6 residue 417 VAL Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 562 SER 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 55 VAL Chi-restraints excluded: chain 7 residue 177 MET 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 464 GLN Chi-restraints excluded: chain 7 residue 616 LEU Chi-restraints excluded: chain 7 residue 621 MET Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 228 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 61 optimal weight: 0.0670 chunk 68 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 452 optimal weight: 1.9990 chunk 395 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 413 optimal weight: 0.0010 chunk 431 optimal weight: 7.9990 overall best weight: 0.5526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 129 GLN 2 212 HIS 2 838 GLN 3 553 HIS ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 479 ASN A 796 GLN ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN E 193 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.142552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.112485 restraints weight = 114876.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.116801 restraints weight = 61799.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.117933 restraints weight = 36422.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.118195 restraints weight = 30683.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.118372 restraints weight = 30197.939| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 47099 Z= 0.108 Angle : 0.582 14.162 64139 Z= 0.291 Chirality : 0.041 0.383 7308 Planarity : 0.004 0.069 7758 Dihedral : 16.028 179.247 7396 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.13 % Allowed : 17.51 % Favored : 80.36 % 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: 0.77 (0.12), residues: 5310 helix: 1.61 (0.10), residues: 2558 sheet: -0.16 (0.18), residues: 834 loop : -0.61 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 7 514 TYR 0.028 0.001 TYR F 121 PHE 0.046 0.001 PHE 7 77 TRP 0.031 0.002 TRP E 278 HIS 0.015 0.001 HIS C 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (47080) covalent geometry : angle 0.57903 / 0.29 (64115) hydrogen bonds : bond 0.03546 / 2.35 ( 2115) hydrogen bonds : angle 4.06887 / 2.86 ( 5999) metal coordination : bond 0.00561 / 0.33 ( 19) metal coordination : angle 3.31337 / 2.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 487 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 20 MET cc_start: 0.6611 (tpp) cc_final: 0.6370 (ttm) REVERT: F 122 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7691 (tm-30) REVERT: F 130 GLN cc_start: 0.8005 (tm-30) cc_final: 0.6775 (mp10) REVERT: F 146 LEU cc_start: 0.8214 (tp) cc_final: 0.7665 (pp) REVERT: 2 193 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8569 (tp) REVERT: 3 47 LEU cc_start: 0.7947 (tp) cc_final: 0.7699 (mt) REVERT: 4 284 THR cc_start: 0.5844 (OUTLIER) cc_final: 0.5546 (p) REVERT: 4 684 MET cc_start: 0.7569 (tpp) cc_final: 0.7311 (tpp) REVERT: 5 429 MET cc_start: 0.7626 (mmt) cc_final: 0.7346 (mmt) REVERT: 6 47 LEU cc_start: 0.7366 (tp) cc_final: 0.7045 (pp) REVERT: 6 450 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7949 (mtt) REVERT: 6 527 MET cc_start: 0.7758 (mmm) cc_final: 0.7251 (ttp) REVERT: 7 18 GLN cc_start: 0.8603 (pt0) cc_final: 0.8236 (pm20) REVERT: 7 430 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6342 (mt-10) REVERT: A 756 ASP cc_start: 0.8851 (p0) cc_final: 0.8438 (t0) REVERT: B 278 LYS cc_start: 0.7535 (ptpt) cc_final: 0.7200 (ptpp) REVERT: B 383 ASP cc_start: 0.8030 (m-30) cc_final: 0.7701 (t70) REVERT: C 354 ARG cc_start: 0.2575 (mtt180) cc_final: 0.1629 (tpp80) REVERT: C 358 LEU cc_start: 0.7671 (tp) cc_final: 0.7290 (tp) REVERT: C 562 CYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7314 (p) REVERT: D 218 MET cc_start: 0.4776 (mpp) cc_final: 0.3782 (mtm) REVERT: D 281 MET cc_start: 0.8130 (mmm) cc_final: 0.7804 (mmp) REVERT: D 351 ASN cc_start: 0.8834 (t0) cc_final: 0.8587 (t0) REVERT: E 94 ILE cc_start: 0.8754 (mm) cc_final: 0.8272 (mm) REVERT: E 130 LEU cc_start: 0.8311 (mt) cc_final: 0.7983 (tt) REVERT: E 141 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6610 (t80) REVERT: E 188 GLN cc_start: 0.5447 (tp40) cc_final: 0.5225 (tp-100) REVERT: E 219 CYS cc_start: 0.5484 (t) cc_final: 0.5185 (p) outliers start: 103 outliers final: 77 residues processed: 557 average time/residue: 0.2244 time to fit residues: 215.3380 Evaluate side-chains 535 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 453 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain 2 residue 288 LEU Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 379 GLN Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 534 LYS Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 834 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 260 LEU Chi-restraints excluded: chain 3 residue 307 ILE Chi-restraints excluded: chain 3 residue 393 LEU Chi-restraints excluded: chain 3 residue 398 MET Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 