Starting phenix.real_space_refine on Tue Jul 7 06:59:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s0d_19622/07_2026/8s0d_19622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s0d_19622/07_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_19622/07_2026/8s0d_19622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s0d_19622/07_2026/8s0d_19622.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s0d_19622/07_2026/8s0d_19622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s0d_19622/07_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-dev-6108/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: 8.58, per 1000 atoms: 0.19 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: 4.11 Conformation dependent library (CDL) restraints added in 2.2 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: 5.02 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: 10.59 Time building geometry restraints manager: 5.52 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: 63372 2.04 - 4.07: 637 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: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 48.690 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.090 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.310 ------------------------------------------------------------------------------- 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 : 0.568 30.733 64139 Z= 0.318 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 0.51569 / 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 : 1.822 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: 0.5716 (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: 0.6942 (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: 0.2992 time to fit residues: 569.0121 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 : 1.783 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.143520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.113272 restraints weight = 117927.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.117198 restraints weight = 66001.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.117998 restraints weight = 41230.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.118557 restraints weight = 35185.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.118720 restraints weight = 33127.148| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 47099 Z= 0.241 Angle : 0.713 15.413 64139 Z= 0.368 Chirality : 0.045 0.222 7308 Planarity : 0.005 0.078 7758 Dihedral : 16.555 175.371 7396 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.11 % Allowed : 10.73 % Favored : 87.16 % 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: 1.54 (0.10), residues: 2545 sheet: -0.08 (0.18), residues: 833 loop : -0.70 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 3 13 TYR 0.026 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 0.00555 / 0.24 (47080) covalent geometry : angle 0.70021 / 0.37 (64115) hydrogen bonds : bond 0.04863 / 3.21 ( 2115) hydrogen bonds : angle 4.55663 / 3.22 ( 5999) metal coordination : bond 0.01392 / 0.93 ( 19) metal coordination : angle 6.96235 / 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 678 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 576 time to evaluate : 1.688 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: 0.6299 (OUTLIER) cc_final: 0.6093 (mm) REVERT: F 122 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7385 (tm-30) REVERT: 2 185 TRP cc_start: 0.8486 (t-100) cc_final: 0.8214 (t-100) REVERT: 3 398 MET cc_start: 0.8781 (ttm) cc_final: 0.8519 (mtp) REVERT: 4 216 LYS cc_start: 0.7822 (tttt) cc_final: 0.7497 (tppt) REVERT: 6 32 ASP cc_start: 0.7713 (t0) cc_final: 0.6225 (t0) REVERT: 6 47 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7123 (pp) REVERT: 6 450 MET cc_start: 0.8488 (mtm) cc_final: 0.8154 (mtt) REVERT: 6 527 MET cc_start: 0.7948 (mmm) cc_final: 0.7347 (ttp) REVERT: 6 779 ARG cc_start: 0.8481 (ttt90) cc_final: 0.8275 (ttt90) REVERT: 7 18 GLN cc_start: 0.8714 (pt0) cc_final: 0.8296 (pm20) REVERT: 7 108 MET cc_start: 0.5215 (ppp) cc_final: 0.4609 (ppp) REVERT: A 756 ASP cc_start: 0.8822 (p0) cc_final: 0.8603 (t0) REVERT: A 808 MET cc_start: 0.8476 (mtp) cc_final: 0.8240 (tmm) REVERT: B 278 LYS cc_start: 0.7509 (ptpt) cc_final: 0.6945 (tmtt) REVERT: C 222 MET cc_start: 0.8508 (tmm) cc_final: 0.8202 (tmm) REVERT: C 354 ARG cc_start: 0.2835 (mtt180) cc_final: 0.1784 (tpp80) REVERT: D 210 PHE cc_start: 0.7015 (t80) cc_final: 0.6723 (t80) REVERT: D 281 MET cc_start: 0.7827 (mmm) cc_final: 0.7546 (mmm) REVERT: E 94 ILE cc_start: 0.8527 (mm) cc_final: 0.8247 (mm) REVERT: E 130 LEU cc_start: 0.8442 (mt) cc_final: 0.8068 (tt) REVERT: E 133 MET cc_start: 0.6434 (mmt) cc_final: 0.5645 (mmt) REVERT: E 189 LYS cc_start: 0.6649 (mtmt) cc_final: 0.6393 (ptpt) outliers start: 102 outliers final: 67 residues processed: 636 average time/residue: 0.2724 time to fit residues: 287.9931 Evaluate side-chains 536 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 467 time to evaluate : 1.776 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 54 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 375 optimal weight: 8.9990 chunk 392 optimal weight: 0.6980 chunk 293 optimal weight: 0.5980 chunk 188 optimal weight: 0.0010 chunk 273 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 517 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 7 541 HIS 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.146088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.116132 restraints weight = 116969.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.120262 restraints weight = 62282.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.121430 restraints weight = 40335.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.122115 restraints weight = 32295.