Starting phenix.real_space_refine on Tue Aug 26 22:41:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jav_36135/08_2025/8jav_36135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jav_36135/08_2025/8jav_36135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jav_36135/08_2025/8jav_36135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jav_36135/08_2025/8jav_36135.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jav_36135/08_2025/8jav_36135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jav_36135/08_2025/8jav_36135.map" } resolution = 3.44 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4765 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 233 5.16 5 C 25104 2.51 5 N 6700 2.21 5 O 7294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39339 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4622 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 6, 'TRANS': 565} Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1616 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain breaks: 1 Chain: "D" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "S" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "B" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4622 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 6, 'TRANS': 565} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "G" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 782 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 8, 'TRANS': 90} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "I" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5223 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 618} Chain breaks: 1 Chain: "R" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 679 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "J" Number of atoms: 4619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4619 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 565} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4613 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 6, 'TRANS': 564} Chain: "L" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1176 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain breaks: 1 Chain: "M" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain breaks: 1 Chain: "N" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain breaks: 1 Chain: "O" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "P" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "Q" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "T" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "V" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 661 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "U" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5223 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 618} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 410 SG CYS A 54 75.142 79.609 73.080 1.00 13.28 S ATOM 8228 SG CYS B 54 72.572 80.650 75.819 1.00 38.57 S ATOM 19495 SG CYS R 53 74.538 169.467 77.321 1.00 35.88 S ATOM 19518 SG CYS R 56 70.810 169.137 76.798 1.00 43.45 S ATOM 19602 SG CYS R 68 72.305 172.618 77.625 1.00 40.26 S ATOM 19409 SG CYS R 42 80.273 173.928 78.923 1.00 27.18 S ATOM 19428 SG CYS R 45 79.913 172.156 75.589 1.00 26.75 S ATOM 19723 SG CYS R 83 78.747 170.396 78.619 1.00 30.52 S ATOM 19652 SG CYS R 75 85.708 179.158 88.756 1.00 34.56 S ATOM 19819 SG CYS R 94 86.390 176.422 86.827 1.00 29.34 S ATOM 20348 SG CYS J 54 118.511 174.539 73.208 1.00 9.91 S ATOM 24967 SG CYS K 54 120.896 173.669 76.158 1.00 27.85 S ATOM 33665 SG CYS V 53 118.838 85.099 77.222 1.00 72.16 S ATOM 33688 SG CYS V 56 122.622 85.395 77.306 1.00 78.92 S ATOM 33772 SG CYS V 68 120.900 82.040 78.138 1.00 75.92 S ATOM 33579 SG CYS V 42 113.048 80.247 78.776 1.00 57.29 S ATOM 33598 SG CYS V 45 113.662 82.153 75.612 1.00 55.65 S ATOM 33893 SG CYS V 83 114.806 83.688 78.783 1.00 64.49 S ATOM 33822 SG CYS V 75 107.850 75.227 89.091 1.00 74.26 S ATOM 33989 SG CYS V 94 107.189 77.627 86.983 1.00 63.75 S Time building chain proxies: 7.24, per 1000 atoms: 0.18 Number of scatterers: 39339 At special positions: 0 Unit cell: (194.34, 251.74, 141.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 233 16.00 O 7294 8.00 N 6700 7.00 C 25104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS B 89 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 89 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 54 " pdb="ZN ZN A 601 " - pdb=" SG CYS B 54 " pdb=" ZN J 601 " pdb="ZN ZN J 601 " - pdb=" NE2 HIS K 89 " pdb="ZN ZN J 601 " - pdb=" NE2 HIS J 89 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 54 " pdb="ZN ZN J 601 " - pdb=" SG CYS K 54 " pdb=" ZN R 200 " pdb="ZN ZN R 200 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 56 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb=" ZN V 200 " pdb="ZN ZN V 200 " - pdb=" ND1 HIS V 82 " pdb="ZN ZN V 200 " - pdb=" SG CYS V 53 " pdb="ZN ZN V 200 " - pdb=" SG CYS V 68 " pdb="ZN ZN V 200 " - pdb=" SG CYS V 56 " pdb=" ZN V 201 " pdb="ZN ZN V 201 " - pdb=" ND1 HIS V 80 " pdb="ZN ZN V 201 " - pdb=" SG CYS V 45 " pdb="ZN ZN V 201 " - pdb=" SG CYS V 83 " pdb="ZN ZN V 201 " - pdb=" SG CYS V 42 " pdb=" ZN V 202 " pdb="ZN ZN V 202 " - pdb=" SG CYS V 75 " pdb="ZN ZN V 202 " - pdb=" SG CYS V 94 " pdb="ZN ZN V 202 " - pdb=" ND1 HIS V 77 " Number of angles added : 16 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9274 Finding SS restraints... Secondary structure from input PDB file: 227 helices and 21 sheets defined 70.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 28 through 33 removed outlier: 4.074A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 50 removed outlier: 3.763A pdb=" N TYR A 48 " --> pdb=" O TYR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 112 through 133 removed outlier: 3.620A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 removed outlier: 4.473A pdb=" N LYS A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 removed outlier: 3.658A pdb=" N HIS A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 199 removed outlier: 3.629A pdb=" N GLU A 184 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 221 through 236 Processing helix chain 'A' and resid 241 through 257 Processing helix chain 'A' and resid 261 through 280 removed outlier: 3.664A pdb=" N GLN A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 300 removed outlier: 3.668A pdb=" N PHE A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 322 removed outlier: 3.816A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 344 removed outlier: 3.554A pdb=" N ALA A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 368 removed outlier: 3.946A pdb=" N ALA A 360 " --> pdb=" O HIS A 356 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.508A pdb=" N ALA A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 421 Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 444 through 464 removed outlier: 3.703A pdb=" N GLU A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 485 removed outlier: 3.621A pdb=" N SER A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 506 Processing helix chain 'A' and resid 510 through 528 removed outlier: 4.108A pdb=" N GLU A 514 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 551 removed outlier: 3.922A pdb=" N VAL A 533 " --> pdb=" O ASN A 529 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 566 through 578 Processing helix chain 'E' and resid 9 through 26 removed outlier: 3.968A pdb=" N THR E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 removed outlier: 3.677A pdb=" N TYR E 43 " --> pdb=" O PHE E 39 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 78 Processing helix chain 'E' and resid 82 through 105 removed outlier: 3.809A pdb=" N MET E 86 " --> pdb=" O GLN E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.991A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 173 removed outlier: 3.562A pdb=" N LYS E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 186 removed outlier: 3.758A pdb=" N VAL E 184 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 191 Processing helix chain 'E' and resid 200 through 207 Processing helix chain 'C' and resid 24 through 36 removed outlier: 3.639A pdb=" N ILE C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 39 through 46 removed outlier: 3.611A pdb=" N LYS D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 83 Processing helix chain 'D' and resid 99 through 111 Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.717A pdb=" N SER B 19 " --> pdb=" O ASN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 33 removed outlier: 5.810A pdb=" N ARG B 30 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASP B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 removed outlier: 4.018A pdb=" N ASP B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 62 through 71 Processing helix chain 'B' and resid 76 through 90 Processing helix chain 'B' and resid 92 through 109 Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 136 through 151 removed outlier: 4.404A pdb=" N LYS B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 175 removed outlier: 3.563A pdb=" N LEU B 170 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 198 removed outlier: 3.666A pdb=" N GLU B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 221 through 236 Processing helix chain 'B' and resid 241 through 259 removed outlier: 3.671A pdb=" N VAL B 258 " --> pdb=" O LYS B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 280 removed outlier: 3.692A pdb=" N GLN B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 300 Processing helix chain 'B' and resid 303 through 322 removed outlier: 3.842A pdb=" N ALA B 309 " --> pdb=" O CYS B 305 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 344 Processing helix chain 'B' and resid 352 through 368 removed outlier: 3.605A pdb=" N ILE B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 393 Processing helix chain 'B' and resid 396 through 422 Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 444 through 464 Processing helix chain 'B' and resid 467 through 484 Processing helix chain 'B' and resid 487 through 506 removed outlier: 3.638A pdb=" N LYS B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 510 removed outlier: 3.996A pdb=" N TYR B 510 " --> pdb=" O GLY B 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 511 through 528 removed outlier: 4.208A pdb=" N TYR B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 550 Processing helix chain 'B' and resid 569 through 577 Processing helix chain 'G' and resid 23 through 36 Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'H' and resid 32 through 37 Processing helix chain 'H' and resid 39 through 47 Processing helix chain 'H' and resid 66 through 83 removed outlier: 4.108A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 removed outlier: 3.518A pdb=" N ASN H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 25 removed outlier: 3.602A pdb=" N THR I 19 " --> pdb=" O ASN I 15 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR I 20 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL I 25 " --> pdb=" O ILE I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 47 removed outlier: 3.594A pdb=" N PHE I 39 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 78 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.603A pdb=" N GLU I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 