Starting phenix.real_space_refine on Fri Mar 22 09:49:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvx_34301/03_2024/8gvx_34301_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvx_34301/03_2024/8gvx_34301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvx_34301/03_2024/8gvx_34301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvx_34301/03_2024/8gvx_34301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvx_34301/03_2024/8gvx_34301_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvx_34301/03_2024/8gvx_34301_trim.pdb" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.039 sd= 0.121 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 16 5.49 5 S 180 5.16 5 C 21284 2.51 5 N 5392 2.21 5 O 5992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 32": "OE1" <-> "OE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32872 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 5590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5590 Classifications: {'peptide': 686} Link IDs: {'PTRANS': 27, 'TRANS': 658} Chain breaks: 3 Chain: "F" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2480 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 3, 'TRANS': 301} Chain breaks: 1 Chain: "E" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2480 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 3, 'TRANS': 301} Chain breaks: 1 Chain: "G" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2480 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 3, 'TRANS': 301} Chain breaks: 1 Chain: "H" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2480 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 3, 'TRANS': 301} Chain breaks: 1 Chain: "A" Number of atoms: 5590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5590 Classifications: {'peptide': 686} Link IDs: {'PTRANS': 27, 'TRANS': 658} Chain breaks: 3 Chain: "C" Number of atoms: 5590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5590 Classifications: {'peptide': 686} Link IDs: {'PTRANS': 27, 'TRANS': 658} Chain breaks: 3 Chain: "D" Number of atoms: 5590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5590 Classifications: {'peptide': 686} Link IDs: {'PTRANS': 27, 'TRANS': 658} Chain breaks: 3 Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 116 Unusual residues: {' CA': 1, ' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 116 Unusual residues: {' CA': 1, ' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 116 Unusual residues: {' CA': 1, ' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "D" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 116 Unusual residues: {' CA': 1, ' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1274 SG CYS B 176 112.442 71.417 103.189 1.00182.40 S ATOM 1288 SG CYS B 178 114.790 73.922 101.370 1.00194.05 S ATOM 1310 SG CYS B 181 111.047 74.024 100.621 1.00194.94 S ATOM 16784 SG CYS A 176 71.403 24.636 103.176 1.00182.40 S ATOM 16798 SG CYS A 178 73.908 22.289 101.356 1.00194.05 S ATOM 16820 SG CYS A 181 74.010 26.032 100.608 1.00194.94 S ATOM 22374 SG CYS C 176 65.658 112.455 103.197 1.00182.40 S ATOM 22388 SG CYS C 178 63.154 114.804 101.378 1.00194.05 S ATOM 22410 SG CYS C 181 63.051 111.061 100.628 1.00194.94 S ATOM 27964 SG CYS D 176 24.620 65.673 103.185 1.00182.40 S ATOM 27978 SG CYS D 178 22.272 63.169 101.364 1.00194.05 S ATOM 28000 SG CYS D 181 26.015 63.067 100.615 1.00194.94 S Time building chain proxies: 17.16, per 1000 atoms: 0.52 Number of scatterers: 32872 At special positions: 0 Unit cell: (138.176, 138.176, 179.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 180 16.00 P 16 15.00 O 5992 8.00 N 5392 7.00 C 21284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 13.97 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 181 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 176 " pdb=" ZN B 803 " pdb="ZN ZN B 803 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 176 " pdb=" ZN C 803 " pdb="ZN ZN C 803 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 181 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 176 " pdb=" ZN D 803 " pdb="ZN ZN D 803 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 176 " Number of angles added : 12 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7616 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 8 sheets defined 71.0% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.940A pdb=" N GLU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.578A pdb=" N HIS B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.889A pdb=" N ARG B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 163 removed outlier: 3.618A pdb=" N ILE B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 213 removed outlier: 3.552A pdb=" N SER B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.586A pdb=" N TYR B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.551A pdb=" N PHE B 359 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 360 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 384 Processing helix chain 'B' and resid 401 through 424 