4 residue 284 THR Chi-restraints excluded: chain 4 residue 286 SER Chi-restraints excluded: chain 5 residue 96 LEU Chi-restraints excluded: chain 5 residue 99 LEU Chi-restraints excluded: chain 5 residue 296 VAL 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 5 residue 637 VAL Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 6 residue 79 ILE Chi-restraints excluded: chain 6 residue 112 VAL Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 217 ARG Chi-restraints excluded: chain 6 residue 234 GLU Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 293 SER Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 346 LEU Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 562 SER 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 242 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 464 GLN Chi-restraints excluded: chain 7 residue 479 ASN Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 193 HIS Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain E residue 414 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 186 optimal weight: 0.9990 chunk 514 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 524 optimal weight: 0.8980 chunk 479 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 312 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 533 optimal weight: 5.9990 chunk 468 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 838 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 479 ASN C 31 ASN ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 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 = 0.4260 r_free = 0.4260 target = 0.139885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.109763 restraints weight = 115417.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.112709 restraints weight = 60329.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.114043 restraints weight = 38557.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.114225 restraints weight = 34479.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.114347 restraints weight = 32118.175| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 47099 Z= 0.165 Angle : 0.630 13.498 64139 Z= 0.317 Chirality : 0.042 0.342 7308 Planarity : 0.004 0.065 7758 Dihedral : 16.009 176.380 7396 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.47 % Allowed : 17.57 % Favored : 79.97 % 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: 0.62 (0.12), residues: 5310 helix: 1.51 (0.10), residues: 2544 sheet: -0.28 (0.18), residues: 824 loop : -0.68 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG 3 364 TYR 0.024 0.002 TYR F 121 PHE 0.045 0.002 PHE 7 77 TRP 0.030 0.002 TRP C 187 HIS 0.028 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (47080) covalent geometry : angle 0.62694 / 0.32 (64115) hydrogen bonds : bond 0.03905 / 2.60 ( 2115) hydrogen bonds : angle 4.24068 / 2.99 ( 5999) metal coordination : bond 0.00729 / 0.45 ( 19) metal coordination : angle 3.25349 / 2.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 457 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 68 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6788 (tt) REVERT: F 122 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7817 (tm-30) REVERT: F 130 GLN cc_start: 0.8036 (tm-30) cc_final: 0.6935 (mp10) REVERT: F 146 LEU cc_start: 0.8232 (tp) cc_final: 0.7675 (pp) REVERT: 2 193 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8568 (tp) REVERT: 4 216 LYS cc_start: 0.7949 (tttt) cc_final: 0.7495 (tppt) REVERT: 4 684 MET cc_start: 0.7607 (tpp) cc_final: 0.7320 (tpp) REVERT: 5 434 MET cc_start: 0.8063 (mtt) cc_final: 0.7834 (mtp) REVERT: 6 47 LEU cc_start: 0.7407 (tp) cc_final: 0.7090 (pp) REVERT: 6 450 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8071 (mtt) REVERT: 6 527 MET cc_start: 0.7871 (mmm) cc_final: 0.7329 (ttp) REVERT: 7 18 GLN cc_start: 0.8631 (pt0) cc_final: 0.8226 (pm20) REVERT: 7 108 MET cc_start: 0.5748 (ppp) cc_final: 0.4814 (ppp) REVERT: 7 223 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6550 (tt0) REVERT: 7 269 ASP cc_start: 0.7493 (t0) cc_final: 0.7144 (t0) REVERT: 7 430 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6486 (mt-10) REVERT: A 756 ASP cc_start: 0.8889 (p0) cc_final: 0.8361 (t0) REVERT: A 758 MET cc_start: 0.2513 (tmm) cc_final: 0.2278 (tmm) REVERT: B 278 LYS cc_start: 0.7611 (ptpt) cc_final: 0.7267 (ptpp) REVERT: B 383 ASP cc_start: 0.8283 (m-30) cc_final: 0.7812 (t70) REVERT: B 393 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.7180 (m90) REVERT: C 354 ARG cc_start: 0.2667 (mtt180) cc_final: 0.1670 (tpp80) REVERT: C 358 LEU cc_start: 0.7740 (tp) cc_final: 0.7392 (tp) REVERT: C 562 CYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7358 (p) REVERT: D 218 MET cc_start: 0.5026 (mpp) cc_final: 0.3897 (mtm) REVERT: D 281 MET cc_start: 0.8213 (mmm) cc_final: 0.7910 (mmt) REVERT: D 351 ASN cc_start: 0.8808 (t0) cc_final: 0.8562 (t0) REVERT: E 94 ILE cc_start: 0.8849 (mm) cc_final: 0.8391 (mm) REVERT: E 130 LEU cc_start: 0.8270 (mt) cc_final: 0.7944 (tt) REVERT: E 