112 Processing helix chain 'I' and resid 138 through 151 removed outlier: 4.317A pdb=" N LEU I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 172 removed outlier: 3.724A pdb=" N ARG I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 187 removed outlier: 3.960A pdb=" N ILE I 181 " --> pdb=" O ASN I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 196 removed outlier: 4.865A pdb=" N VAL I 191 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN I 193 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N TYR I 194 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS I 195 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS I 196 " --> pdb=" O GLN I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 200 No H-bonds generated for 'chain 'I' and resid 198 through 200' Processing helix chain 'I' and resid 201 through 207 Processing helix chain 'I' and resid 207 through 228 removed outlier: 3.581A pdb=" N SER I 224 " --> pdb=" O LYS I 220 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN I 228 " --> pdb=" O SER I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 231 through 254 removed outlier: 3.812A pdb=" N MET I 236 " --> pdb=" O CYS I 232 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP I 245 " --> pdb=" O GLY I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 257 No H-bonds generated for 'chain 'I' and resid 255 through 257' Processing helix chain 'I' and resid 258 through 271 removed outlier: 3.879A pdb=" N HIS I 264 " --> pdb=" O THR I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 287 removed outlier: 3.508A pdb=" N GLU I 281 " --> pdb=" O PHE I 277 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N HIS I 283 " --> pdb=" O HIS I 279 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 304 removed outlier: 4.549A pdb=" N ASN I 296 " --> pdb=" O ASN I 292 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU I 300 " --> pdb=" O ASN I 296 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU I 301 " --> pdb=" O MET I 297 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA I 303 " --> pdb=" O VAL I 299 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL I 304 " --> pdb=" O LEU I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 327 removed outlier: 3.906A pdb=" N MET I 311 " --> pdb=" O GLY I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 357 removed outlier: 4.026A pdb=" N GLN I 352 " --> pdb=" O GLY I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 377 Processing helix chain 'I' and resid 386 through 400 removed outlier: 3.575A pdb=" N LYS I 400 " --> pdb=" O ASP I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 407 through 424 removed outlier: 3.720A pdb=" N VAL I 411 " --> pdb=" O THR I 407 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR I 420 " --> pdb=" O THR I 416 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL I 421 " --> pdb=" O SER I 417 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR I 424 " --> pdb=" O THR I 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 427 through 445 removed outlier: 3.740A pdb=" N PHE I 431 " --> pdb=" O ASP I 427 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS I 441 " --> pdb=" O ARG I 437 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS I 445 " --> pdb=" O LYS I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 465 removed outlier: 3.503A pdb=" N GLN I 463 " --> pdb=" O ASN I 459 " (cutoff:3.500A) Processing helix chain 'I' and resid 471 through 477 Processing helix chain 'I' and resid 479 through 496 removed outlier: 3.638A pdb=" N ALA I 484 " --> pdb=" O MET I 480 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP I 485 " --> pdb=" O SER I 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 533 through 548 removed outlier: 3.698A pdb=" N MET I 539 " --> pdb=" O LYS I 535 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE I 540 " --> pdb=" O SER I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 556 through 560 Processing helix chain 'I' and resid 578 through 591 removed outlier: 4.375A pdb=" N VAL I 584 " --> pdb=" O TYR I 580 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU I 585 " --> pdb=" O GLN I 581 " (cutoff:3.500A) Processing helix chain 'I' and resid 596 through 604 removed outlier: 3.506A pdb=" N ASP I 601 " --> pdb=" O LYS I 597 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER I 602 " --> pdb=" O GLU I 598 " (cutoff:3.500A) Processing helix chain 'I' and resid 606 through 621 removed outlier: 4.038A pdb=" N LEU I 610 " --> pdb=" O ASN I 606 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR I 611 " --> pdb=" O GLU I 607 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS I 612 " --> pdb=" O LYS I 608 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS I 615 " --> pdb=" O THR I 611 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU I 617 " --> pdb=" O THR I 613 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL I 620 " --> pdb=" O SER I 616 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 60 removed outlier: 3.753A pdb=" N ASN R 59 " --> pdb=" O GLU R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 68 Processing helix chain 'R' and resid 81 through 91 removed outlier: 3.575A pdb=" N THR R 90 " --> pdb=" O ARG R 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 24 removed outlier: 3.847A pdb=" N SER J 19 " --> pdb=" O ASN J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 29 Processing helix chain 'J' and resid 31 through 35 Processing helix chain 'J' and resid 36 through 50 removed outlier: 3.615A pdb=" N ASP J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR J 48 " --> pdb=" O TYR J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 61 removed outlier: 3.597A pdb=" N SER J 58 " --> pdb=" O CYS J 54 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU J 59 " --> pdb=" O GLN J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 71 removed outlier: 4.528A pdb=" N LYS J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 74 No H-bonds generated for 'chain 'J' and resid 72 through 74' Processing helix chain 'J' and resid 75 through 88 removed outlier: 3.775A pdb=" N HIS J 81 " --> pdb=" O HIS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 109 Processing helix chain 'J' and resid 112 through 133 removed outlier: 3.816A pdb=" N LYS J 118 " --> pdb=" O ALA J 114 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA J 119 " --> pdb=" O VAL J 115 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP J 132 " --> pdb=" O GLY J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 151 removed outlier: 4.831A pdb=" N LYS J 141 " --> pdb=" O SER J 137 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL J 142 " --> pdb=" O ASP J 138 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 175 removed outlier: 3.944A pdb=" N PHE J 160 " --> pdb=" O MET J 156 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG J 161 " --> pdb=" O LEU J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 198 removed outlier: 3.717A pdb=" N GLU J 184 " --> pdb=" O HIS J 180 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP J 194 " --> pdb=" O GLN J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 219 Processing helix chain 'J' and resid 221 through 235 removed outlier: 3.942A pdb=" N ILE J 230 " --> pdb=" O TYR J 226 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU J 231 " --> pdb=" O LYS J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 259 Processing helix chain 'J' and resid 261 through 280 removed outlier: 3.650A pdb=" N GLN J 267 " --> pdb=" O LYS J 263 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU J 268 " --> pdb=" O LYS J 264 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR J 274 " --> pdb=" O LYS J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 300 removed outlier: 3.708A pdb=" N PHE J 296 " --> pdb=" O LEU J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 322 removed outlier: 4.720A pdb=" N ALA J 309 " --> pdb=" O CYS J 305 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE J 310 " --> pdb=" O GLN J 306 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA J 313 " --> pdb=" O ALA J 309 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE J 317 " --> pdb=" O ALA J 313 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER J 320 " --> pdb=" O ASP J 316 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 344 removed outlier: 3.541A pdb=" N TYR J 338 " --> pdb=" O GLU J 334 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 368 removed outlier: 3.857A pdb=" N ALA J 360 " --> pdb=" O HIS J 356 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS J 366 " --> pdb=" O GLY J 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 393 removed outlier: 3.647A pdb=" N ALA J 376 " --> pdb=" O HIS J 372 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER J 378 " --> pdb=" O LEU J 374 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL J 381 " --> pdb=" O SER J 377 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU J 388 " --> pdb=" O LEU J 384 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA J 390 " --> pdb=" O LEU J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 421 removed outlier: 3.506A pdb=" N ARG J 401 " --> pdb=" O GLU J 397 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA J 420 " --> pdb=" O LEU J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 440 removed outlier: 3.599A pdb=" N HIS J 431 " --> pdb=" O GLN J 427 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR J 432 " --> pdb=" O THR J 428 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 463 removed outlier: 3.530A pdb=" N GLU J 449 " --> pdb=" O PHE J 445 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU J 450 " --> pdb=" O LYS J 446 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE J 458 " --> pdb=" O LYS J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 467 through 484 removed outlier: 3.601A pdb=" N ALA J 471 " --> pdb=" O ASP J 467 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER J 473 " --> pdb=" O GLU J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 488 through 506 removed outlier: 4.142A pdb=" N LYS J 493 " --> pdb=" O GLU J 489 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU J 494 " --> pdb=" O ASN J 490 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU J 496 " --> pdb=" O GLU J 492 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG J 497 " --> pdb=" O LYS J 493 " (cutoff:3.500A) Processing helix chain 'J' and resid 510 through 512 No H-bonds generated for 'chain 'J' and resid 510 through 512' Processing helix chain 'J' and resid 513 through 522 removed outlier: 3.805A pdb=" N GLY J 519 " --> pdb=" O TYR J 515 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS J 522 " --> pdb=" O ARG J 518 " (cutoff:3.500A) Processing helix chain 'J' and resid 530 through 551 removed outlier: 4.435A pdb=" N ARG J 549 " --> pdb=" O ARG J 545 " (cutoff:3.500A) Processing helix chain 'J' and resid 555 through 560 Processing helix chain 'J' and resid 566 through 578 Processing helix chain 'K' and resid 12 through 23 removed outlier: 3.702A pdb=" N SER K 19 " --> pdb=" O ASN K 15 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP K 23 " --> pdb=" O SER K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 33 removed outlier: 5.374A pdb=" N ARG K 30 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASP K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG K 33 " --> pdb=" O ARG K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 50 removed outlier: 3.562A pdb=" N ASP K 42 " --> pdb=" O ASN K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 61 removed outlier: 4.559A pdb=" N GLU K 59 " --> pdb=" O GLN K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 69 Processing helix chain 'K' and resid 75 through 89 removed outlier: 3.668A pdb=" N HIS K 81 " --> pdb=" O HIS K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 106 Processing helix chain 'K' and resid 114 through 134 removed outlier: 3.629A pdb=" N ASP K 132 " --> pdb=" O GLY K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 151 removed outlier: 4.265A pdb=" N LYS K 141 " --> pdb=" O SER K 137 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL K 142 " --> pdb=" O ASP K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 173 removed outlier: 3.506A pdb=" N TRP K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE K 160 " --> pdb=" O MET K 156 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG K 161 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG K 168 " --> pdb=" O GLU K 164 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS K 171 " --> pdb=" O VAL K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 199 removed outlier: 4.287A pdb=" N GLU K 184 " --> pdb=" O HIS K 180 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU K 196 " --> pdb=" O TYR K 192 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS K 199 " --> pdb=" O LYS K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 219 removed outlier: 3.580A pdb=" N LEU K 212 " --> pdb=" O LEU K 208 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE K 217 " --> pdb=" O CYS K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 234 removed outlier: 3.680A pdb=" N LYS K 227 " --> pdb=" O ASP K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 259 Processing helix chain 'K' and resid 262 through 279 removed outlier: 4.191A pdb=" N GLN K 267 " --> pdb=" O LYS K 263 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU K 268 " --> pdb=" O LYS K 264 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS K 279 " --> pdb=" O LEU K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 301 Processing helix chain 'K' and resid 303 through 306 removed outlier: 3.656A pdb=" N GLN K 306 " --> pdb=" O ASN K 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 303 through 306' Processing helix chain 'K' and resid 307 through 322 Processing helix chain 'K' and resid 326 through 344 Processing helix chain 'K' and resid 351 through 368 removed outlier: 4.037A pdb=" N HIS K 366 " --> pdb=" O GLY K 362 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 393 removed outlier: 3.758A pdb=" N VAL K 381 " --> pdb=" O SER K 377 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS K 382 " --> pdb=" O SER K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 421 Processing helix chain 'K' and resid 425 through 442 Processing helix chain 'K' and resid 444 through 463 removed outlier: 3.938A pdb=" N GLU K 450 " --> pdb=" O LYS K 446 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS K 452 " --> pdb=" O ALA K 448 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 484 removed outlier: 3.633A pdb=" N HIS K 476 " --> pdb=" O LEU K 472 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP K 484 " --> pdb=" O LEU K 480 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 507 removed outlier: 4.059A pdb=" N LYS K 493 " --> pdb=" O GLU K 489 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU K 494 " --> pdb=" O ASN K 490 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE K 501 " --> pdb=" O ARG K 497 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU K 505 " --> pdb=" O ILE K 501 " (cutoff:3.500A) Processing helix chain 'K' and resid 510 through 512 No H-bonds generated for 'chain 'K' and resid 510 through 512' Processing helix chain 'K' and resid 513 through 526 removed outlier: 3.811A pdb=" N GLY K 519 " --> pdb=" O TYR K 515 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER K 526 " --> pdb=" O LYS K 522 " (cutoff:3.500A) Processing helix chain 'K' and resid 530 through 552 removed outlier: 3.644A pdb=" N PHE K 534 " --> pdb=" O TYR K 530 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL K 539 " --> pdb=" O GLU K 535 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG K 549 " --> pdb=" O ARG K 545 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLN K 550 " --> pdb=" O LEU K 546 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER K 552 " --> pdb=" O ASP K 548 " (cutoff:3.500A) Processing helix chain 'K' and resid 555 through 560 removed outlier: 3.738A pdb=" N VAL K 560 " --> pdb=" O ALA K 556 " (cutoff:3.500A) Processing helix chain 'K' and resid 569 through 577 removed outlier: 3.782A pdb=" N SER K 577 " --> pdb=" O SER K 573 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 26 removed outlier: 3.805A pdb=" N THR L 20 " --> pdb=" O LYS L 16 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA L 23 " --> pdb=" O THR L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 47 removed outlier: 3.847A pdb=" N PHE L 39 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER L 40 " --> pdb=" O ASN L 36 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA L 44 " --> pdb=" O SER L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 78 Processing helix chain 'L' and resid 82 through 105 removed outlier: 3.851A pdb=" N HIS L 88 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG L 89 " --> pdb=" O VAL L 85 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU L 92 " --> pdb=" O HIS L 88 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU L 93 " --> pdb=" O ARG L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 112 Processing helix chain 'L' and resid 141 through 151 removed outlier: 3.916A pdb=" N ARG L 148 " --> pdb=" O LEU L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 156 Processing helix chain 'M' and resid 23 through 36 removed outlier: 3.815A pdb=" N LEU M 27 " --> pdb=" O THR M 23 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE M 34 " --> pdb=" O ILE M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.901A pdb=" N GLY M 61 " --> pdb=" O GLY M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 67 removed outlier: 3.634A pdb=" N ALA M 67 " --> pdb=" O SER M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 37 Processing helix chain 'N' and resid 39 through 47 Processing helix chain 'N' and resid 66 through 83 removed outlier: 4.132A pdb=" N LYS N 72 " --> pdb=" O HIS N 68 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR N 78 " --> pdb=" O CYS N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 111 removed outlier: 4.744A pdb=" N LEU N 101 " --> pdb=" O PRO N 97 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLU N 102 " --> pdb=" O GLU N 98 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET N 105 " --> pdb=" O LEU N 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 33 removed outlier: 3.689A pdb=" N LEU Q 27 " --> pdb=" O THR Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 49 removed outlier: 3.543A pdb=" N ASP Q 48 " --> pdb=" O TYR Q 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 34 through 38 Processing helix chain 'T' and resid 39 through 47 Processing helix chain 'T' and resid 66 through 83 removed outlier: 4.329A pdb=" N LYS T 72 " --> pdb=" O HIS T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 109 removed outlier: 3.799A pdb=" N ASN T 108 " --> pdb=" O LEU T 104 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE T 109 " --> pdb=" O MET T 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 81 through 88 removed outlier: 3.501A pdb=" N ARG V 86 " --> pdb=" O HIS V 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 26 removed outlier: 3.585A pdb=" N THR U 19 " --> pdb=" O ASN U 15 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR U 20 " --> pdb=" O LYS U 16 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET U 26 " --> pdb=" O LYS U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 47 removed outlier: 4.073A pdb=" N SER U 40 " --> pdb=" O ASN U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 78 removed outlier: 3.501A pdb=" N LEU U 57 " --> pdb=" O LEU U 53 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG U 70 " --> pdb=" O GLU U 66 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU U 78 " --> pdb=" O LYS U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 105 removed outlier: 3.832A pdb=" N GLU U 93 " --> pdb=" O ARG U 89 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR U 94 " --> pdb=" O TYR U 90 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS U 96 " --> pdb=" O GLU U 92 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP U 99 " --> pdb=" O SER U 95 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET U 101 " --> pdb=" O GLY U 97 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 112 Processing helix chain 'U' and resid 138 through 151 removed outlier: 4.187A pdb=" N LEU U 144 " --> pdb=" O GLY U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 155 through 172 removed outlier: 3.876A pdb=" N ARG U 161 " --> pdb=" O ALA U 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET U 162 " --> pdb=" O ILE U 158 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP U 170 " --> pdb=" O GLU U 166 " (cutoff:3.500A) Processing helix chain 'U' and resid 177 through 191 removed outlier: 3.603A pdb=" N PHE U 188 " --> pdb=" O VAL U 184 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL U 189 " --> pdb=" O ILE U 185 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL U 191 " --> pdb=" O SER U 187 " (cutoff:3.500A) Processing helix chain 'U' and resid 202 through 207 Processing helix chain 'U' and resid 207 through 229 removed outlier: 3.783A pdb=" N SER U 224 " --> pdb=" O LYS U 220 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN U 228 " --> pdb=" O SER U 224 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU U 229 " --> pdb=" O ASN U 225 " (cutoff:3.500A) Processing helix chain 'U' and resid 231 through 254 removed outlier: 3.916A pdb=" N MET U 236 " --> pdb=" O CYS U 232 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU U 237 " --> pdb=" O SER U 233 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR U 253 " --> pdb=" O ARG U 249 " (cutoff:3.500A) Processing helix chain 'U' and resid 255 through 257 No H-bonds generated for 'chain 'U' and resid 255 through 257' Processing helix chain 'U' and resid 258 through 269 removed outlier: 3.544A pdb=" N ILE U 263 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS U 264 " --> pdb=" O THR U 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 274 through 283 removed outlier: 3.605A pdb=" N GLU U 281 " --> pdb=" O PHE U 277 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N HIS U 283 " --> pdb=" O HIS U 279 " (cutoff:3.500A) Processing helix chain 'U' and resid 284 through 289 removed outlier: 5.181A pdb=" N ARG U 287 " --> pdb=" O ASN U 284 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN U 288 " --> pdb=" O ILE U 285 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU U 289 " --> pdb=" O ILE U 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 284 through 289' Processing helix chain 'U' and resid 290 through 304 removed outlier: 3.804A pdb=" N