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.122623 restraints weight = 29589.090| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3145 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= 0.119 Angle : 0.597 17.027 64139 Z= 0.302 Chirality : 0.041 0.243 7308 Planarity : 0.004 0.061 7758 Dihedral : 16.412 178.753 7396 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.20 % Allowed : 12.12 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.12), residues: 5310 helix: 1.72 (0.10), residues: 2535 sheet: 0.08 (0.18), residues: 823 loop : -0.57 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 680 TYR 0.027 0.001 TYR 4 249 PHE 0.023 0.001 PHE 4 263 TRP 0.037 0.002 TRP B 433 HIS 0.008 0.001 HIS 7 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (47080) covalent geometry : angle 0.58879 / 0.30 (64115) hydrogen bonds : bond 0.03979 / 2.63 ( 2115) hydrogen bonds : angle 4.17490 / 2.94 ( 5999) metal coordination : bond 0.00737 / 0.43 ( 19) metal coordination : angle 5.16483 / 3.30 ( 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 641 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 535 time to evaluate : 1.778 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: F 121 TYR cc_start: 0.6981 (t80) cc_final: 0.6728 (t80) REVERT: F 146 LEU cc_start: 0.8255 (tp) cc_final: 0.7683 (pp) REVERT: 2 185 TRP cc_start: 0.8428 (t-100) cc_final: 0.8187 (t-100) REVERT: 2 193 LEU cc_start: 0.8799 (tt) cc_final: 0.8541 (tp) REVERT: 3 47 LEU cc_start: 0.7917 (tp) cc_final: 0.7618 (mt) REVERT: 3 322 LEU cc_start: 0.7162 (mp) cc_final: 0.6938 (mp) REVERT: 3 449 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6779 (mp) REVERT: 4 684 MET cc_start: 0.7291 (tpp) cc_final: 0.7079 (tpp) REVERT: 6 47 LEU cc_start: 0.7254 (tp) cc_final: 0.6950 (pp) REVERT: 6 179 ILE cc_start: 0.8487 (tp) cc_final: 0.8184 (mm) REVERT: 6 450 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7937 (mtt) REVERT: 6 527 MET cc_start: 0.7919 (mmm) cc_final: 0.7285 (ttp) REVERT: 7 18 GLN cc_start: 0.8577 (pt0) cc_final: 0.8319 (pm20) REVERT: 7 108 MET cc_start: 0.5461 (ppp) cc_final: 0.4753 (ppp) REVERT: 7 430 GLU cc_start: 0.6621 (mt-10) cc_final: 0.6334 (mt-10) REVERT: A 756 ASP cc_start: 0.8888 (p0) cc_final: 0.8490 (t0) REVERT: B 273 ARG cc_start: 0.6374 (mpt180) cc_final: 0.6174 (mpt180) REVERT: B 278 LYS cc_start: 0.7487 (ptpt) cc_final: 0.6903 (tmtt) REVERT: B 333 ASP cc_start: 0.6871 (t70) cc_final: 0.6634 (t0) REVERT: B 446 TYR cc_start: 0.7226 (m-80) cc_final: 0.6979 (m-80) REVERT: C 189 MET cc_start: 0.8453 (ppp) cc_final: 0.8196 (ppp) REVERT: C 222 MET cc_start: 0.8509 (tmm) cc_final: 0.8194 (tmm) REVERT: C 231 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8131 (mp10) REVERT: C 354 ARG cc_start: 0.2882 (mtt180) cc_final: 0.1648 (tpp80) REVERT: C 556 VAL cc_start: 0.7315 (t) cc_final: 0.7045 (m) REVERT: C 680 ARG cc_start: 0.8261 (ttm110) cc_final: 0.8017 (ttm110) REVERT: D 189 VAL cc_start: 0.7815 (t) cc_final: 0.7325 (p) REVERT: D 218 MET cc_start: 0.5139 (mpp) cc_final: 0.3810 (mtm) REVERT: D 281 MET cc_start: 0.7742 (mmm) cc_final: 0.7527 (mmm) REVERT: D 287 LEU cc_start: 0.8223 (mt) cc_final: 0.8020 (mt) REVERT: D 303 MET cc_start: 0.5687 (mmp) cc_final: 0.5342 (mmt) REVERT: D 351 ASN cc_start: 0.8705 (t0) cc_final: 0.8462 (t0) REVERT: E 94 ILE cc_start: 0.8438 (mm) cc_final: 0.8161 (mm) REVERT: E 115 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8496 (tp) REVERT: E 130 LEU cc_start: 0.8411 (mt) cc_final: 0.8014 (tt) REVERT: E 133 MET cc_start: 0.6153 (mmt) cc_final: 0.5515 (mmt) REVERT: E 189 LYS cc_start: 0.6418 (mtmt) cc_final: 0.6016 (ptpt) REVERT: E 429 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7442 (ptpt) outliers start: 106 outliers final: 54 residues processed: 599 average time/residue: 0.2584 time to fit residues: 261.2169 Evaluate side-chains 529 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 470 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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 720 LEU Chi-restraints excluded: chain 2 residue 764 VAL Chi-restraints excluded: chain 2 residue 805 THR 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 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 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 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 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 338 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 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 495 GLU 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 115 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 278 TRP Chi-restraints excluded: chain E residue 414 ASP 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: 5.9990 chunk 462 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 461 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 55 optimal weight: 0.0050 chunk 442 optimal weight: 7.9990 chunk 496 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 299 optimal weight: 9.9990 chunk 515 optimal weight: 5.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 461 GLN 4 494 HIS ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 542 GLN A 769 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.142190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.112340 restraints weight = 115993.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.115873 restraints weight = 63330.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.116695 restraints weight = 39560.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.117326 restraints weight = 35503.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.117449 restraints weight = 34428.647| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 47099 Z= 0.167 Angle : 0.613 14.930 64139 Z= 0.310 Chirality : 0.042 0.209 7308 Planarity : 0.004 0.064 7758 Dihedral : 16.377 173.674 7396 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.49 % Allowed : 14.00 % Favored : 83.51 % 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: 0.75 (0.12), residues: 5310 helix: 1.59 (0.10), residues: 2533 sheet: -0.07 (0.18), residues: 829 loop : -0.65 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 436 TYR 0.020 0.002 TYR 4 249 PHE 0.044 0.002 PHE 7 77 TRP 0.020 0.002 TRP B 433 HIS 0.007 0.001 HIS C 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (47080) covalent geometry : angle 0.60514 / 0.31 (64115) hydrogen bonds : bond 0.04135 / 2.74 ( 2115) hydrogen bonds : angle 4.23498 / 2.99 ( 5999) metal coordination : bond 0.00924 / 0.60 ( 19) metal coordination : angle 4.96779 / 3.02 ( 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 620 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 500 time to evaluate : 1.406 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: 2 193 LEU