141 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6804 (t80) REVERT: E 188 GLN cc_start: 0.5480 (tp40) cc_final: 0.5233 (tp-100) outliers start: 119 outliers final: 91 residues processed: 536 average time/residue: 0.1985 time to fit residues: 183.4938 Evaluate side-chains 545 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 447 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 68 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 2 residue 288 LEU Chi-restraints excluded: chain 2 residue 379 GLN Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 414 LEU Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 2 residue 534 LYS Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 684 VAL Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 805 THR Chi-restraints excluded: chain 2 residue 834 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 240 THR Chi-restraints excluded: chain 3 residue 260 LEU Chi-restraints excluded: chain 3 residue 307 ILE Chi-restraints excluded: chain 3 residue 393 LEU Chi-restraints excluded: chain 3 residue 398 MET Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 4 residue 610 ARG Chi-restraints excluded: chain 5 residue 96 LEU 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 637 VAL Chi-restraints excluded: chain 6 residue 79 ILE Chi-restraints excluded: chain 6 residue 112 VAL Chi-restraints excluded: chain 6 residue 152 VAL Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 217 ARG Chi-restraints excluded: chain 6 residue 234 GLU Chi-restraints excluded: chain 6 residue 243 ASP 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 346 LEU Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 562 SER 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 55 VAL 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 298 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 464 GLN Chi-restraints excluded: chain 7 residue 621 MET Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain E residue 414 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 107 optimal weight: 4.9990 chunk 492 optimal weight: 0.9980 chunk 331 optimal weight: 0.9990 chunk 469 optimal weight: 0.6980 chunk 526 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 521 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 410 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 838 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 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 = 0.4283 r_free = 0.4283 target = 0.141572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.110899 restraints weight = 115673.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.115234 restraints weight = 60848.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.116421 restraints weight = 38535.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.117169 restraints weight = 29732.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.117491 restraints weight = 27520.282| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 47099 Z= 0.114 Angle : 0.608 16.172 64139 Z= 0.301 Chirality : 0.041 0.357 7308 Planarity : 0.004 0.063 7758 Dihedral : 15.954 178.555 7396 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.89 % Allowed : 18.23 % Favored : 79.88 % 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: 0.72 (0.12), residues: 5310 helix: 1.56 (0.10), residues: 2556 sheet: -0.21 (0.18), residues: 826 loop : -0.61 (0.15), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 2 812 TYR 0.037 0.001 TYR F 121 PHE 0.045 0.001 PHE 7 77 TRP 0.080 0.002 TRP E 278 HIS 0.005 0.001 HIS 6 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (47080) covalent geometry : angle 0.60536 / 0.30 (64115) hydrogen bonds : bond 0.03541 / 2.36 ( 2115) hydrogen bonds : angle 4.12811 / 2.91 ( 5999) metal coordination : bond 0.00517 / 0.31 ( 19) metal coordination : angle 3.02628 / 1.90 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10620 Ramachandran restraints generated. 5310 Oldfield, 0 Emsley, 5310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 475 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 68 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6800 (tt) REVERT: F 122 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7734 (tm-30) REVERT: F 130 GLN cc_start: 0.8042 (tm-30) cc_final: 0.6929 (mp10) REVERT: F 146 LEU cc_start: 0.8171 (tp) cc_final: 0.7627 (pp) REVERT: 2 193 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8546 (tp) REVERT: 2 811 MET cc_start: 0.7696 (tmm) cc_final: 0.7116 (tmm) REVERT: 3 47 LEU cc_start: 0.7983 (tp) cc_final: 0.7644 (mt) REVERT: 3 603 MET cc_start: 0.7035 (pmm) cc_final: 0.6805 (pmm) REVERT: 4 684 MET cc_start: 0.7624 (tpp) cc_final: 0.7345 (tpp) REVERT: 5 434 MET cc_start: 0.7820 (mtt) cc_final: 0.7583 (mtp) REVERT: 6 47 LEU cc_start: 0.7363 (tp) cc_final: 0.7045 (pp) REVERT: 6 450 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7966 (mtt) REVERT: 6 527 MET cc_start: 0.7832 (mmm) cc_final: 0.7278 (ttp) REVERT: 7 18 GLN cc_start: 0.8608 (pt0) cc_final: 0.8211 (pm20) REVERT: 