MET U 297 " --> pdb=" O ASP U 293 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL U 299 " --> pdb=" O ALA U 295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU U 300 " --> pdb=" O ASN U 296 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA U 303 " --> pdb=" O VAL U 299 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL U 304 " --> pdb=" O LEU U 300 " (cutoff:3.500A) Processing helix chain 'U' and resid 307 through 328 removed outlier: 3.691A pdb=" N MET U 311 " --> pdb=" O GLY U 307 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN U 313 " --> pdb=" O PRO U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 334 through 357 removed outlier: 3.867A pdb=" N LEU U 338 " --> pdb=" O ASN U 334 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN U 352 " --> pdb=" O GLY U 348 " (cutoff:3.500A) Processing helix chain 'U' and resid 361 through 377 removed outlier: 3.507A pdb=" N SER U 374 " --> pdb=" O LYS U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 386 through 400 removed outlier: 3.717A pdb=" N LYS U 400 " --> pdb=" O ASP U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 407 through 424 removed outlier: 3.530A pdb=" N SER U 417 " --> pdb=" O ASP U 413 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE U 419 " --> pdb=" O LEU U 415 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR U 420 " --> pdb=" O THR U 416 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL U 421 " --> pdb=" O SER U 417 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR U 424 " --> pdb=" O THR U 420 " (cutoff:3.500A) Processing helix chain 'U' and resid 427 through 445 removed outlier: 3.722A pdb=" N PHE U 431 " --> pdb=" O ASP U 427 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET U 438 " --> pdb=" O PHE U 434 " (cutoff:3.500A) Processing helix chain 'U' and resid 450 through 466 removed outlier: 3.568A pdb=" N GLU U 454 " --> pdb=" O SER U 450 " (cutoff:3.500A) Processing helix chain 'U' and resid 466 through 496 removed outlier: 3.851A pdb=" N THR U 470 " --> pdb=" O GLY U 466 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYS U 472 " --> pdb=" O GLU U 468 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LEU U 473 " --> pdb=" O PHE U 469 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET U 480 " --> pdb=" O MET U 476 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP U 485 " --> pdb=" O SER U 481 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 548 removed outlier: 4.015A pdb=" N LYS U 535 " --> pdb=" O GLN U 531 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N SER U 536 " --> pdb=" O GLU U 532 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN U 546 " --> pdb=" O LEU U 542 " (cutoff:3.500A) Processing helix chain 'U' and resid 557 through 559 No H-bonds generated for 'chain 'U' and resid 557 through 559' Processing helix chain 'U' and resid 579 through 591 removed outlier: 3.868A pdb=" N VAL U 584 " --> pdb=" O TYR U 580 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE U 588 " --> pdb=" O VAL U 584 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN U 589 " --> pdb=" O LEU U 585 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN U 590 " --> pdb=" O LEU U 586 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER U 591 " --> pdb=" O ALA U 587 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 604 removed outlier: 3.599A pdb=" N THR U 603 " --> pdb=" O LEU U 599 " (cutoff:3.500A) Processing helix chain 'U' and resid 606 through 620 removed outlier: 3.716A pdb=" N LEU U 610 " --> pdb=" O ASN U 606 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS U 612 " --> pdb=" O LYS U 608 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS U 615 " --> pdb=" O THR U 611 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER U 616 " --> pdb=" O LYS U 612 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU U 617 " --> pdb=" O THR U 613 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 16 through 18 removed outlier: 6.986A pdb=" N PHE C 4 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VAL C 75 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N MET C 6 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU C 77 " --> pdb=" O MET C 6 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG C 8 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 28 through 32 Processing sheet with id=AA3, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AA4, first strand: chain 'G' and resid 12 through 13 removed outlier: 4.011A pdb=" N ALA G 73 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL G 75 " --> pdb=" O MET G 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'I' and resid 506 through 513 Processing sheet with id=AA7, first strand: chain 'I' and resid 506 through 513 removed outlier: 3.634A pdb=" N ASN R 28 " --> pdb=" O THR I 561 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR I 561 " --> pdb=" O ASN R 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 574 through 576 removed outlier: 6.342A pdb=" N VAL I 574 " --> pdb=" O PHE I 651 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'I' and resid 593 through 595 removed outlier: 3.582A pdb=" N VAL I 594 " --> pdb=" O PHE I 638 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 70 through 71 Processing sheet with id=AB2, first strand: chain 'M' and resid 16 through 18 removed outlier: 3.552A pdb=" N THR M 16 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU M 5 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA M 73 " --> pdb=" O PHE M 4 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 45 through 46 Processing sheet with id=AB4, first strand: chain 'N' and resid 18 through 19 removed outlier: 3.581A pdb=" N VAL N 31 " --> pdb=" O VAL N 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 12 through 13 removed outlier: 3.580A pdb=" N THR Q 16 " --> pdb=" O LEU Q 5 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 12 through 13 removed outlier: 4.253A pdb=" N ALA Q 73 " --> pdb=" O PHE Q 4 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL Q 75 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'T' and resid 31 through 32 removed outlier: 3.675A pdb=" N ASN T 58 " --> pdb=" O TYR T 18 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 508 through 513 removed outlier: 6.759A pdb=" N ALA V 29 " --> pdb=" O TYR U 510 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU U 512 " --> pdb=" O ALA V 29 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA V 31 " --> pdb=" O LEU U 512 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'V' and resid 70 through 71 Processing sheet with id=AC2, first strand: chain 'U' and resid 561 through 566 removed outlier: 3.884A pdb=" N VAL U 564 " --> pdb=" O ALA U 575 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA U 575 " --> pdb=" O VAL U 564 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET U 566 " --> pdb=" O TYR U 573 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR U 573 " --> pdb=" O MET U 566 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL U 574 " --> pdb=" O PHE U 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 593 through 594 2304 hydrogen bonds defined for protein. 6804 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12776 1.34 - 1.46: 6776 1.46 - 1.58: 20268 1.58 - 1.69: 0 1.69 - 1.81: 354 Bond restraints: 40174 Sorted by residual: bond pdb=" CA ASP R 51 " pdb=" C ASP R 51 " ideal model delta sigma weight residual 1.528 1.500 0.028 1.37e-02 5.33e+03 4.05e+00 bond pdb=" CA ASP V 51 " pdb=" C ASP V 51 " ideal model delta sigma weight residual 1.528 1.500 0.027 1.37e-02 5.33e+03 3.95e+00 bond pdb=" CG1 ILE A 385 " pdb=" CD1 ILE A 385 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.93e+00 bond pdb=" CB GLU E 60 " pdb=" CG GLU E 60 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.84e+00 bond pdb=" C LYS V 105 " pdb=" N TYR V 106 " ideal model delta sigma weight residual 1.331 1.312 0.019 1.51e-02 4.39e+03 1.58e+00 ... (remaining 40169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 53773 2.23 - 4.46: 387 4.46 - 6.69: 52 6.69 - 8.92: 6 8.92 - 11.15: 1 Bond angle restraints: 54219 Sorted by residual: angle pdb=" N GLU A 231 " pdb=" CA GLU A 231 " pdb=" CB GLU A 231 " ideal model delta sigma weight residual 110.28 115.40 -5.12 1.55e+00 4.16e-01 1.09e+01 angle pdb=" O LYS V 105 " pdb=" C LYS V 105 " pdb=" N TYR V 106 " ideal model delta sigma weight residual 123.48 120.12 3.36 1.12e+00 7.97e-01 8.98e+00 angle pdb=" C LYS C 46 " pdb=" N ASP C 47 " pdb=" CA ASP C 47 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.65e+00 angle pdb=" N TYR R 106 " pdb=" CA TYR R 106 " pdb=" C TYR R 106 " ideal model delta sigma weight residual 110.24 105.95 4.29 1.47e+00 4.63e-01 8.51e+00 angle pdb=" C THR H 84 " pdb=" N ASN H 85 " pdb=" CA ASN H 85 " ideal model delta sigma weight residual 122.46 126.50 -4.04 1.41e+00 5.03e-01 8.20e+00 ... (remaining 54214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 21457 17.88 - 35.76: 2246 35.76 - 53.64: 374 53.64 - 71.52: 67 71.52 - 89.40: 52 Dihedral angle restraints: 24196 sinusoidal: 9859 harmonic: 14337 Sorted by residual: dihedral pdb=" CA PHE T 52 " pdb=" C PHE T 52 " pdb=" N ALA T 53 " pdb=" CA ALA T 53 " ideal model delta harmonic sigma weight residual -180.00 -160.34 -19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LEU H 37 " pdb=" C LEU H 37 " pdb=" N THR H 38 " pdb=" CA THR H 38 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLN R 104 " pdb=" C GLN R 104 " pdb=" N LYS R 105 " pdb=" CA LYS R 105 " ideal model delta harmonic sigma weight residual -180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 24193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 5002 0.053 - 0.106: 847 0.106 - 0.159: 80 0.159 - 0.213: 5 0.213 - 0.266: 4 Chirality restraints: 5938 Sorted by residual: chirality pdb=" CB ILE T 95 " pdb=" CA ILE T 95 " pdb=" CG1 ILE T 95 " pdb=" CG2 ILE T 95 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB VAL I 47 " pdb=" CA VAL I 47 " pdb=" CG1 VAL I 47 " pdb=" CG2 VAL I 47 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB ILE U 529 " pdb=" CA ILE U 529 " pdb=" CG1 ILE U 529 " pdb=" CG2 ILE U 529 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 5935 not shown) Planarity restraints: 6914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS R 105 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C LYS R 105 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS R 105 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR R 106 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU U 308 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO U 309 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO U 309 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO U 309 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 48 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO H 49 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO H 49 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 49 " -0.030 5.00e-02 4.00e+02 ... (remaining 6911 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 373 2.63 - 3.20: 36152 3.20 - 3.77: 64027 3.77 - 4.33: 86498 4.33 - 4.90: 141400 Nonbonded interactions: 328450 Sorted by model distance: nonbonded pdb=" OD1 ASP V 97 " pdb="ZN ZN V 202 " model vdw 2.067 2.230 nonbonded pdb=" OE1 GLU J 334 " pdb=" OG SER J 378 " model vdw 2.175 3.040 nonbonded