cc_start: 0.8804 (tt) cc_final: 0.8554 (tp) REVERT: 4 684 MET cc_start: 0.7417 (tpp) cc_final: 0.7165 (tpp) REVERT: 5 429 MET cc_start: 0.7392 (mmt) cc_final: 0.7100 (mmt) REVERT: 6 47 LEU cc_start: 0.7319 (tp) cc_final: 0.7017 (pp) REVERT: 6 450 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8292 (mtm) REVERT: 6 527 MET cc_start: 0.7886 (mmm) cc_final: 0.7291 (ttp) REVERT: 7 18 GLN cc_start: 0.8672 (pt0) cc_final: 0.8324 (pm20) REVERT: 7 108 MET cc_start: 0.5905 (ppp) cc_final: 0.5160 (ppp) REVERT: 7 430 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6448 (mt-10) REVERT: 7 565 MET cc_start: 0.5944 (tmm) cc_final: 0.5731 (tmm) REVERT: A 756 ASP cc_start: 0.8905 (p0) cc_final: 0.8511 (t0) REVERT: B 273 ARG cc_start: 0.6158 (mpt180) cc_final: 0.5839 (mpt180) REVERT: B 333 ASP cc_start: 0.6974 (t70) cc_final: 0.6700 (t0) REVERT: C 189 MET cc_start: 0.8545 (ppp) cc_final: 0.8249 (ppp) REVERT: C 354 ARG cc_start: 0.2802 (mtt180) cc_final: 0.1340 (tpp80) REVERT: C 556 VAL cc_start: 0.7272 (t) cc_final: 0.6981 (m) REVERT: D 218 MET cc_start: 0.5155 (mpp) cc_final: 0.3898 (mtm) REVERT: D 281 MET cc_start: 0.8030 (mmm) cc_final: 0.7710 (mmm) REVERT: D 302 LEU cc_start: 0.6755 (tp) cc_final: 0.5762 (mp) REVERT: D 303 MET cc_start: 0.5954 (mmp) cc_final: 0.5531 (mmt) REVERT: D 351 ASN cc_start: 0.8834 (t0) cc_final: 0.8560 (t0) REVERT: E 94 ILE cc_start: 0.8570 (mm) cc_final: 0.8263 (mm) REVERT: E 130 LEU cc_start: 0.8351 (mt) cc_final: 0.7976 (tt) REVERT: E 189 LYS cc_start: 0.6447 (mtmt) cc_final: 0.5986 (ptpt) outliers start: 120 outliers final: 81 residues processed: 575 average time/residue: 0.2402 time to fit residues: 234.3234 Evaluate side-chains 549 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 467 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 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 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 393 LEU 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 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 7 residue 13 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 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 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 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 391 LEU Chi-restraints excluded: chain B residue 451 TYR 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 495 GLU 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 298 THR Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain D residue 379 LEU 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 414 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 167 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 335 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 512 optimal weight: 0.8980 chunk 185 optimal weight: 0.0980 chunk 444 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 chunk 489 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 549 GLN 2 606 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.143626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.114054 restraints weight = 115419.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.117373 restraints weight = 62381.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.117818 restraints weight = 39482.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.118462 restraints weight = 37467.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.118466 restraints weight = 34788.889| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 47099 Z= 0.109 Angle : 0.561 15.677 64139 Z= 0.283 Chirality : 0.040 0.221 7308 Planarity : 0.004 0.059 7758 Dihedral : 16.206 173.551 7396 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.18 % Allowed : 15.45 % Favored : 82.37 % 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: 0.90 (0.12), residues: 5310 helix: 1.72 (0.10), residues: 2545 sheet: 0.02 (0.18), residues: 823 loop : -0.59 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 7 302 TYR 0.025 0.001 TYR F 121 PHE 0.027 0.001 PHE 7 77 TRP 0.029 0.001 TRP E 278 HIS 0.006 0.001 HIS 7 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (47080) covalent geometry : angle 0.55497 / 0.28 (64115) hydrogen bonds : bond 0.03621 / 2.39 ( 2115) hydrogen bonds : angle 4.04544 / 2.85 ( 5999) metal coordination : bond 0.00666 / 0.41 ( 19) metal coordination : angle 4.25266 / 2.62 ( 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 615 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 510 time to evaluate : 1.851 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: F 122 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7577 (tm-30) REVERT: F 130 GLN cc_start: 0.7866 (tm-30) cc_final: 0.6893 (mp10) REVERT: F 146 LEU cc_start: 0.8221 (tp) cc_final: 0.7663 (pp) REVERT: 2 185 TRP cc_start: 0.8282 (t-100) cc_final: 0.8051 (t-100) REVERT: 2 193 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8528 (tp) REVERT: 3 47 LEU cc_start: 0.7919 (tp) cc_final: 0.7550 (mt) REVERT: 4 684 MET cc_start: 0.7545 (tpp) cc_final: 0.7284 (tpp) REVERT: 5 429 MET cc_start: 0.7310 (mmt) cc_final: 0.6979 (mmt) REVERT: 6 47 LEU cc_start: 0.7327 (tp) cc_final: 0.7015 (pp) REVERT: 6 450 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8029 (mtt) REVERT: 6 527 MET cc_start: 0.7823 (mmm) cc_final: 0.7223 (ttp) REVERT: 7 18 GLN cc_start: 0.8626 (pt0) cc_final: 0.8268 (pm20) REVERT: 7 108 MET cc_start: 0.6009 (ppp) cc_final: 0.5277 (ppp) REVERT: 7 430 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6448 (mt-10) REVERT: 7 565 MET cc_start: 0.6046 (tmm) cc_final: 0.5824 (tmm) REVERT: 7 616 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5773 (tp) REVERT: A 756 ASP cc_start: 0.8897 (p0) cc_final: 0.8523 (t0) REVERT: A 769 ASN cc_start: 0.7593 (t160) cc_final: 0.7271 (p0) REVERT: B 278 LYS cc_start: 0.7593 (ptpt) cc_final: 0.6891 (tmtt) REVERT: B 333 ASP cc_start: 0.7016 (t70) cc_final: 0.6702 (t0) REVERT: B 446 TYR cc_start: 0.7220 (m-80) cc_final: 0.6972 (m-80) REVERT: C 189 MET cc_start: 0.8618 (ppp) cc_final: 0.8358 (ppp) REVERT: C 354 ARG cc_start: 0.2775 (mtt180) cc_final: 0.1326 (tpp80) REVERT: C 562 CYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7614 (p) REVERT: D 218 MET cc_start: 0.5033 (mpp) cc_final: 0.3928 (mtm) REVERT: D 281 MET cc_start: 0.7980 (mmm) cc_final: 0.7702 (mmm) REVERT: D 303 MET