7 108 MET cc_start: 0.5798 (ppp) cc_final: 0.4886 (ppp) REVERT: 7 269 ASP cc_start: 0.7442 (t0) cc_final: 0.7088 (t0) REVERT: 7 430 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6405 (mt-10) REVERT: A 756 ASP cc_start: 0.8896 (p0) cc_final: 0.8389 (t0) REVERT: A 759 PHE cc_start: 0.6311 (OUTLIER) cc_final: 0.5894 (m-10) REVERT: A 816 MET cc_start: 0.7516 (ttp) cc_final: 0.6991 (tpp) REVERT: B 278 LYS cc_start: 0.7545 (ptpt) cc_final: 0.7205 (ptpp) REVERT: B 383 ASP cc_start: 0.8232 (m-30) cc_final: 0.7751 (t70) REVERT: C 354 ARG cc_start: 0.2559 (mtt180) cc_final: 0.1604 (tpp80) REVERT: C 358 LEU cc_start: 0.7567 (tp) cc_final: 0.7238 (tp) REVERT: C 562 CYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7472 (p) REVERT: D 69 ARG cc_start: 0.6740 (tpp80) cc_final: 0.6412 (tpp80) REVERT: D 218 MET cc_start: 0.4759 (mpp) cc_final: 0.3894 (mtp) REVERT: D 281 MET cc_start: 0.8234 (mmm) cc_final: 0.7858 (mmm) REVERT: D 351 ASN cc_start: 0.8797 (t0) cc_final: 0.8467 (t0) REVERT: E 94 ILE cc_start: 0.8818 (mm) cc_final: 0.8358 (mm) REVERT: E 130 LEU cc_start: 0.8213 (mt) cc_final: 0.7923 (tt) REVERT: E 141 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6691 (t80) REVERT: E 188 GLN cc_start: 0.5504 (tp40) cc_final: 0.5288 (tp-100) outliers start: 91 outliers final: 82 residues processed: 532 average time/residue: 0.1821 time to fit residues: 166.6544 Evaluate side-chains 543 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 455 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 68 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 2 residue 288 LEU Chi-restraints excluded: chain 2 residue 335 VAL Chi-restraints excluded: chain 2 residue 379 GLN Chi-restraints excluded: chain 2 residue 406 CYS Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 2 residue 534 LYS Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 834 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 240 THR Chi-restraints excluded: chain 3 residue 260 LEU Chi-restraints excluded: chain 3 residue 307 ILE Chi-restraints excluded: chain 3 residue 393 LEU Chi-restraints excluded: chain 3 residue 398 MET Chi-restraints excluded: chain 3 residue 456 TYR Chi-restraints excluded: chain 4 residue 207 PHE Chi-restraints excluded: chain 4 residue 488 THR Chi-restraints excluded: chain 4 residue 610 ARG Chi-restraints excluded: chain 5 residue 96 LEU Chi-restraints excluded: chain 5 residue 99 LEU 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 637 VAL Chi-restraints excluded: chain 6 residue 79 ILE Chi-restraints excluded: chain 6 residue 112 VAL Chi-restraints excluded: chain 6 residue 152 VAL Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 217 ARG Chi-restraints excluded: chain 6 residue 234 GLU Chi-restraints excluded: chain 6 residue 243 ASP 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 346 LEU Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 562 SER 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 55 VAL Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 464 GLN Chi-restraints excluded: chain 7 residue 479 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 429 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 340 optimal weight: 1.9990 chunk 398 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 504 optimal weight: 0.2980 chunk 488 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 442 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 437 optimal weight: 5.9990 chunk 313 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 HIS ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.140871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.110743 restraints weight = 115310.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.114426 restraints weight = 60509.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.115342 restraints weight = 37100.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.115546 restraints weight = 34276.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.115776 restraints weight = 32182.646| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 47099 Z= 0.128 Angle : 0.611 14.022 64139 Z= 0.303 Chirality : 0.041 0.337 7308 Planarity : 0.004 0.063 7758 Dihedral : 15.910 178.820 7396 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.22 % Allowed : 18.02 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.12), residues: 5310 helix: 1.57 (0.10), residues: 2547 sheet: -0.22 (0.18), residues: 826 loop : -0.61 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 2 812 TYR 0.033 0.001 TYR F 121 PHE 0.046 0.001 PHE 7 77 TRP 0.062 0.002 TRP E 278 HIS 0.016 0.001 HIS D 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (47080) covalent geometry : angle 0.60883 / 0.30 (64115) hydrogen bonds : bond 0.03610 / 2.41 ( 2115) hydrogen bonds : angle 4.14634 / 2.92 ( 5999) metal coordination : bond 0.00565 / 0.34 ( 19) metal coordination : angle 2.91888 / 1.86 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8714.57 seconds wall clock time: 150 minutes 43.69 seconds (9043.69 seconds total)