pdb=" OE1 GLU A 334 " pdb=" OG SER A 378 " model vdw 2.194 3.040 nonbonded pdb=" OH TYR I 467 " pdb=" OG SER R 62 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASP U 633 " pdb=" OG SER U 636 " model vdw 2.219 3.040 ... (remaining 328445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 577)) selection = (chain 'B' and (resid 7 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 577)) selection = (chain 'J' and resid 7 through 577) selection = (chain 'K' and (resid 7 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 577)) } ncs_group { reference = (chain 'C' and resid 2 through 100) selection = (chain 'G' and (resid 2 through 79 or resid 88 through 100)) selection = (chain 'M' and resid 2 through 100) } ncs_group { reference = (chain 'D' and (resid 17 through 50 or resid 57 through 112)) selection = (chain 'H' and (resid 17 through 50 or resid 57 through 112)) selection = chain 'N' selection = (chain 'T' and (resid 17 through 50 or resid 57 through 112)) } ncs_group { reference = chain 'F' selection = chain 'O' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = (chain 'R' and resid 27 through 202) selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 32.740 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 40204 Z= 0.170 Angle : 0.531 11.150 54235 Z= 0.282 Chirality : 0.040 0.266 5938 Planarity : 0.004 0.057 6914 Dihedral : 14.990 89.397 14922 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.12), residues: 4788 helix: -0.64 (0.09), residues: 3184 sheet: -1.88 (0.43), residues: 143 loop : -1.08 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 56 TYR 0.014 0.001 TYR H 76 PHE 0.020 0.001 PHE E 39 TRP 0.014 0.001 TRP U 35 HIS 0.006 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00399 (40174) covalent geometry : angle 0.52817 (54219) hydrogen bonds : bond 0.23478 ( 2293) hydrogen bonds : angle 7.85625 ( 6804) metal coordination : bond 0.01170 ( 30) metal coordination : angle 3.48563 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 789 time to evaluate : 1.570 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: A 546 LEU cc_start: 0.7204 (mm) cc_final: 0.6997 (mm) REVERT: E 13 THR cc_start: 0.7911 (m) cc_final: 0.7578 (p) REVERT: B 282 SER cc_start: 0.8917 (m) cc_final: 0.8690 (t) REVERT: B 294 TYR cc_start: 0.8404 (t80) cc_final: 0.8166 (t80) REVERT: B 300 ASN cc_start: 0.8184 (t160) cc_final: 0.7889 (t0) REVERT: I 338 LEU cc_start: 0.8184 (tt) cc_final: 0.7747 (mt) REVERT: R 98 ASN cc_start: 0.8500 (t0) cc_final: 0.8176 (t0) REVERT: J 230 ILE cc_start: 0.7754 (mm) cc_final: 0.7332 (mp) REVERT: J 280 PHE cc_start: 0.7870 (m-10) cc_final: 0.7664 (m-10) REVERT: K 8 TRP cc_start: 0.6377 (m-90) cc_final: 0.5879 (m-90) REVERT: K 156 MET cc_start: 0.7225 (tmm) cc_final: 0.7021 (tmm) REVERT: K 168 ARG cc_start: 0.7535 (mtt90) cc_final: 0.7163 (mtt180) REVERT: K 231 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8176 (mm-30) REVERT: L 86 MET cc_start: 0.1759 (ppp) cc_final: 0.0935 (ppp) REVERT: L 114 LYS cc_start: 0.8450 (mmtt) cc_final: 0.8079 (mmtt) REVERT: N 82 ARG cc_start: 0.7684 (tmt-80) cc_final: 0.7367 (tpt90) REVERT: Q 25 PHE cc_start: 0.5952 (t80) cc_final: 0.5735 (t80) REVERT: V 40 ASP cc_start: 0.7878 (p0) cc_final: 0.7585 (p0) REVERT: U 151 MET cc_start: 0.9124 (tpt) cc_final: 0.8795 (tpt) REVERT: U 314 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6861 (tp30) REVERT: U 582 MET cc_start: 0.7584 (tmm) cc_final: 0.7237 (tmm) REVERT: U 622 MET cc_start: 0.6362 (tpt) cc_final: 0.6152 (tpt) outliers start: 0 outliers final: 0 residues processed: 789 average time/residue: 0.2318 time to fit residues: 294.4988 Evaluate side-chains 486 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.5980 chunk 470 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 529 ASN E 204 GLN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 HIS B 395 ASN B 425 ASN G 70 GLN ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 ASN J 572 GLN K 81 HIS K 544 ASN L 67 ASN P -5 GLN Q 70 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.174003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.142207 restraints weight = 68696.390| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.34 r_work: 0.3855 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40204 Z= 0.149 Angle : 0.583 11.735 54235 Z= 0.308 Chirality : 0.039 0.226 5938 Planarity : 0.004 0.103 6914 Dihedral : 4.161 29.502 5298 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 8.99 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.12), residues: 4788 helix: 0.12 (0.09), residues: 3258 sheet: -1.92 (0.37), residues: 179 loop : -1.07 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 29 TYR 0.033 0.001 TYR K 510 PHE 0.022 0.002 PHE A 445 TRP 0.015 0.001 TRP U 35 HIS 0.009 0.001 HIS T 35 Details of bonding type rmsd covalent geometry : bond 0.00322 (40174) covalent geometry : angle 0.58052 (54219) hydrogen bonds : bond 0.05495 ( 2293) hydrogen bonds : angle 5.03368 ( 6804) metal coordination : bond 0.00857 ( 30) metal coordination : angle 3.20086 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 547 time to evaluate : 1.450 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: A 8 TRP cc_start: 0.7869 (m-10) cc_final: 0.7232 (m-10) REVERT: A 156 MET cc_start: 0.7681 (mmp) cc_final: 0.7119 (mmm) REVERT: A 457 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8641 (tm-30) REVERT: C 42 GLN cc_start: 0.2035 (pp30) cc_final: 0.1722 (pt0) REVERT: D 17 MET cc_start: 0.6717 (tpp) cc_final: 0.6472 (tmm) REVERT: S -3 ARG cc_start: 0.8106 (ptp-170) cc_final: 0.7839 (ptt180) REVERT: B 174 ASN cc_start: 0.8396 (m-40) cc_final: 0.8184 (m110) REVERT: B 294 TYR cc_start: 0.8724 (t80) cc_final: 0.8501 (t80) REVERT: B 300 ASN cc_start: 0.8468 (t0) cc_final: 0.8129 (t0) REVERT: I 338 LEU cc_start: 0.8080 (tt) cc_final: 0.7650 (mt) REVERT: I 438 MET cc_start: 0.8342 (ptp) cc_final: 0.7760 (ptp) REVERT: I 534 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7259 (mm-30) REVERT: I 605 MET cc_start: 0.4167 (ppp) cc_final: 0.3751 (ppp) REVERT: R 41 ASN cc_start: 0.8298 (m-40) cc_final: 0.8043 (m-40) REVERT: R 98 ASN cc_start: 0.8731 (t0) cc_final: 0.8407 (t0) REVERT: J 230 ILE cc_start: 0.8287 (mm) cc_final: 0.8087 (mp) REVERT: K 156 MET cc_start: 0.7641 (tmm) cc_final: 0.7390 (tmm) REVERT: K 168 ARG cc_start: 0.7755 (mtt90) cc_final: 0.7347 (mtt180) REVERT: K 266 GLU cc_start: 0.7795 (pt0) cc_final: 0.7593 (pt0) REVERT: L 71 HIS cc_start: 0.8079 (m-70) cc_final: 0.7590 (m90) REVERT: M 101 ASP cc_start: 0.7281 (t0) cc_final: 0.6804 (t0) REVERT: N 82 ARG cc_start: 0.8386 (tmt-80) cc_final: 0.8168 (tpt90) REVERT: Q 25 PHE cc_start: 0.6375 (t80) cc_final: 0.6069 (t80) REVERT: Q 68 ARG cc_start: 0.6256 (ttm110) cc_final: 0.6055 (ptt180) REVERT: T 56 GLU cc_start: 0.6337 (tp30) cc_final: 0.5883 (mt-10) REVERT: V 40 ASP cc_start: 0.8314 (p0) cc_final: 0.8032 (p0) REVERT: U 542 LEU cc_start: 0.9077 (tp) cc_final: 0.8856 (tt) REVERT: U 582 MET cc_start: 0.7673 (tmm) cc_final: 0.7249 (tmm) REVERT: U 622 MET cc_start: 0.6619 (tpt) cc_final: 0.6185 (tpt) outliers start: 53 outliers final: 35 residues processed: 575 average time/residue: 0.2046 time to fit residues: 196.1501 Evaluate side-chains 487 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 452 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 98 GLU Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain U residue 26 MET Chi-restraints excluded: chain U residue 201 LYS Chi-restraints excluded: chain U residue 268 GLN Chi-restraints excluded: chain U residue 407 THR Chi-restraints excluded: chain U residue 444 ILE Chi-restraints excluded: chain U residue 618 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 113 optimal weight: 1.9990 chunk 270 optimal weight: 0.5980 chunk 354 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 386 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 451 optimal weight: 3.9990 chunk 392 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 380 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN I 589 ASN K 55 GLN K 333 HIS K 352 ASN ** K 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 HIS M 10 HIS U 88 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.172435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.138375 restraints weight = 71031.851| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 2.07 r_work: 0.3870 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 40204 Z= 0.230 Angle : 0.606 13.771 54235 Z= 0.316 Chirality : 0.041 0.378 5938 Planarity : 0.004 0.076 6914 Dihedral : 4.224 29.435 5298 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.08 % Allowed : 11.97 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.12), residues: 4788 helix: 0.21 (0.09), residues: 3265 sheet: -2.05 (0.37), residues: 172 loop : -1.00 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 32 TYR 0.026 0.002 TYR U 558 PHE 0.023 0.002 PHE J 445 TRP 0.021 0.002 TRP U 35 HIS 0.008 0.001 HIS J 333 Details of bonding type rmsd covalent geometry : bond 0.00538 (40174) covalent geometry : angle 0.60358 (54219) hydrogen bonds : bond 0.04789 ( 2293) hydrogen bonds : angle 4.80013 ( 6804) metal coordination : bond 0.01629 ( 30) metal coordination : angle 3.48218 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 492 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8126 (mp) REVERT: E 53 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7917 (pp) REVERT: C 42 GLN cc_start: 0.2265 (pp30) cc_final: 0.2049 (pt0) REVERT: D 17 MET cc_start: 0.6669 (tpp) cc_final: 0.6428 (tmm) REVERT: B 294 TYR cc_start: 0.8661 (t80) cc_final: 0.8409 (t80) REVERT: B 442 MET cc_start: 0.7730 (mtp) cc_final: 0.7521 (mtp) REVERT: I 338 LEU cc_start: 0.8086 (tt) cc_final: 0.7598 (mt) REVERT: I 438 MET cc_start: 0.8126 (ptp) cc_final: 0.7667 (ptp) REVERT: I 534 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7225 (mm-30) REVERT: I 605 MET cc_start: 0.4467 (ppp) cc_final: 0.3820 (ppp) REVERT: R 41 ASN cc_start: 0.8281 (m-40) cc_final: 0.8047 (m-40) REVERT: R 98 ASN cc_start: 0.8704 (t0) cc_final: 0.8408 (t0) REVERT: J 247 ASP cc_start: 0.7116 (m-30) cc_final: 0.6878 (m-30) REVERT: J 385 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8067 (mp) REVERT: K 168 ARG cc_start: 0.7665 (mtt90) cc_final: 0.7225 (mtt180) REVERT: N 82 ARG cc_start: 0.8340 (tmt-80) cc_final: 0.8131 (tpt90) REVERT: Q 25 PHE cc_start: 0.6394 (t80) cc_final: 0.6042 (t80) REVERT: Q 80 ARG cc_start: 0.7004 (ttp80) cc_final: 0.6790 (ttp80) REVERT: V 40 ASP cc_start: 0.8135 (p0) cc_final: 0.7872 (p0) REVERT: U 476 MET cc_start: 0.8523 (mtm) cc_final: 0.8200 (mtm) REVERT: U 582 MET cc_start: 0.7651 (tmm) cc_final: 0.7189 (tmm) REVERT: U 622 MET cc_start: 0.6581 (tpt) cc_final: 0.6230 (tpt) outliers start: 89 outliers final: 58 residues processed: 541 average time/residue: 0.2093 time to fit residues: 188.9699 Evaluate side-chains 510 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 449 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 328 SER Chi-restraints excluded: chain I residue 357 VAL Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 310 ILE Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain J residue 385 ILE Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 571 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 98 GLU Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 