cc_start: 0.5857 (mmp) cc_final: 0.5398 (mmt) REVERT: D 351 ASN cc_start: 0.8770 (t0) cc_final: 0.8510 (t0) REVERT: E 94 ILE cc_start: 0.8631 (mm) cc_final: 0.8329 (mm) REVERT: E 130 LEU cc_start: 0.8382 (mt) cc_final: 0.8004 (tt) REVERT: E 189 LYS cc_start: 0.6430 (mtmt) cc_final: 0.5994 (ptpt) outliers start: 105 outliers final: 69 residues processed: 573 average time/residue: 0.2450 time to fit residues: 239.0986 Evaluate side-chains 547 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 474 time to evaluate : 1.616 ------------------------------------------------------------------------------- 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 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 592 MET Chi-restraints excluded: chain 2 residue 606 GLN 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 456 TYR 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 574 LEU Chi-restraints excluded: chain 5 residue 619 ILE 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 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 618 VAL Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 8 LEU 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 616 LEU Chi-restraints excluded: chain 7 residue 621 MET 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 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 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 495 GLU Chi-restraints excluded: chain C residue 562 CYS 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 266 GLN 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: 2.9990 chunk 154 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 325 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 340 optimal weight: 2.9990 chunk 417 optimal weight: 0.8980 chunk 476 optimal weight: 8.9990 chunk 494 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 129 GLN 2 419 HIS 2 606 GLN 2 838 GLN 4 350 GLN 6 187 ASN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 265 HIS ** 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 = 0.4292 r_free = 0.4292 target = 0.142137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.112460 restraints weight = 116108.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.115643 restraints weight = 63078.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.116198 restraints weight = 40732.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.116629 restraints weight = 38190.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.116751 restraints weight = 35558.096| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3811 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= 0.149 Angle : 0.583 14.539 64139 Z= 0.295 Chirality : 0.041 0.224 7308 Planarity : 0.004 0.060 7758 Dihedral : 16.155 178.448 7396 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.57 % Allowed : 16.08 % Favored : 81.35 % 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: 0.83 (0.12), residues: 5310 helix: 1.66 (0.10), residues: 2540 sheet: -0.03 (0.18), residues: 828 loop : -0.61 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 2 812 TYR 0.028 0.001 TYR F 121 PHE 0.048 0.002 PHE 7 77 TRP 0.026 0.002 TRP B 433 HIS 0.005 0.001 HIS 7 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (47080) covalent geometry : angle 0.57796 / 0.29 (64115) hydrogen bonds : bond 0.03833 / 2.55 ( 2115) hydrogen bonds : angle 4.13173 / 2.91 ( 5999) metal coordination : bond 0.00764 / 0.48 ( 19) metal coordination : angle 3.85469 / 2.39 ( 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 605 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 481 time to evaluate : 1.551 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: F 15 LEU cc_start: 0.8324 (mt) cc_final: 0.8044 (mp) REVERT: F 146 LEU cc_start: 0.8228 (tp) cc_final: 0.7670 (pp) REVERT: 2 193 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8564 (tp) REVERT: 2 773 MET cc_start: 0.7783 (tpp) cc_final: 0.7571 (tpp) REVERT: 3 47 LEU cc_start: 0.7932 (tp) cc_final: 0.7576 (mt) REVERT: 4 684 MET cc_start: 0.7611 (tpp) cc_final: 0.7365 (tpp) REVERT: 5 429 MET cc_start: 0.7385 (mmt) cc_final: 0.7118 (mmt) REVERT: 6 47 LEU cc_start: 0.7276 (tp) cc_final: 0.6957 (pp) REVERT: 6 450 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8229 (mtm) REVERT: 6 527 MET cc_start: 0.7774 (mmm) cc_final: 0.7271 (ttp) REVERT: 7 18 GLN cc_start: 0.8655 (pt0) cc_final: 0.8287 (pm20) REVERT: 7 108 MET cc_start: 0.6008 (ppp) cc_final: 0.5287 (ppp) REVERT: 7 430 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6431 (mt-10) REVERT: 7 565 MET cc_start: 0.6097 (tmm) cc_final: 0.5872 (tmm) REVERT: 7 616 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.5885 (tp) REVERT: A 756 ASP cc_start: 0.8891 (p0) cc_final: 0.8499 (t0) REVERT: B 278 LYS cc_start: 0.7591 (ptpt) cc_final: 0.7252 (ptpp) REVERT: B 333 ASP cc_start: 0.6932 (t70) cc_final: 0.6653 (t0) REVERT: C 189 MET cc_start: 0.8593 (ppp) cc_final: 0.8365 (ppp) REVERT: C 354 ARG cc_start: 0.2585 (mtt180) cc_final: 0.1391 (tpp80) REVERT: C 562 CYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7353 (p) REVERT: D 218 MET cc_start: 0.4949 (mpp) cc_final: 0.3728 (mtm) REVERT: D 281 MET cc_start: 0.8022 (mmm) cc_final: 0.7681 (mmm) REVERT: D 303 MET cc_start: 0.5871 (mmp) cc_final: 0.5535 (mmt) REVERT: D 351 ASN cc_start: 0.8816 (t0) cc_final: 0.8549 (t0) REVERT: E 94 ILE cc_start: 0.8713 (mm) cc_final: 0.8267 (mm) REVERT: E 130 LEU cc_start: 0.8332 (mt) cc_final: 0.7959 (tt) outliers start: 124 outliers final: 94 residues processed: 556 average time/residue: 0.2272 time to fit residues: 215.5348 Evaluate side-chains 554 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 456 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 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 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 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 393 LEU Chi-restraints excluded: chain 3 residue 398 MET 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 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 458 ILE Chi-restraints excluded: chain 5 residue 574 LEU 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 8 LEU 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 385 VAL 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 303 LEU 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 