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.915A pdb=" N ILE B 431 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 460 removed outlier: 3.527A pdb=" N ASP B 439 " --> pdb=" O TRP B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 499 removed outlier: 4.091A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 4.171A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 549 through 553 removed outlier: 3.693A pdb=" N ASN B 552 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS B 553 " --> pdb=" O PRO B 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 549 through 553' Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.794A pdb=" N THR B 588 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'B' and resid 615 through 650 removed outlier: 4.187A pdb=" N ASP B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE B 637 " --> pdb=" O ASP B 633 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 731 Processing helix chain 'B' and resid 740 through 761 Processing helix chain 'F' and resid 45 through 58 Processing helix chain 'F' and resid 62 through 69 removed outlier: 3.670A pdb=" N TYR F 69 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.227A pdb=" N GLY F 89 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 110 removed outlier: 3.750A pdb=" N ASP F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 132 Processing helix chain 'F' and resid 133 through 142 Processing helix chain 'F' and resid 143 through 146 Processing helix chain 'F' and resid 151 through 158 Processing helix chain 'F' and resid 158 through 163 Processing helix chain 'F' and resid 170 through 176 Processing helix chain 'F' and resid 204 through 215 removed outlier: 4.482A pdb=" N LYS F 209 " --> pdb=" O SER F 206 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS F 210 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE F 212 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS F 213 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE F 215 " --> pdb=" O ILE F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 230 No H-bonds generated for 'chain 'F' and resid 228 through 230' Processing helix chain 'F' and resid 241 through 256 Processing helix chain 'F' and resid 257 through 260 removed outlier: 3.758A pdb=" N THR F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 257 through 260' Processing helix chain 'F' and resid 270 through 279 removed outlier: 4.162A pdb=" N LYS F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 286 Processing helix chain 'F' and resid 295 through 309 Processing helix chain 'F' and resid 328 through 347 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 62 through 69 removed outlier: 3.670A pdb=" N TYR E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 4.228A pdb=" N GLY E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 110 removed outlier: 3.750A pdb=" N ASP E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 132 Processing helix chain 'E' and resid 133 through 142 Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 151 through 158 Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 170 through 176 Processing helix chain 'E' and resid 204 through 215 removed outlier: 4.482A pdb=" N LYS E 209 " --> pdb=" O SER E 206 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS E 210 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE E 212 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS E 213 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 215 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 241 through 256 Processing helix chain 'E' and resid 257 through 260 removed outlier: 3.758A pdb=" N THR E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 257 through 260' Processing helix chain 'E' and resid 270 through 279 removed outlier: 4.162A pdb=" N LYS E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 286 Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 328 through 347 Processing helix chain 'G' and resid 45 through 58 Processing helix chain 'G' and resid 62 through 69 removed outlier: 3.670A pdb=" N TYR G 69 " --> pdb=" O GLU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.228A pdb=" N GLY G 89 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG G 90 " --> pdb=" O ARG G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 110 removed outlier: 3.750A pdb=" N ASP G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 132 Processing helix chain 'G' and resid 133 through 142 Processing helix chain 'G' and resid 143 through 146 Processing helix chain 'G' and resid 151 through 158 Processing helix chain 'G' and resid 158 through 163 Processing helix chain 'G' and resid 170 through 176 Processing helix chain 'G' and resid 204 through 215 removed outlier: 4.483A pdb=" N LYS G 209 " --> pdb=" O SER G 206 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS G 210 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE G 212 " --> pdb=" O LYS G 209 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS G 213 " --> pdb=" O LYS G 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE G 215 " --> pdb=" O ILE G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 230 No H-bonds generated for 'chain 'G' and resid 228 through 230' Processing helix chain 'G' and resid 241 through 256 Processing helix chain 'G' and resid 257 through 260 removed outlier: 3.757A pdb=" N THR G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 257 through 260' Processing helix chain 'G' and resid 270 through 279 removed outlier: 4.161A pdb=" N LYS G 279 " --> pdb=" O GLU G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 286 Processing helix chain 'G' and resid 295 through 309 Processing helix chain 'G' and resid 328 through 347 Processing helix chain 'H' and resid 45 through 58 Processing helix chain 'H' and resid 62 through 69 removed outlier: 3.672A pdb=" N TYR H 69 " --> pdb=" O GLU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.228A pdb=" N GLY H 89 " --> pdb=" O ILE H 85 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG H 90 " --> pdb=" O ARG H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 removed outlier: 3.750A pdb=" N ASP H 103 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 132 Processing helix chain 'H' and resid 133 through 142 Processing helix chain 'H' and resid 143 through 146 Processing helix chain 'H' and resid 151 through 158 Processing helix chain 'H' and resid 158 through 163 Processing helix chain 'H' and resid 170 through 176 Processing helix chain 'H' and resid 204 through 215 removed outlier: 4.482A pdb=" N LYS H 209 " --> pdb=" O SER H 206 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS H 210 " --> pdb=" O GLU H 207 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE H 212 " --> pdb=" O LYS H 209 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS H 213 " --> pdb=" O LYS H 210 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE H 215 " --> pdb=" O ILE H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 230 No H-bonds generated for 'chain 'H' and resid 228 through 230' Processing helix chain 'H' and resid 241 through 256 Processing helix chain 'H' and resid 257 through 260 removed outlier: 3.759A pdb=" N THR H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 257 through 260' Processing helix chain 'H' and resid 270 through 279 removed outlier: 4.161A pdb=" N LYS H 279 " --> pdb=" O GLU H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 286 Processing helix chain 'H' and resid 295 through 309 Processing helix chain 'H' and resid 328 through 347 Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.941A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.578A pdb=" N HIS A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.888A pdb=" N ARG A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.618A pdb=" N ILE A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.552A pdb=" N SER A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.587A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.551A pdb=" N PHE A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 360 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 401 through 424 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.915A pdb=" N ILE A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 460 removed outlier: 3.528A pdb=" N ASP A 439 " --> pdb=" O TRP A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 499 removed outlier: 4.091A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 4.170A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.694A pdb=" N ASN A 552 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS A 553 " --> pdb=" O PRO A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 553' Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.794A pdb=" N THR A 588 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'A' and resid 615 through 650 removed outlier: 4.187A pdb=" N ASP A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 731 Processing helix chain 'A' and resid 740 through 761 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.940A pdb=" N GLU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.578A pdb=" N HIS C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 108 through 119 removed outlier: 3.889A pdb=" N ARG C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 removed outlier: 3.618A pdb=" N ILE C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 213 removed outlier: 3.552A pdb=" N SER C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.586A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 339 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.551A pdb=" N PHE C 359 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 360 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 384 Processing helix chain 'C' and resid 401 through 424 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.915A pdb=" N ILE C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 460 removed outlier: 3.527A pdb=" N ASP C 439 " --> pdb=" O TRP C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 499 removed outlier: 4.091A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 