55 ASN Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain U residue 26 MET Chi-restraints excluded: chain U residue 162 MET Chi-restraints excluded: chain U residue 201 LYS Chi-restraints excluded: chain U residue 292 ASN Chi-restraints excluded: chain U residue 308 LEU Chi-restraints excluded: chain U residue 391 LEU Chi-restraints excluded: chain U residue 407 THR Chi-restraints excluded: chain U residue 444 ILE Chi-restraints excluded: chain U residue 499 THR Chi-restraints excluded: chain U residue 605 MET Chi-restraints excluded: chain U residue 609 GLU Chi-restraints excluded: chain U residue 618 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 260 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 374 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 253 optimal weight: 0.7980 chunk 258 optimal weight: 1.9990 chunk 440 optimal weight: 3.9990 chunk 411 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 248 optimal weight: 0.0070 chunk 278 optimal weight: 0.8980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 457 GLN ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN I 359 ASN ** J 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 ASN K 306 GLN ** K 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.173956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.141798 restraints weight = 70873.009| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.09 r_work: 0.3916 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40204 Z= 0.145 Angle : 0.546 14.748 54235 Z= 0.282 Chirality : 0.039 0.355 5938 Planarity : 0.004 0.058 6914 Dihedral : 4.113 29.593 5298 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.26 % Allowed : 13.70 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.12), residues: 4788 helix: 0.47 (0.09), residues: 3283 sheet: -2.09 (0.37), residues: 172 loop : -1.02 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 32 TYR 0.028 0.001 TYR K 510 PHE 0.021 0.001 PHE J 41 TRP 0.016 0.001 TRP U 35 HIS 0.007 0.001 HIS T 35 Details of bonding type rmsd covalent geometry : bond 0.00326 (40174) covalent geometry : angle 0.54302 (54219) hydrogen bonds : bond 0.04218 ( 2293) hydrogen bonds : angle 4.54011 ( 6804) metal coordination : bond 0.00891 ( 30) metal coordination : angle 3.20432 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 492 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7897 (m-10) cc_final: 0.7271 (m-10) REVERT: A 120 ILE cc_start: 0.8687 (mm) cc_final: 0.8442 (tt) REVERT: A 156 MET cc_start: 0.7488 (mmp) cc_final: 0.7018 (mmm) REVERT: A 227 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8286 (mmmt) REVERT: A 385 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8111 (mp) REVERT: E 149 LYS cc_start: 0.8174 (mmtp) cc_final: 0.7529 (ptpp) REVERT: D 17 MET cc_start: 0.6568 (tpp) cc_final: 0.6315 (tmm) REVERT: B 294 TYR cc_start: 0.8644 (t80) cc_final: 0.8406 (t80) REVERT: B 467 ASP cc_start: 0.6811 (t70) cc_final: 0.6573 (t0) REVERT: I 338 LEU cc_start: 0.8055 (tt) cc_final: 0.7574 (mp) REVERT: I 438 MET cc_start: 0.8134 (ptp) cc_final: 0.7681 (ptp) REVERT: I 605 MET cc_start: 0.4643 (ppp) cc_final: 0.3806 (ppp) REVERT: R 41 ASN cc_start: 0.8330 (m-40) cc_final: 0.8104 (m-40) REVERT: R 98 ASN cc_start: 0.8580 (t0) cc_final: 0.8311 (t0) REVERT: J 157 LEU cc_start: 0.8445 (tt) cc_final: 0.8227 (pp) REVERT: J 385 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8099 (mp) REVERT: K 156 MET cc_start: 0.7651 (tmm) cc_final: 0.7412 (tmm) REVERT: K 168 ARG cc_start: 0.7616 (mtt90) cc_final: 0.7223 (mtt180) REVERT: K 510 TYR cc_start: 0.6146 (t80) cc_final: 0.5848 (t80) REVERT: L 90 TYR cc_start: 0.5649 (m-80) cc_final: 0.5280 (m-80) REVERT: M 101 ASP cc_start: 0.7035 (t0) cc_final: 0.6727 (t0) REVERT: N 70 LEU cc_start: 0.8926 (tp) cc_final: 0.8671 (tp) REVERT: N 82 ARG cc_start: 0.8422 (tmt-80) cc_final: 0.8081 (tpt90) REVERT: Q 25 PHE cc_start: 0.6322 (t80) cc_final: 0.5940 (t80) REVERT: U 476 MET cc_start: 0.8567 (mtm) cc_final: 0.8237 (mtm) REVERT: U 527 PHE cc_start: 0.7809 (t80) cc_final: 0.6955 (t80) REVERT: U 582 MET cc_start: 0.7787 (tmm) cc_final: 0.7259 (tmm) REVERT: U 622 MET cc_start: 0.6638 (tpt) cc_final: 0.6217 (tpt) outliers start: 97 outliers final: 59 residues processed: 546 average time/residue: 0.2161 time to fit residues: 198.2698 Evaluate side-chains 509 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 448 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 328 SER Chi-restraints excluded: chain I residue 357 VAL Chi-restraints excluded: chain I residue 539 MET Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain J residue 385 ILE Chi-restraints excluded: chain J residue 468 TYR Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 282 SER Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 571 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 98 GLU Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 55 ASN Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain U residue 26 MET Chi-restraints excluded: chain U residue 162 MET Chi-restraints excluded: chain U residue 196 LYS Chi-restraints excluded: chain U residue 201 LYS Chi-restraints excluded: chain U residue 292 ASN Chi-restraints excluded: chain U residue 308 LEU Chi-restraints excluded: chain U residue 391 LEU Chi-restraints excluded: chain U residue 407 THR Chi-restraints excluded: chain U residue 444 ILE Chi-restraints excluded: chain U residue 533 LEU Chi-restraints excluded: chain U residue 605 MET Chi-restraints excluded: chain U residue 618 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 468 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 407 optimal weight: 0.2980 chunk 381 optimal weight: 0.8980 chunk 358 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 361 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 297 optimal weight: 2.9990 chunk 383 optimal weight: 0.1980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 HIS N 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.175055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.143477 restraints weight = 70641.876| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.15 r_work: 0.3930 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 40204 Z= 0.124 Angle : 0.530 15.275 54235 Z= 0.272 Chirality : 0.038 0.458 5938 Planarity : 0.003 0.058 6914 Dihedral : 4.033 28.405 5298 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.05 % Allowed : 14.94 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.12), residues: 4788 helix: 0.63 (0.09), residues: 3290 sheet: -2.13 (0.36), residues: 172 loop : -0.98 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 32 TYR 0.023 0.001 TYR K 510 PHE 0.025 0.001 PHE J 280 TRP 0.014 0.001 TRP U 35 HIS 0.007 0.001 HIS T 35 Details of bonding type rmsd covalent geometry : bond 0.00272 (40174) covalent geometry : angle 0.52819 (54219) hydrogen bonds : bond 0.03988 ( 2293) hydrogen bonds : angle 4.40832 ( 6804) metal coordination : bond 0.00677 ( 30) metal coordination : angle 2.92186 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 499 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7927 (m-10) cc_final: 0.7268 (m-10) REVERT: A 156 MET cc_start: 0.7577 (mmp) cc_final: 0.6973 (mmm) REVERT: A 385 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8069 (mp) REVERT: E 149 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7473 (ptpp) REVERT: C 103 MET cc_start: 0.7807 (mmt) cc_final: 0.7039 (mmt) REVERT: D 17 MET cc_start: 0.6538 (tpp) cc_final: 0.6197 (tmm) REVERT: B 156 MET cc_start: 0.5622 (tpp) cc_final: 0.5063 (ttm) REVERT: B 294 TYR cc_start: 0.8652 (t80) cc_final: 0.8399 (t80) REVERT: B 442 MET cc_start: 0.7701 (mtp) cc_final: 0.7442 (mtp) REVERT: I 438 MET cc_start: 0.8120 (ptp) cc_final: 0.7688 (ptp) REVERT: I 605 MET cc_start: 0.4666 (ppp) cc_final: 0.3708 (ppp) REVERT: R 41 ASN cc_start: 0.8340 (m-40) cc_final: 0.8070 (m-40) REVERT: R 98 ASN cc_start: 0.8611 (t0) cc_final: 0.8311 (t0) REVERT: J 157 LEU cc_start: 0.8524 (tt) cc_final: 0.8287 (pp) REVERT: J 385 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8036 (mp) REVERT: K 156 MET cc_start: 0.7670 (tmm) cc_final: 0.7413 (tmm) REVERT: K 168 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7252 (mtt180) REVERT: K 399 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6340 (mp0) REVERT: K 510 TYR cc_start: 0.6203 (t80) cc_final: 0.5815 (t80) REVERT: L 90 TYR cc_start: 0.5584 (m-80) cc_final: 0.5286 (m-80) REVERT: L 137 MET cc_start: 0.7551 (tmm) cc_final: 0.7342 (tmm) REVERT: N 82 ARG cc_start: 0.8415 (tmt-80) cc_final: 0.8048 (tpt90) REVERT: Q 25 PHE cc_start: 0.6357 (t80) cc_final: 0.6007 (t80) REVERT: Q 68 ARG cc_start: 0.6120 (ttm110) cc_final: 0.5894 (ptt180) REVERT: U 527 PHE cc_start: 0.7795 (t80) cc_final: 0.7085 (t80) REVERT: U 582 MET cc_start: 0.7843 (tmm) cc_final: 0.7258 (tmm) REVERT: U 622 MET cc_start: 0.6661 (tpt) cc_final: 0.6192 (tpt) outliers start: 88 outliers final: 52 residues processed: 547 average time/residue: 0.2181 time to fit residues: 200.6288 Evaluate side-chains 506 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 452 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain E residue 39 PHE Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 328 SER Chi-restraints excluded: chain I residue 357 VAL Chi-restraints excluded: chain I residue 434 PHE Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain J residue 385 ILE Chi-restraints excluded: chain J residue 468 TYR Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 282 SER Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 571 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 73 HIS Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 98 GLU Chi-restraints excluded: chain Q residue 2 ASP Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain U residue 162 MET Chi-restraints excluded: chain U residue 201 LYS Chi-restraints excluded: chain U residue 308 LEU Chi-restraints excluded: chain U residue 391 LEU Chi-restraints excluded: chain U residue 533 LEU Chi-restraints excluded: chain U residue 605 MET Chi-restraints excluded: chain U residue 618 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 5.9990 chunk 436 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 281 optimal weight: 0.7980 chunk 235 optimal weight: 0.9990 chunk 342 optimal weight: 0.6980 chunk 283 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 308 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 230 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 ASN D 35 HIS ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 372 HIS ** K 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.175128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.144186 restraints weight = 70693.201| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.18 r_work: 0.3918 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40204 Z= 0.122 Angle : 0.533 15.946 54235 Z= 0.271 Chirality : 0.038 0.340 5938 Planarity : 0.003 0.058 6914 Dihedral : 4.003 27.805 5298 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.91 % Allowed : 16.20 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.12), residues: 4788 helix: 0.72 (0.09), residues: 3300 sheet: -2.16 (0.36), residues: 172 loop : -0.97 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 29 TYR 0.026 0.001 TYR U 558 PHE 0.029 0.001 PHE K 186 TRP 