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 433 TRP 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 495 GLU Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 647 VAL 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 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 236 TYR 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: 8.9990 chunk 128 optimal weight: 0.0050 chunk 22 optimal weight: 2.9990 chunk 345 optimal weight: 8.9990 chunk 386 optimal weight: 30.0000 chunk 64 optimal weight: 3.9990 chunk 417 optimal weight: 5.9990 chunk 363 optimal weight: 0.1980 chunk 402 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 473 optimal weight: 0.7980 overall best weight: 1.3998 ------------------------------------------------------------------------------- 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 A 796 GLN ** 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 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.142273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.112487 restraints weight = 115009.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.115805 restraints weight = 62593.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.117109 restraints weight = 39032.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.117193 restraints weight = 35618.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.117444 restraints weight = 33236.017| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 47099 Z= 0.131 Angle : 0.576 14.218 64139 Z= 0.291 Chirality : 0.041 0.403 7308 Planarity : 0.004 0.062 7758 Dihedral : 16.074 175.653 7396 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.76 % Allowed : 16.12 % Favored : 81.13 % 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: 0.85 (0.12), residues: 5310 helix: 1.67 (0.10), residues: 2547 sheet: -0.06 (0.18), residues: 839 loop : -0.60 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 2 812 TYR 0.020 0.001 TYR E 178 PHE 0.043 0.001 PHE 7 77 TRP 0.027 0.001 TRP B 433 HIS 0.005 0.001 HIS 7 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (47080) covalent geometry : angle 0.57238 / 0.29 (64115) hydrogen bonds : bond 0.03675 / 2.44 ( 2115) hydrogen bonds : angle 4.10020 / 2.89 ( 5999) metal coordination : bond 0.00683 / 0.43 ( 19) metal coordination : angle 3.46367 / 2.16 ( 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: 133 poor density : 480 time to evaluate : 1.349 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: F 20 MET cc_start: 0.6649 (tpp) cc_final: 0.6278 (ttm) REVERT: F 122 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7704 (tm-30) REVERT: F 130 GLN cc_start: 0.7946 (tm-30) cc_final: 0.6901 (mp10) REVERT: F 146 LEU cc_start: 0.8248 (tp) cc_final: 0.7687 (pp) REVERT: 2 193 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8562 (tp) REVERT: 2 811 MET cc_start: 0.7770 (tmm) cc_final: 0.7228 (tmm) REVERT: 3 47 LEU cc_start: 0.7955 (tp) cc_final: 0.7600 (mt) REVERT: 4 284 THR cc_start: 0.5794 (OUTLIER) cc_final: 0.5501 (p) REVERT: 4 684 MET cc_start: 0.7604 (tpp) cc_final: 0.7358 (tpp) REVERT: 5 429 MET cc_start: 0.7421 (mmt) cc_final: 0.7144 (mmt) REVERT: 6 47 LEU cc_start: 0.7262 (tp) cc_final: 0.6949 (pp) REVERT: 6 450 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8064 (mtt) REVERT: 6 527 MET cc_start: 0.7796 (mmm) cc_final: 0.7270 (ttp) REVERT: 7 18 GLN cc_start: 0.8617 (pt0) cc_final: 0.8278 (pm20) REVERT: 7 108 MET cc_start: 0.6140 (ppp) cc_final: 0.5434 (ppp) REVERT: 7 269 ASP cc_start: 0.7406 (t0) cc_final: 0.7063 (t0) REVERT: 7 430 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6255 (mt-10) REVERT: 7 565 MET cc_start: 0.6384 (tmm) cc_final: 0.6173 (tmm) REVERT: 7 616 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.5903 (tp) REVERT: A 756 ASP cc_start: 0.8832 (p0) cc_final: 0.8403 (t0) REVERT: B 278 LYS cc_start: 0.7568 (ptpt) cc_final: 0.7233 (ptpp) REVERT: B 333 ASP cc_start: 0.6882 (t70) cc_final: 0.6610 (t0) REVERT: B 393 HIS cc_start: 0.7850 (OUTLIER) cc_final: 0.7131 (m90) REVERT: C 189 MET cc_start: 0.8562 (ppp) cc_final: 0.8350 (ppp) REVERT: C 354 ARG cc_start: 0.2697 (mtt180) cc_final: 0.1596 (tpp80) REVERT: C 358 LEU cc_start: 0.8059 (tp) cc_final: 0.7768 (tp) REVERT: C 562 CYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7330 (p) REVERT: D 218 MET cc_start: 0.4734 (mpp) cc_final: 0.3674 (mtm) REVERT: D 281 MET cc_start: 0.8056 (mmm) cc_final: 0.7703 (mmm) REVERT: D 303 MET cc_start: 0.5904 (mmp) cc_final: 0.5566 (mmt) REVERT: D 351 ASN cc_start: 0.8830 (t0) cc_final: 0.8569 (t0) REVERT: E 94 ILE cc_start: 0.8681 (mm) cc_final: 0.8206 (mm) REVERT: E 130 LEU cc_start: 0.8278 (mt) cc_final: 0.7948 (tt) outliers start: 133 outliers final: 98 residues processed: 563 average time/residue: 0.2155 time to fit residues: 209.1106 Evaluate side-chains 568 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 464 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 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 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 805 THR Chi-restraints excluded: chain 2 residue 834 PHE Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 268 MET Chi-restraints excluded: chain 3 residue 379 THR 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 239 MET Chi-restraints excluded: chain 4 residue 284 THR Chi-restraints excluded: chain 4 residue 286 SER 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 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 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 8 LEU 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 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 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 303 LEU 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 342 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 433 TRP 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 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 495 GLU 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 264 GLU Chi-restraints excluded: chain D residue 265 VAL 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 123 VAL 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: 4.9990 chunk 87 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 199 optimal weight: 0.0980 chunk 452 optimal weight: 0.8980 chunk 395 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 413 optimal weight: 0.9990 chunk 431 optimal weight: 7.