4.170A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.693A pdb=" N ASN C 552 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS C 553 " --> pdb=" O PRO C 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 549 through 553' Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 585 through 589 removed outlier: 3.794A pdb=" N THR C 588 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'C' and resid 615 through 650 removed outlier: 4.188A pdb=" N ASP C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP C 636 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE C 637 " --> pdb=" O ASP C 633 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 649 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 731 Processing helix chain 'C' and resid 740 through 761 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.940A pdb=" N GLU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.579A pdb=" N HIS D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.888A pdb=" N ARG D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.618A pdb=" N ILE D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 213 removed outlier: 3.552A pdb=" N SER D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.587A pdb=" N TYR D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 339 Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.551A pdb=" N PHE D 359 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE D 360 " --> pdb=" O GLY D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 384 Processing helix chain 'D' and resid 401 through 424 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 426 through 431 removed outlier: 3.915A pdb=" N ILE D 431 " --> pdb=" O PHE D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 460 removed outlier: 3.527A pdb=" N ASP D 439 " --> pdb=" O TRP D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 499 removed outlier: 4.092A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 4.170A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 549 through 553 removed outlier: 3.692A pdb=" N ASN D 552 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS D 553 " --> pdb=" O PRO D 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 549 through 553' Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 585 through 589 removed outlier: 3.794A pdb=" N THR D 588 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 615 Processing helix chain 'D' and resid 615 through 650 removed outlier: 4.187A pdb=" N ASP D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE D 637 " --> pdb=" O ASP D 633 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER D 649 " --> pdb=" O LYS D 645 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 731 Processing helix chain 'D' and resid 740 through 761 Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 168 Processing sheet with id=AA3, first strand: chain 'F' and resid 184 through 191 removed outlier: 6.408A pdb=" N VAL F 34 " --> pdb=" O LYS F 197 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE F 199 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU F 36 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL F 201 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS F 35 " --> pdb=" O ALA F 220 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE F 222 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU F 37 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N CYS F 224 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU F 39 " --> pdb=" O CYS F 224 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ALA F 226 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE F 264 " --> pdb=" O TYR F 320 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N HIS F 322 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU F 266 " --> pdb=" O HIS F 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 184 through 191 removed outlier: 6.407A pdb=" N VAL E 34 " --> pdb=" O LYS E 197 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE E 199 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU E 36 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL E 201 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU E 38 " --> pdb=" O VAL E 201 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS E 35 " --> pdb=" O ALA E 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE E 222 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU E 37 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N CYS E 224 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU E 39 " --> pdb=" O CYS E 224 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ALA E 226 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE E 264 " --> pdb=" O TYR E 320 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N HIS E 322 " --> pdb=" O ILE E 264 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU E 266 " --> pdb=" O HIS E 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 184 through 191 removed outlier: 6.408A pdb=" N VAL G 34 " --> pdb=" O LYS G 197 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE G 199 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU G 36 " --> pdb=" O PHE G 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL G 201 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU G 38 " --> pdb=" O VAL G 201 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS G 35 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE G 222 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU G 37 " --> pdb=" O ILE G 222 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N CYS G 224 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU G 39 " --> pdb=" O CYS G 224 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ALA G 226 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE G 264 " --> pdb=" O TYR G 320 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N HIS G 322 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU G 266 " --> pdb=" O HIS G 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 184 through 191 removed outlier: 6.407A pdb=" N VAL H 34 " --> pdb=" O LYS H 197 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE H 199 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU H 36 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL H 201 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU H 38 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS H 35 " --> pdb=" O ALA H 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE H 222 " --> pdb=" O LYS H 35 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU H 37 " --> pdb=" O ILE H 222 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N CYS H 224 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU H 39 " --> pdb=" O CYS H 224 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ALA H 226 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE H 264 " --> pdb=" O TYR H 320 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N HIS H 322 " --> pdb=" O ILE H 264 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU H 266 " --> pdb=" O HIS H 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 167 through 168 Processing sheet with id=AA8, first strand: chain 'C' and resid 18 through 19 1916 hydrogen bonds defined for protein. 5556 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: 11.18 Time building geometry restraints manager: 15.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5670 1.32 - 1.45: 8799 1.45 - 1.58: 18751 1.58 - 1.70: 76 1.70 - 1.83: 284 Bond restraints: 33580 Sorted by residual: bond pdb=" C SER E 263 " pdb=" N ILE E 264 " ideal model delta sigma weight residual 1.329 1.448 -0.120 1.31e-02 5.83e+03 8.33e+01 bond pdb=" C SER F 263 " pdb=" N ILE F 264 " ideal model delta sigma weight residual 1.329 1.448 -0.119 1.31e-02 5.83e+03 8.30e+01 bond pdb=" C SER G 263 " pdb=" N ILE G 264 " ideal model delta sigma weight residual 1.329 1.448 -0.119 1.31e-02 5.83e+03 8.29e+01 bond pdb=" C SER H 263 " pdb=" N ILE H 264 " ideal model delta sigma weight residual 1.329 1.448 -0.119 1.31e-02 5.83e+03 8.25e+01 bond pdb=" CA VAL E 50 " pdb=" CB VAL E 50 " ideal model delta sigma weight residual 1.540 1.597 -0.057 1.25e-02 6.40e+03 2.07e+01 ... (remaining 33575 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.43: 856 106.43 - 113.40: 17908 113.40 - 120.37: 13408 120.37 - 127.33: 12907 127.33 - 134.30: 345 Bond angle restraints: 45424 Sorted by residual: angle pdb=" C ASP H 133 " pdb=" N GLY H 134 " pdb=" CA GLY H 134 " ideal model delta sigma weight residual 120.00 111.74 8.26 1.10e+00 8.26e-01 5.64e+01 angle pdb=" C ASP F 133 " pdb=" N GLY F 134 " pdb=" CA GLY F 134 " ideal model delta sigma weight residual 120.00 111.75 8.25 1.10e+00 8.26e-01 5.63e+01 angle pdb=" C ASP E 133 " pdb=" N GLY E 134 " pdb=" CA GLY E 134 " ideal model delta sigma weight residual 120.00 111.79 8.21 1.10e+00 8.26e-01 5.58e+01 angle pdb=" O ASP H 133 " pdb=" C ASP H 133 " pdb=" N GLY H 134 " ideal model delta sigma weight residual 122.86 131.66 -8.80 1.18e+00 7.18e-01 5.56e+01 angle pdb=" C ASP G 133 " pdb=" N GLY G 134 " pdb=" CA GLY G 134 " ideal model delta sigma weight residual 120.00 111.80 8.20 1.10e+00 8.26e-01 5.56e+01 ... (remaining 45419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 19888 35.30 - 70.60: 440 70.60 - 105.89: 24 105.89 - 141.19: 28 141.19 - 176.49: 12 Dihedral angle restraints: 20392 sinusoidal: 8668 harmonic: 11724 Sorted by residual: dihedral pdb=" CB CYS A 553 " pdb=" SG CYS A 553 " pdb=" SG CYS A 558 " pdb=" CB CYS A 558 " ideal model delta sinusoidal sigma weight residual 93.00 152.35 -59.35 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CB CYS D 553 " pdb=" SG CYS D 553 " pdb=" SG CYS D 558 " pdb=" CB CYS D 558 " ideal model delta sinusoidal sigma weight residual 93.00 152.35 -59.35 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CB CYS B 553 " pdb=" SG CYS B 553 " pdb=" SG CYS B 558 " pdb=" CB CYS B 558 " ideal model delta sinusoidal sigma weight residual 93.00 152.35 -59.35 1 1.00e+01 1.00e-02 4.71e+01 ... (remaining 20389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4276 0.077 - 0.155: 658 