0.013 0.001 TRP U 35 HIS 0.006 0.001 HIS T 35 Details of bonding type rmsd covalent geometry : bond 0.00271 (40174) covalent geometry : angle 0.53067 (54219) hydrogen bonds : bond 0.03841 ( 2293) hydrogen bonds : angle 4.32360 ( 6804) metal coordination : bond 0.00702 ( 30) metal coordination : angle 2.80887 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 480 time to evaluate : 1.491 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: A 8 TRP cc_start: 0.7923 (m-10) cc_final: 0.7260 (m-10) REVERT: A 385 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8056 (mp) REVERT: E 101 MET cc_start: 0.8681 (mmm) cc_final: 0.8441 (mmt) REVERT: E 146 MET cc_start: 0.6768 (ttm) cc_final: 0.6538 (ttm) REVERT: C 103 MET cc_start: 0.7765 (mmt) cc_final: 0.6957 (mmt) REVERT: D 17 MET cc_start: 0.6386 (tpp) cc_final: 0.6046 (tmm) REVERT: D 82 ARG cc_start: 0.8641 (tpt90) cc_final: 0.8375 (tpt90) REVERT: B 156 MET cc_start: 0.5609 (tpp) cc_final: 0.5065 (ttm) REVERT: B 294 TYR cc_start: 0.8633 (t80) cc_final: 0.8354 (t80) REVERT: I 605 MET cc_start: 0.4653 (ppp) cc_final: 0.3631 (ppp) REVERT: R 41 ASN cc_start: 0.8333 (m-40) cc_final: 0.8060 (m-40) REVERT: R 98 ASN cc_start: 0.8609 (t0) cc_final: 0.8348 (t0) REVERT: J 385 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8035 (mp) REVERT: K 156 MET cc_start: 0.7673 (tmm) cc_final: 0.7418 (tmm) REVERT: K 168 ARG cc_start: 0.7662 (mtt90) cc_final: 0.7260 (mtt180) REVERT: K 399 GLU cc_start: 0.6531 (mt-10) cc_final: 0.6287 (mp0) REVERT: K 510 TYR cc_start: 0.6118 (t80) cc_final: 0.5728 (t80) REVERT: N 82 ARG cc_start: 0.8499 (tmt-80) cc_final: 0.8113 (tpt90) REVERT: Q 25 PHE cc_start: 0.6354 (t80) cc_final: 0.5980 (t80) REVERT: U 476 MET cc_start: 0.8580 (mtm) cc_final: 0.8203 (mtm) REVERT: U 527 PHE cc_start: 0.7718 (t80) cc_final: 0.7016 (t80) REVERT: U 582 MET cc_start: 0.7861 (tmm) cc_final: 0.7252 (tmm) REVERT: U 622 MET cc_start: 0.6622 (tpt) cc_final: 0.6179 (tpt) outliers start: 82 outliers final: 52 residues processed: 524 average time/residue: 0.2398 time to fit residues: 209.8385 Evaluate side-chains 503 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 449 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 39 PHE Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 335 MET Chi-restraints excluded: chain I residue 434 PHE Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain J residue 385 ILE Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 571 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 73 HIS Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 162 MET Chi-restraints excluded: chain U residue 196 LYS Chi-restraints excluded: chain U residue 201 LYS Chi-restraints excluded: chain U residue 533 LEU Chi-restraints excluded: chain U residue 605 MET Chi-restraints excluded: chain U residue 618 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 105 optimal weight: 0.7980 chunk 453 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 328 optimal weight: 0.8980 chunk 362 optimal weight: 20.0000 chunk 452 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 393 optimal weight: 7.9990 chunk 149 optimal weight: 0.3980 chunk 206 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN K 372 HIS ** K 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 HIS Q 70 GLN U 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.174763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.142471 restraints weight = 70609.717| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 1.91 r_work: 0.3934 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40204 Z= 0.134 Angle : 0.550 16.267 54235 Z= 0.279 Chirality : 0.039 0.351 5938 Planarity : 0.003 0.057 6914 Dihedral : 3.987 27.754 5298 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.22 % Allowed : 16.69 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.12), residues: 4788 helix: 0.74 (0.09), residues: 3309 sheet: -2.17 (0.37), residues: 172 loop : -0.94 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 29 TYR 0.025 0.001 TYR B 495 PHE 0.034 0.001 PHE U 493 TRP 0.014 0.001 TRP U 35 HIS 0.032 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00303 (40174) covalent geometry : angle 0.54778 (54219) hydrogen bonds : bond 0.03787 ( 2293) hydrogen bonds : angle 4.30682 ( 6804) metal coordination : bond 0.00803 ( 30) metal coordination : angle 2.81409 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 485 time to evaluate : 1.610 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: A 8 TRP cc_start: 0.8000 (m-10) cc_final: 0.7316 (m-10) REVERT: A 156 MET cc_start: 0.7542 (mmp) cc_final: 0.7025 (mmm) REVERT: A 385 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8000 (mp) REVERT: A 569 GLU cc_start: 0.8755 (mp0) cc_final: 0.8537 (mp0) REVERT: E 60 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: E 111 GLN cc_start: 0.8074 (mm110) cc_final: 0.7773 (mm-40) REVERT: E 146 MET cc_start: 0.6772 (ttm) cc_final: 0.6520 (ttm) REVERT: D 17 MET cc_start: 0.6331 (tpp) cc_final: 0.5999 (tmm) REVERT: D 82 ARG cc_start: 0.8641 (tpt90) cc_final: 0.8329 (tpt90) REVERT: B 156 MET cc_start: 0.5582 (tpp) cc_final: 0.5082 (ttm) REVERT: B 294 TYR cc_start: 0.8641 (t80) cc_final: 0.8402 (t80) REVERT: I 297 MET cc_start: 0.8921 (tpp) cc_final: 0.8290 (tmm) REVERT: I 605 MET cc_start: 0.4609 (ppp) cc_final: 0.3691 (ppp) REVERT: R 41 ASN cc_start: 0.8299 (m-40) cc_final: 0.8007 (m-40) REVERT: R 98 ASN cc_start: 0.8590 (t0) cc_final: 0.8328 (t0) REVERT: J 385 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8018 (mp) REVERT: K 156 MET cc_start: 0.7644 (tmm) cc_final: 0.7383 (tmm) REVERT: K 168 ARG cc_start: 0.7610 (mtt90) cc_final: 0.7236 (mtt180) REVERT: K 399 GLU cc_start: 0.6467 (mt-10) cc_final: 0.6226 (mp0) REVERT: K 510 TYR cc_start: 0.6192 (t80) cc_final: 0.5777 (t80) REVERT: N 105 MET cc_start: 0.7897 (mtt) cc_final: 0.7287 (mtt) REVERT: Q 25 PHE cc_start: 0.6331 (t80) cc_final: 0.5947 (t80) REVERT: U 476 MET cc_start: 0.8578 (mtm) cc_final: 0.8171 (mtm) REVERT: U 527 PHE cc_start: 0.7738 (t80) cc_final: 0.7406 (t80) REVERT: U 582 MET cc_start: 0.7929 (tmm) cc_final: 0.7323 (tmm) REVERT: U 622 MET cc_start: 0.6656 (tpt) cc_final: 0.6196 (tpt) outliers start: 95 outliers final: 64 residues processed: 540 average time/residue: 0.2380 time to fit residues: 216.4702 Evaluate side-chains 517 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 450 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 39 PHE Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 357 VAL Chi-restraints excluded: chain I residue 434 PHE Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain I residue 566 MET Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain J residue 385 ILE Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 571 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 73 HIS Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 162 MET Chi-restraints excluded: chain U residue 196 LYS Chi-restraints excluded: chain U residue 201 LYS Chi-restraints excluded: chain U residue 292 ASN Chi-restraints excluded: chain U residue 308 LEU Chi-restraints excluded: chain U residue 407 THR Chi-restraints excluded: chain U residue 499 THR Chi-restraints excluded: chain U residue 533 LEU Chi-restraints excluded: chain U residue 605 MET Chi-restraints excluded: chain U residue 618 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 121 optimal weight: 0.1980 chunk 272 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 198 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 346 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 HIS ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 452 HIS K 77 HIS K 372 HIS ** K 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN M 10 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.176011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.142880 restraints weight = 70402.526| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.81 r_work: 0.3947 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3834 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40204 Z= 0.126 Angle : 0.557 16.605 54235 Z= 0.279 Chirality : 0.039 0.366 5938 Planarity : 0.004 0.143 6914 Dihedral : 3.969 27.530 5298 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.08 % Allowed : 17.20 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.12), residues: 4788 helix: 0.82 (0.09), residues: 3308 sheet: -2.18 (0.37), residues: 172 loop : -0.91 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 80 TYR 0.021 0.001 TYR K 226 PHE 0.040 0.001 PHE J 186 TRP 0.014 0.001 TRP U 35 HIS 0.009 0.001 HIS J 279 Details of bonding type rmsd covalent geometry : bond 0.00282 (40174) covalent geometry : angle 0.55499 (54219) hydrogen bonds : bond 0.03695 ( 2293) hydrogen bonds : angle 4.27170 ( 6804) metal coordination : bond 0.00684 ( 30) metal coordination : angle 2.71031 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 482 time to evaluate : 1.290 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: A 8 TRP cc_start: 0.7974 (m-10) cc_final: 0.7347 (m-10) REVERT: A 138 ASP cc_start: 0.7779 (m-30) cc_final: 0.7384 (m-30) REVERT: A 156 MET cc_start: 0.7495 (mmp) cc_final: 0.6978 (mmm) REVERT: A 385 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.7989 (mp) REVERT: E 60 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: E 111 GLN cc_start: 0.8077 (mm110) cc_final: 0.7740 (mm-40) REVERT: E 146 MET cc_start: 0.6811 (ttm) cc_final: 0.6569 (ttm) REVERT: D 17 MET cc_start: 0.6421 (tpp) cc_final: 0.6045 (tmm) REVERT: D 82 ARG cc_start: 0.8615 (tpt90) cc_final: 0.8303 (tpt90) REVERT: B 156 MET cc_start: 0.5534 (tpp) cc_final: 0.5086 (ttm) REVERT: I 605 MET cc_start: 0.4697 (ppp) cc_final: 0.3775 (ppp) REVERT: R 41 ASN cc_start: 0.8244 (m-40) cc_final: 0.7954 (m-40) REVERT: R 98 ASN cc_start: 0.8537 (t0) cc_final: 0.8249 (t0) REVERT: J 385 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.7984 (mp) REVERT: K 156 MET cc_start: 0.7627 (tmm) cc_final: 0.7378 (tmm) REVERT: K 168 ARG cc_start: 0.7551 (mtt90) cc_final: 0.7210 (mtt180) REVERT: K 399 GLU cc_start: 0.6482 (mt-10) cc_final: 0.6266 (mp0) REVERT: N 82 ARG cc_start: 0.8418 (tmt-80) cc_final: 0.8119 (tpt90) REVERT: N 83 TYR cc_start: 0.8104 (m-80) cc_final: 0.7795 (m-80) REVERT: N 105 MET cc_start: 0.7836 (mtt) cc_final: 0.7257 (mtt) REVERT: Q 25 PHE cc_start: 0.6228 (t80) cc_final: 0.5861 (t80) REVERT: U 476 MET cc_start: 0.8552 (mtm) cc_final: 0.8136 (mtm) REVERT: U 527 PHE cc_start: 0.7630 (t80) cc_final: 0.7083 (t80) REVERT: U 582 MET cc_start: 0.7932 (tmm) cc_final: 0.7353 (tmm) REVERT: U 622 MET cc_start: 0.6635 (tpt) cc_final: 0.6176 (tpt) outliers start: 89 outliers final: 64 residues processed: 533 average time/residue: 0.2180 time to fit residues: 195.7591 Evaluate side-chains 517 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 450 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 372 HIS Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain E residue 39 PHE Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 338 LEU Chi-restraints excluded: chain I residue 351 VAL Chi-restraints excluded: chain I residue 357 VAL Chi-restraints excluded: chain I residue 434 PHE Chi-restraints excluded: chain I residue 542 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain J residue 385 ILE Chi-restraints excluded: chain J residue 468 