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 838 GLN 3 553 HIS ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 644 HIS 7 479 ASN B 340 ASN ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN E 188 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.143043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.113136 restraints weight = 115597.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.116203 restraints weight = 64095.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.117778 restraints weight = 41228.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.118134 restraints weight = 34791.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.118371 restraints weight = 33304.519| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 47099 Z= 0.104 Angle : 0.562 13.882 64139 Z= 0.280 Chirality : 0.040 0.222 7308 Planarity : 0.004 0.061 7758 Dihedral : 15.967 177.922 7396 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.97 % Allowed : 17.17 % Favored : 80.86 % 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: 0.96 (0.12), residues: 5310 helix: 1.75 (0.10), residues: 2550 sheet: 0.03 (0.18), residues: 840 loop : -0.54 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 2 812 TYR 0.026 0.001 TYR F 121 PHE 0.038 0.001 PHE 7 77 TRP 0.030 0.002 TRP C 649 HIS 0.005 0.001 HIS 6 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (47080) covalent geometry : angle 0.55890 / 0.28 (64115) hydrogen bonds : bond 0.03412 / 2.26 ( 2115) hydrogen bonds : angle 3.98270 / 2.80 ( 5999) metal coordination : bond 0.00546 / 0.32 ( 19) metal coordination : angle 3.01380 / 1.88 ( 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 597 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 502 time to evaluate : 1.568 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: F 122 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7576 (tm-30) REVERT: F 130 GLN cc_start: 0.7958 (tm-30) cc_final: 0.6915 (mp10) REVERT: F 146 LEU cc_start: 0.8236 (tp) cc_final: 0.7680 (pp) REVERT: 2 185 TRP cc_start: 0.8221 (t-100) cc_final: 0.7891 (t-100) REVERT: 2 193 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8552 (tp) REVERT: 2 773 MET cc_start: 0.7762 (tpp) cc_final: 0.7518 (tpp) REVERT: 3 47 LEU cc_start: 0.7945 (tp) cc_final: 0.7597 (mt) REVERT: 4 284 THR cc_start: 0.5558 (OUTLIER) cc_final: 0.5282 (p) REVERT: 4 684 MET cc_start: 0.7573 (tpp) cc_final: 0.7261 (tpp) REVERT: 5 429 MET cc_start: 0.7447 (mmt) cc_final: 0.7170 (mmt) REVERT: 6 47 LEU cc_start: 0.7292 (tp) cc_final: 0.6962 (pp) REVERT: 6 450 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8050 (mtt) REVERT: 6 527 MET cc_start: 0.7729 (mmm) cc_final: 0.7210 (ttp) REVERT: 7 18 GLN cc_start: 0.8620 (pt0) cc_final: 0.8264 (pm20) REVERT: 7 108 MET cc_start: 0.6243 (ppp) cc_final: 0.5585 (ppp) REVERT: 7 269 ASP cc_start: 0.7380 (t0) cc_final: 0.7034 (t0) REVERT: 7 430 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6246 (mt-10) REVERT: 7 565 MET cc_start: 0.6448 (tmm) cc_final: 0.6244 (tmm) REVERT: 7 616 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5782 (tp) REVERT: A 756 ASP cc_start: 0.8845 (p0) cc_final: 0.8428 (t0) REVERT: B 278 LYS cc_start: 0.7580 (ptpt) cc_final: 0.7250 (ptpp) REVERT: B 330 MET cc_start: 0.7175 (mmm) cc_final: 0.6814 (mmp) REVERT: B 333 ASP cc_start: 0.6889 (t70) cc_final: 0.6653 (t0) REVERT: B 383 ASP cc_start: 0.8236 (m-30) cc_final: 0.7793 (t70) REVERT: B 446 TYR cc_start: 0.7117 (m-80) cc_final: 0.6760 (m-80) REVERT: C 318 ASP cc_start: 0.7204 (p0) cc_final: 0.6998 (p0) REVERT: C 354 ARG cc_start: 0.2631 (mtt180) cc_final: 0.1198 (tpp80) REVERT: C 358 LEU cc_start: 0.8027 (tp) cc_final: 0.7715 (tp) REVERT: C 562 CYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7319 (p) REVERT: D 218 MET cc_start: 0.4775 (mpp) cc_final: 0.3775 (mtm) REVERT: D 281 MET cc_start: 0.8117 (mmm) cc_final: 0.7767 (mmm) REVERT: D 303 MET cc_start: 0.5794 (mmp) cc_final: 0.5456 (mmt) REVERT: D 351 ASN cc_start: 0.8814 (t0) cc_final: 0.8548 (t0) REVERT: E 94 ILE cc_start: 0.8702 (mm) cc_final: 0.8203 (mm) REVERT: E 130 LEU cc_start: 0.8271 (mt) cc_final: 0.7964 (tt) REVERT: E 141 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6612 (t80) outliers start: 95 outliers final: 75 residues processed: 558 average time/residue: 0.2166 time to fit residues: 206.8986 Evaluate side-chains 547 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 466 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 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 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 795 ILE 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 260 LEU Chi-restraints excluded: chain 3 residue 379 THR 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 284 THR Chi-restraints excluded: chain 4 residue 300 GLN 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 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 618 VAL Chi-restraints excluded: chain 6 residue 782 HIS Chi-restraints excluded: chain 7 residue 8 LEU Chi-restraints excluded: chain 7 residue 16 PHE Chi-restraints excluded: chain 7 residue 21 TYR Chi-restraints excluded: chain 7 residue 223 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 479 ASN 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 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 303 LEU 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 433 TRP Chi-restraints excluded: chain C residue 114 HIS 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 447 ILE Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 141 PHE 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: 3.9990 chunk 514 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 524 optimal weight: 2.9990 chunk 479 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 312 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 533 optimal weight: 8.9990 chunk 468 optimal weight: 0.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 421 ASN 2 838 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 597 GLN 7 479 ASN B 340 ASN C 31 ASN ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 HIS D 267 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 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 = 0.4272 r_free = 0.4272 target = 0.140870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.110933 restraints weight = 115234.