0.155 - 0.232: 126 0.232 - 0.309: 16 0.309 - 0.387: 12 Chirality restraints: 5088 Sorted by residual: chirality pdb=" CA GLU G 58 " pdb=" N GLU G 58 " pdb=" C GLU G 58 " pdb=" CB GLU G 58 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CA GLU H 58 " pdb=" N GLU H 58 " pdb=" C GLU H 58 " pdb=" CB GLU H 58 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CA GLU E 58 " pdb=" N GLU E 58 " pdb=" C GLU E 58 " pdb=" CB GLU E 58 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 5085 not shown) Planarity restraints: 5644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 743 " 0.034 2.00e-02 2.50e+03 6.05e-02 6.41e+01 pdb=" CG PHE A 743 " -0.133 2.00e-02 2.50e+03 pdb=" CD1 PHE A 743 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE A 743 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 PHE A 743 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 743 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 743 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 743 " -0.033 2.00e-02 2.50e+03 6.05e-02 6.40e+01 pdb=" CG PHE C 743 " 0.133 2.00e-02 2.50e+03 pdb=" CD1 PHE C 743 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 PHE C 743 " -0.068 2.00e-02 2.50e+03 pdb=" CE1 PHE C 743 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE C 743 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 743 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 743 " -0.034 2.00e-02 2.50e+03 6.05e-02 6.40e+01 pdb=" CG PHE B 743 " 0.133 2.00e-02 2.50e+03 pdb=" CD1 PHE B 743 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE B 743 " -0.067 2.00e-02 2.50e+03 pdb=" CE1 PHE B 743 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 743 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE B 743 " 0.006 2.00e-02 2.50e+03 ... (remaining 5641 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 989 2.72 - 3.26: 33980 3.26 - 3.81: 53043 3.81 - 4.35: 67339 4.35 - 4.90: 112320 Nonbonded interactions: 267671 Sorted by model distance: nonbonded pdb=" OE1 GLN B 537 " pdb=" OG SER C 385 " model vdw 2.173 2.440 nonbonded pdb=" OG SER B 385 " pdb=" OE1 GLN A 537 " model vdw 2.174 2.440 nonbonded pdb=" OE1 GLN C 537 " pdb=" OG SER D 385 " model vdw 2.175 2.440 nonbonded pdb=" OG SER A 385 " pdb=" OE1 GLN D 537 " model vdw 2.175 2.440 nonbonded pdb=" O ILE C 209 " pdb=" OG SER C 213 " model vdw 2.199 2.440 ... (remaining 267666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.630 Check model and map are aligned: 0.480 Set scattering table: 0.310 Process input model: 90.680 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.200 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 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 : 0.008 0.120 33580 Z= 0.534 Angle : 1.010 14.076 45424 Z= 0.617 Chirality : 0.061 0.387 5088 Planarity : 0.006 0.067 5644 Dihedral : 16.267 176.489 12764 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.68 % Allowed : 2.37 % Favored : 96.96 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.11), residues: 3916 helix: -0.45 (0.08), residues: 2552 sheet: -1.41 (0.48), residues: 116 loop : -0.68 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 416 HIS 0.007 0.001 HIS H 322 PHE 0.133 0.003 PHE A 743 TYR 0.024 0.003 TYR H 155 ARG 0.023 0.001 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 204 time to evaluate : 4.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 MET cc_start: 0.7805 (mmp) cc_final: 0.7327 (mmm) REVERT: B 344 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7379 (tp) REVERT: B 743 PHE cc_start: 0.7836 (m-10) cc_final: 0.7478 (m-80) REVERT: F 243 MET cc_start: 0.7828 (tpp) cc_final: 0.7376 (tpp) REVERT: F 247 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8387 (mtt) REVERT: G 247 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8392 (mtt) REVERT: H 243 MET cc_start: 0.7783 (tpp) cc_final: 0.6963 (tpp) REVERT: H 247 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8351 (mtt) REVERT: A 335 MET cc_start: 0.7776 (mmp) cc_final: 0.7374 (mmm) REVERT: A 344 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7420 (tp) REVERT: A 437 LEU cc_start: 0.8304 (mt) cc_final: 0.8098 (tt) REVERT: A 524 TYR cc_start: 0.8634 (t80) cc_final: 0.8430 (t80) REVERT: A 648 MET cc_start: 0.9225 (mtm) cc_final: 0.8979 (mtm) REVERT: A 743 PHE cc_start: 0.7974 (m-10) cc_final: 0.7575 (m-80) REVERT: C 319 PHE cc_start: 0.9095 (m-80) cc_final: 0.8793 (m-10) REVERT: C 335 MET cc_start: 0.7847 (mmp) cc_final: 0.7351 (mmm) REVERT: C 524 TYR cc_start: 0.8645 (t80) cc_final: 0.8329 (t80) REVERT: C 603 THR cc_start: 0.8929 (m) cc_final: 0.8516 (p) REVERT: C 648 MET cc_start: 0.9236 (mtm) cc_final: 0.9017 (mtp) REVERT: C 743 PHE cc_start: 0.7965 (m-10) cc_final: 0.7625 (m-80) REVERT: D 335 MET cc_start: 0.7807 (mmp) cc_final: 0.7392 (mmm) REVERT: D 344 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7401 (tp) REVERT: D 437 LEU cc_start: 0.8329 (mt) cc_final: 0.8122 (tt) REVERT: D 524 TYR cc_start: 0.8665 (t80) cc_final: 0.8214 (t80) REVERT: D 743 PHE cc_start: 0.7883 (m-10) cc_final: 0.7525 (m-80) outliers start: 24 outliers final: 5 residues processed: 224 average time/residue: 0.4857 time to fit residues: 173.0400 Evaluate side-chains 147 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 247 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 7.9990 chunk 297 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 307 optimal weight: 8.9990 chunk 118 optimal weight: 0.0020 chunk 186 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 355 optimal weight: 0.0670 overall best weight: 2.