TYR Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 571 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 73 HIS Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 162 MET Chi-restraints excluded: chain U residue 196 LYS Chi-restraints excluded: chain U residue 201 LYS Chi-restraints excluded: chain U residue 292 ASN Chi-restraints excluded: chain U residue 308 LEU Chi-restraints excluded: chain U residue 407 THR Chi-restraints excluded: chain U residue 499 THR Chi-restraints excluded: chain U residue 533 LEU Chi-restraints excluded: chain U residue 605 MET Chi-restraints excluded: chain U residue 618 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 100 optimal weight: 0.0170 chunk 259 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 467 optimal weight: 6.9990 chunk 294 optimal weight: 0.9990 chunk 140 optimal weight: 0.3980 chunk 152 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 300 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 372 HIS ** K 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 HIS U 513 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.176624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.144559 restraints weight = 71015.961| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 1.93 r_work: 0.3955 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 40204 Z= 0.119 Angle : 0.563 16.827 54235 Z= 0.281 Chirality : 0.039 0.464 5938 Planarity : 0.004 0.107 6914 Dihedral : 3.950 27.159 5298 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.61 % Allowed : 17.86 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.12), residues: 4788 helix: 0.87 (0.09), residues: 3313 sheet: -2.18 (0.36), residues: 172 loop : -0.94 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 80 TYR 0.028 0.001 TYR K 510 PHE 0.050 0.001 PHE J 186 TRP 0.016 0.001 TRP J 8 HIS 0.008 0.001 HIS U 320 Details of bonding type rmsd covalent geometry : bond 0.00265 (40174) covalent geometry : angle 0.56138 (54219) hydrogen bonds : bond 0.03633 ( 2293) hydrogen bonds : angle 4.24082 ( 6804) metal coordination : bond 0.00587 ( 30) metal coordination : angle 2.61130 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 484 time to evaluate : 1.056 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: A 8 TRP cc_start: 0.7964 (m-10) cc_final: 0.7349 (m-10) REVERT: A 156 MET cc_start: 0.7490 (mmp) cc_final: 0.6922 (mmm) REVERT: A 385 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8008 (mp) REVERT: E 60 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: E 111 GLN cc_start: 0.8070 (mm110) cc_final: 0.7740 (mm-40) REVERT: E 146 MET cc_start: 0.6926 (ttm) cc_final: 0.6700 (ttm) REVERT: D 17 MET cc_start: 0.6283 (tpp) cc_final: 0.5956 (tmm) REVERT: D 82 ARG cc_start: 0.8621 (tpt90) cc_final: 0.8298 (tpt90) REVERT: B 156 MET cc_start: 0.5627 (tpp) cc_final: 0.5259 (ttm) REVERT: I 297 MET cc_start: 0.8868 (tpp) cc_final: 0.8282 (tmm) REVERT: I 605 MET cc_start: 0.4685 (ppp) cc_final: 0.3683 (ppp) REVERT: R 98 ASN cc_start: 0.8540 (t0) cc_final: 0.8253 (t0) REVERT: J 385 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8001 (mp) REVERT: K 156 MET cc_start: 0.7616 (tmm) cc_final: 0.7360 (tmm) REVERT: K 168 ARG cc_start: 0.7590 (mtt90) cc_final: 0.7230 (mtt180) REVERT: K 399 GLU cc_start: 0.6473 (mt-10) cc_final: 0.6248 (mp0) REVERT: N 17 MET cc_start: 0.6938 (tmm) cc_final: 0.5922 (tmm) REVERT: N 82 ARG cc_start: 0.8491 (tmt-80) cc_final: 0.8197 (tpt90) REVERT: N 83 TYR cc_start: 0.8104 (m-80) cc_final: 0.7763 (m-80) REVERT: N 105 MET cc_start: 0.7798 (mtt) cc_final: 0.7229 (mtt) REVERT: Q 25 PHE cc_start: 0.6225 (t80) cc_final: 0.5860 (t80) REVERT: T 56 GLU cc_start: 0.6651 (tm-30) cc_final: 0.6234 (tp30) REVERT: U 527 PHE cc_start: 0.7578 (t80) cc_final: 0.7117 (t80) REVERT: U 582 MET cc_start: 0.7909 (tmm) cc_final: 0.7362 (tmm) REVERT: U 622 MET cc_start: 0.6688 (tpt) cc_final: 0.6240 (tpt) outliers start: 69 outliers final: 56 residues processed: 525 average time/residue: 0.2118 time to fit residues: 185.8188 Evaluate side-chains 513 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 454 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 372 HIS Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain E residue 39 PHE Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 338 LEU Chi-restraints excluded: chain I residue 351 VAL Chi-restraints excluded: chain I residue 434 PHE Chi-restraints excluded: chain I residue 539 MET Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 385 ILE Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 571 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 73 HIS Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain U residue 162 MET Chi-restraints excluded: chain U residue 196 LYS Chi-restraints excluded: chain U residue 201 LYS Chi-restraints excluded: chain U residue 292 ASN Chi-restraints excluded: chain U residue 407 THR Chi-restraints excluded: chain U residue 533 LEU Chi-restraints excluded: chain U residue 605 MET Chi-restraints excluded: chain U residue 618 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 184 optimal weight: 0.0000 chunk 388 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 323 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 390 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 469 optimal weight: 9.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN ** K 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 372 HIS ** K 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 HIS Q 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.162175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.132574 restraints weight = 64854.232| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.85 r_work: 0.3608 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40204 Z= 0.131 Angle : 0.576 16.587 54235 Z= 0.287 Chirality : 0.039 0.416 5938 Planarity : 0.003 0.088 6914 Dihedral : 3.954 27.514 5298 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.63 % Allowed : 18.28 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.12), residues: 4788 helix: 0.88 (0.09), residues: 3300 sheet: -2.23 (0.35), residues: 181 loop : -0.93 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 29 TYR 0.032 0.001 TYR K 510 PHE 0.045 0.001 PHE J 186 TRP 0.015 0.001 TRP E 14 HIS 0.007 0.001 HIS J 407 Details of bonding type rmsd covalent geometry : bond 0.00299 (40174) covalent geometry : angle 0.57403 (54219) hydrogen bonds : bond 0.03637 ( 2293) hydrogen bonds : angle 4.23703 ( 6804) metal coordination : bond 0.00708 ( 30) metal coordination : angle 2.70693 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 474 time to evaluate : 1.657 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: A 8 TRP cc_start: 0.7902 (m-10) cc_final: 0.7356 (m-10) REVERT: A 156 MET cc_start: 0.7465 (mmp) cc_final: 0.6880 (mmm) REVERT: A 385 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8022 (mp) REVERT: E 60 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: E 111 GLN cc_start: 0.8190 (mm110) cc_final: 0.7807 (mm-40) REVERT: E 146 MET cc_start: 0.7018 (ttm) cc_final: 0.6810 (ttm) REVERT: D 17 MET cc_start: 0.6357 (tpp) cc_final: 0.6098 (tmm) REVERT: D 82 ARG cc_start: 0.8649 (tpt90) cc_final: 0.8324 (tpt90) REVERT: B 156 MET cc_start: 0.5638 (tpp) cc_final: 0.5259 (ttm) REVERT: I 434 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: I 438 MET cc_start: 0.7954 (ptp) cc_final: 0.7503 (ptp) REVERT: I 605 MET cc_start: 0.4567 (ppp) cc_final: 0.3508 (ppp) REVERT: R 98 ASN cc_start: 0.8509 (t0) cc_final: 0.8240 (t0) REVERT: J 217 PHE cc_start: 0.7985 (t80) cc_final: 0.7566 (t80) REVERT: J 385 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8011 (mp) REVERT: K 156 MET cc_start: 0.7522 (tmm) cc_final: 0.7166 (tmm) REVERT: K 168 ARG cc_start: 0.7618 (mtt90) cc_final: 0.7244 (mtt180) REVERT: N 17 MET cc_start: 0.6984 (tmm) cc_final: 0.6012 (tmm) REVERT: N 82 ARG cc_start: 0.8393 (tmt-80) cc_final: 0.8119 (tpt90) REVERT: N 83 TYR cc_start: 0.8055 (m-80) cc_final: 0.7721 (m-80) REVERT: N 105 MET cc_start: 0.7888 (mtt) cc_final: 0.7356 (mtt) REVERT: Q 25 PHE cc_start: 0.6129 (t80) cc_final: 0.5783 (t80) REVERT: T 56 GLU cc_start: 0.6589 (tm-30) cc_final: 0.6203 (tp30) REVERT: U 308 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8364 (tp) REVERT: U 527 PHE cc_start: 0.7542 (t80) cc_final: 0.7102 (t80) REVERT: U 582 MET cc_start: 0.7876 (tmm) cc_final: 0.7348 (tmm) REVERT: U 622 MET cc_start: 0.6657 (tpt) cc_final: 0.6199 (tpt) outliers start: 70 outliers final: 59 residues processed: 515 average time/residue: 0.2160 time to fit residues: 187.7610 Evaluate side-chains 525 residues out of total 4285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 461 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 372 HIS Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain E residue 39 PHE Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 162 MET Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 338 LEU Chi-restraints excluded: chain I residue 351 VAL Chi-restraints excluded: chain I residue 434 PHE Chi-restraints excluded: chain I residue 539 MET Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain J residue 385 ILE Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 571 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 73 HIS Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 162 MET Chi-restraints excluded: chain U residue 196 LYS Chi-restraints excluded: chain U residue 201 LYS Chi-restraints excluded: chain U residue 292 ASN Chi-restraints excluded: chain U residue 308 LEU Chi-restraints excluded: chain U residue 407 THR Chi-restraints excluded: chain U residue 499 THR Chi-restraints excluded: chain U residue 605 MET Chi-restraints excluded: chain U residue 618 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 143 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 386 optimal weight: 4.9990 chunk 444 optimal weight: 0.7980 chunk 414 optimal weight: 2.9990 chunk 395 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 446 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 chunk 461 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN ** K 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.162048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.132421 restraints weight = 64926.033| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.06 r_work: 0.3585 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 40204 Z= 0.140 Angle : 0.584 16.550 54235 Z= 0.292 Chirality : 0.040 0.390 5938 Planarity : 0.004 0.077 6914 Dihedral : 3.972 28.180 5298 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.77 % Allowed : 18.39 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.12), residues: 4788 helix: 0.87 (0.09), residues: 3302 sheet: -2.23 (0.36), residues: 172 loop : -0.94 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 80 TYR 0.032 0.001 TYR K 510 PHE 0.045 0.002 PHE U 493 TRP 0.014 0.001 TRP U 35 HIS 0.008 0.001 HIS J 407 Details of bonding type rmsd covalent geometry : bond 0.00321 (40174) covalent geometry : angle 0.58222 (54219) hydrogen bonds : bond 0.03665 ( 2293) hydrogen bonds : angle 4.24212 ( 6804) metal coordination : bond 0.00790 ( 30) metal coordination : angle 2.80179 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11725.45 seconds wall clock time: 201 minutes 9.39 seconds (12069.39 seconds total)