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.113793 restraints weight = 60665.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.115040 restraints weight = 39113.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.115303 restraints weight = 35125.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.115453 restraints weight = 32627.906| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 47099 Z= 0.153 Angle : 0.608 13.130 64139 Z= 0.306 Chirality : 0.041 0.203 7308 Planarity : 0.004 0.062 7758 Dihedral : 15.962 174.986 7396 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.38 % Allowed : 17.13 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.12), residues: 5310 helix: 1.62 (0.10), residues: 2546 sheet: -0.09 (0.18), residues: 832 loop : -0.61 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG 3 364 TYR 0.022 0.002 TYR F 121 PHE 0.035 0.002 PHE 7 77 TRP 0.030 0.002 TRP C 187 HIS 0.008 0.001 HIS C 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (47080) covalent geometry : angle 0.60507 / 0.31 (64115) hydrogen bonds : bond 0.03769 / 2.50 ( 2115) hydrogen bonds : angle 4.12699 / 2.90 ( 5999) metal coordination : bond 0.00674 / 0.42 ( 19) metal coordination : angle 2.97458 / 1.87 ( 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 585 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 470 time to evaluate : 1.289 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: F 68 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6757 (tt) REVERT: F 122 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7692 (tm-30) REVERT: F 130 GLN cc_start: 0.7966 (tm-30) cc_final: 0.6827 (mp10) REVERT: F 146 LEU cc_start: 0.8230 (tp) cc_final: 0.7672 (pp) REVERT: 2 193 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8548 (tp) REVERT: 2 534 LYS cc_start: 0.6699 (OUTLIER) cc_final: 0.6177 (mtmm) REVERT: 4 284 THR cc_start: 0.5958 (OUTLIER) cc_final: 0.5646 (p) REVERT: 4 684 MET cc_start: 0.7696 (tpp) cc_final: 0.7403 (tpp) REVERT: 5 145 MET cc_start: 0.8047 (mmm) cc_final: 0.7826 (tpt) REVERT: 6 47 LEU cc_start: 0.7326 (tp) cc_final: 0.6997 (pp) REVERT: 6 450 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8226 (mtm) REVERT: 6 527 MET cc_start: 0.7852 (mmm) cc_final: 0.7321 (ttp) REVERT: 7 18 GLN cc_start: 0.8615 (pt0) cc_final: 0.8223 (pm20) REVERT: 7 108 MET cc_start: 0.6320 (ppp) cc_final: 0.5642 (ppp) REVERT: 7 269 ASP cc_start: 0.7488 (t0) cc_final: 0.7132 (t0) REVERT: 7 430 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6359 (mt-10) REVERT: 7 565 MET cc_start: 0.6610 (tmm) cc_final: 0.6381 (tmm) REVERT: A 756 ASP cc_start: 0.8844 (p0) cc_final: 0.8304 (t0) REVERT: B 278 LYS cc_start: 0.7620 (ptpt) cc_final: 0.7279 (ptpp) REVERT: B 333 ASP cc_start: 0.6865 (t70) cc_final: 0.6644 (t0) REVERT: B 383 ASP cc_start: 0.8405 (m-30) cc_final: 0.7880 (t70) REVERT: C 354 ARG cc_start: 0.2548 (mtt180) cc_final: 0.1639 (tpp80) REVERT: C 358 LEU cc_start: 0.8109 (tp) cc_final: 0.7799 (tp) REVERT: C 562 CYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7381 (p) REVERT: D 218 MET cc_start: 0.5030 (mpp) cc_final: 0.3873 (mtm) REVERT: D 281 MET cc_start: 0.8177 (mmm) cc_final: 0.7862 (mmm) REVERT: D 303 MET cc_start: 0.5875 (mmp) cc_final: 0.5616 (mmt) REVERT: D 351 ASN cc_start: 0.8846 (t0) cc_final: 0.8596 (t0) REVERT: E 94 ILE cc_start: 0.8777 (mm) cc_final: 0.8293 (mm) REVERT: E 130 LEU cc_start: 0.8250 (mt) cc_final: 0.7944 (tt) REVERT: E 141 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6784 (t80) REVERT: E 188 GLN cc_start: 0.5621 (tp40) cc_final: 0.5417 (tp-100) outliers start: 115 outliers final: 85 residues processed: 543 average time/residue: 0.1973 time to fit residues: 185.1677 Evaluate side-chains 545 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 453 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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 795 ILE 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 260 LEU 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 3 residue 494 ASP Chi-restraints excluded: chain 4 residue 157 VAL 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 448 ASP Chi-restraints excluded: chain 5 residue 574 LEU Chi-restraints excluded: chain 5 residue 637 VAL 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 247 THR 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 8 LEU 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 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 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 391 LEU Chi-restraints excluded: chain C residue 114 HIS 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 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 495 GLU 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 264 GLU Chi-restraints excluded: chain D residue 265 VAL 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 256 ASN Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 107 optimal weight: 5.9990 chunk 492 optimal weight: 3.9990 chunk 331 optimal weight: 0.8980 chunk 469 optimal weight: 2.9990 chunk 526 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 521 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 410 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 479 ASN ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 ASN D 362 HIS D 381 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 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 = 0.4267 r_free = 0.4267 target = 0.140455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.109760 restraints weight = 115928.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.114228 restraints weight = 63462.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.114860 restraints weight = 37733.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.115303 restraints weight = 31756.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.115508 restraints weight = 30600.411| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 47099 Z= 0.154 Angle : 0.623 17.606 64139 Z= 0.312 Chirality : 0.042 0.204 7308 Planarity : 0.004 0.063 7758 Dihedral : 15.977 176.550 7396 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.26 % Allowed : 17.34 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.67 (0.12), residues: 5310 helix: 1.53 (0.10), residues: 2552 sheet: -0.20 (0.18), residues: 831 loop : -0.65 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 7 514 TYR 0.034 0.002 TYR F 121 PHE 0.034 0.002 PHE 7 77 TRP 0.040 0.002 TRP 6 751 HIS 0.018 0.001 HIS D 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (47080) covalent geometry : angle 0.62035 / 0.31 (64115) hydrogen bonds : bond 0.03829 / 2.55 ( 2115) hydrogen bonds : angle 4.18596 / 2.95 ( 5999) metal coordination : bond 0.00679 / 0.42 ( 19) metal coordination : angle 2.99079 / 1.86 ( 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 580 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 471 time to evaluate : 1.711 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: F 68 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6789 (tt) REVERT: F 122 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7648 (tm-30) REVERT: F 130 GLN cc_start: 0.8001 (tm-30) cc_final: 0.6780 (mp10) REVERT: 2 193 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8563 (tp) REVERT: 2 773 MET cc_start: 0.7738 (tpp) cc_final: 0.7505 (tpp) REVERT: 3 603 MET cc_start: 0.7057 (pmm) cc_final: 0.6842 (pmm) REVERT: 4 284 THR cc_start: 0.5925 (OUTLIER) cc_final: 0.5658 (p) REVERT: 4 684 MET cc_start: 0.7678 (tpp) cc_final: 0.7395 (tpp) REVERT: 5 145 MET cc_start: 0.8056 (mmm) cc_final: 0.7830 (tpt) REVERT: 6 450 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8229 (mtm) REVERT: 6 527 MET cc_start: 0.7847 (mmm) cc_final: 0.7283 (ttp) REVERT: 7 18 GLN cc_start: 0.8621 (pt0) cc_final: 0.8211 (pm20) REVERT: 7 108 MET cc_start: 0.6298 (ppp) cc_final: 0.5631 (ppp) REVERT: 7 269 ASP cc_start: 0.7431 (t0) cc_final: 0.7079 (t0) REVERT: 7 430 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6331 (mt-10) REVERT: 7 565 MET cc_start: 0.6634 (tmm) cc_final: 0.6411 (tmm) REVERT: A 756 ASP cc_start: 0.8915 (p0) cc_final: 0.8399 (t0) REVERT: B 278 LYS cc_start: 0.7608 (ptpt) cc_final: 0.7267 (ptpp) REVERT: B 333 ASP cc_start: 0.6807 (t70) cc_final: 0.6597 (t0) REVERT: B 383 ASP cc_start: 0.8447 (m-30) cc_final: 0.7862 (t70) REVERT: C 354 ARG cc_start: 0.2542 (mtt180) cc_final: 0.1679 (tpp80) REVERT: C 358 LEU cc_start: 0.8075 (tp) cc_final: 0.7701 (tp) REVERT: C 562 CYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7376 (p) REVERT: D 218 MET cc_start: 0.4920 (mpp) cc_final: 0.3830 (mtp) REVERT: D 281 MET cc_start: 0.8249 (mmm) cc_final: 0.7851 (mmm) REVERT: D 303 MET cc_start: 0.5966 (mmp) cc_final: 0.5715 (mmt) REVERT: D 351 ASN cc_start: 0.8842 (t0) cc_final: 0.8599 (t0) REVERT: E 94 ILE cc_start: 0.8806 (mm) cc_final: 0.8339 (mm) REVERT: E 130 LEU cc_start: 0.8237 (mt) cc_final: 0.7946 (tt) REVERT: E 141 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6702 (t80) REVERT: E 188 GLN cc_start: 0.5475 (tp40) cc_final: 0.5257 (tp-100) outliers start: 109 outliers final: 97 residues processed: 537 average time/residue: 0.2043 time to fit residues: 188.1311 Evaluate side-chains 557 residues out of total 4830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 454 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 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 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 795 ILE 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 260 LEU 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 3 residue 494 ASP Chi-restraints excluded: chain 3 residue 552 LEU Chi-restraints excluded: chain 4 residue 157 VAL 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 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 247 THR 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 443 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 8 LEU 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 531 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 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 391 LEU Chi-restraints excluded: chain C residue 114 HIS 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 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 365 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 141 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 340 optimal weight: 0.9980 chunk 398 optimal weight: 0.0770 chunk 209 optimal weight: 10.0000 chunk 504 optimal weight: 0.1980 chunk 488 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 442 optimal weight: 0.7980 chunk 240 optimal weight: 0.6980 chunk 215 optimal weight: 8.9990 chunk 437 optimal weight: 0.9990 chunk 313 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 252 ASN D 267 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 ASN ** 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 = 0.4294 r_free = 0.4294 target = 0.142548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.111950 restraints weight = 114007.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.116105 restraints weight = 59904.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.117417 restraints weight = 37212.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.118401 restraints weight = 29717.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.118637 restraints weight = 27183.466| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 47099 Z= 0.108 Angle : 0.593 14.824 64139 Z= 0.294 Chirality : 0.040 0.205 7308 Planarity : 0.004 0.078 7758 Dihedral : 15.893 179.798 7396 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.95 % Allowed : 17.78 % Favored : 80.28 % 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: 0.83 (0.12), residues: 5310 helix: 1.62 (0.10), residues: 2554 sheet: -0.06 (0.18), residues: 835 loop : -0.56 (0.15), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 2 812 TYR 0.032 0.001 TYR F 121 PHE 0.037 0.001 PHE C 476 TRP 0.034 0.002 TRP B 433 HIS 0.005 0.001 HIS 7 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (47080) covalent geometry : angle 0.59130 / 0.29 (64115) hydrogen bonds : bond 0.03406 / 2.26 ( 2115) hydrogen bonds : angle 4.03001 / 2.84 ( 5999) metal coordination : bond 0.00445 / 0.26 ( 19) metal coordination : angle 2.67745 / 1.69 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8442.97 seconds wall clock time: 145 minutes 58.65 seconds (8758.65 seconds total)