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN B 634 HIS F 306 GLN E 306 GLN G 306 GLN H 306 GLN A 443 ASN A 533 ASN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN A 634 HIS A 709 GLN C 443 ASN C 533 ASN ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN C 634 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN D 533 ASN ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 GLN D 634 HIS D 709 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33580 Z= 0.218 Angle : 0.551 10.357 45424 Z= 0.291 Chirality : 0.039 0.137 5088 Planarity : 0.004 0.046 5644 Dihedral : 13.331 166.917 4934 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.54 % Allowed : 5.47 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.13), residues: 3916 helix: 1.58 (0.10), residues: 2596 sheet: -1.09 (0.41), residues: 152 loop : -0.23 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 327 HIS 0.005 0.001 HIS B 634 PHE 0.013 0.001 PHE H 196 TYR 0.017 0.001 TYR C 524 ARG 0.006 0.000 ARG H 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 3.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 MET cc_start: 0.7949 (mmp) cc_final: 0.7602 (mmm) REVERT: B 380 MET cc_start: 0.9109 (mmm) cc_final: 0.8794 (tpp) REVERT: B 406 MET cc_start: 0.8746 (ppp) cc_final: 0.8113 (ppp) REVERT: B 634 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8040 (m90) REVERT: F 243 MET cc_start: 0.8155 (tpp) cc_final: 0.7869 (tpp) REVERT: E 187 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7006 (m) REVERT: G 310 LEU cc_start: 0.7649 (mt) cc_final: 0.6762 (mt) REVERT: H 187 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.5666 (m) REVERT: H 310 LEU cc_start: 0.7660 (mt) cc_final: 0.6779 (mt) REVERT: A 335 MET cc_start: 0.7929 (mmp) cc_final: 0.7574 (mmm) REVERT: A 380 MET cc_start: 0.9103 (mmm) cc_final: 0.8847 (tpp) REVERT: A 406 MET cc_start: 0.8765 (ppp) cc_final: 0.8074 (ppp) REVERT: A 437 LEU cc_start: 0.8492 (mt) cc_final: 0.8284 (tt) REVERT: C 319 PHE cc_start: 0.9095 (m-80) cc_final: 0.8781 (m-10) REVERT: C 335 MET cc_start: 0.7978 (mmp) cc_final: 0.7655 (mmm) REVERT: C 336 THR cc_start: 0.9248 (t) cc_final: 0.8983 (p) REVERT: D 319 PHE cc_start: 0.9099 (m-80) cc_final: 0.8776 (m-10) REVERT: D 335 MET cc_start: 0.7947 (mmp) cc_final: 0.7596 (mmm) REVERT: D 344 LEU cc_start: 0.7935 (tp) cc_final: 0.7500 (tp) REVERT: D 437 LEU cc_start: 0.8437 (mt) cc_final: 0.8218 (tt) outliers start: 19 outliers final: 9 residues processed: 166 average time/residue: 0.4154 time to fit residues: 118.7387 Evaluate side-chains 156 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain D residue 604 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 296 optimal weight: 5.9990 chunk 242 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 356 optimal weight: 7.9990 chunk 385 optimal weight: 5.9990 chunk 317 optimal weight: 3.9990 chunk 353 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 286 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33580 Z= 0.245 Angle : 0.537 7.475 45424 Z= 0.282 Chirality : 0.038 0.128 5088 Planarity : 0.004 0.040 5644 Dihedral : 12.554 179.094 4908 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.48 % Allowed : 7.38 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.14), residues: 3916 helix: 2.09 (0.10), residues: 2604 sheet: -0.79 (0.38), residues: 172 loop : -0.24 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 327 HIS 0.040 0.001 HIS B 634 PHE 0.026 0.002 PHE A 341 TYR 0.017 0.001 TYR C 524 ARG 0.004 0.000 ARG H 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 4.362 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: B 335 MET cc_start: 0.8132 (mmp) cc_final: 0.7648 (mmm) REVERT: B 344 LEU cc_start: 0.7772 (tp) cc_final: 0.7270 (tp) REVERT: B 380 MET cc_start: 0.9090 (mmm) cc_final: 0.8060 (tpp) REVERT: B 437 LEU cc_start: 0.8434 (mt) cc_final: 0.8211 (tt) REVERT: B 743 PHE cc_start: 0.8713 (m-80) cc_final: 0.8463 (t80) REVERT: F 243 MET cc_start: 0.8234 (tpp) cc_final: 0.7341 (tpp) REVERT: H 243 MET cc_start: 0.8232 (tpp) cc_final: 0.7482 (tpp) REVERT: A 49 LYS cc_start: 0.9278 (tttt) cc_final: 0.9039 (ttpt) REVERT: A 335 MET cc_start: 0.8065 (mmp) cc_final: 0.7608 (mmm) REVERT: A 344 LEU cc_start: 0.7842 (tp) cc_final: 0.7337 (tp) REVERT: A 380 MET cc_start: 0.9110 (mmm) cc_final: 0.8158 (tpp) REVERT: A 743 PHE cc_start: 0.8732 (m-80) cc_final: 0.8403 (t80) REVERT: C 319 PHE cc_start: 0.9105 (m-80) cc_final: 0.8833 (m-10) REVERT: C 335 MET cc_start: 0.8137 (mmp) cc_final: 0.7717 (mmm) REVERT: C 336 THR cc_start: 0.9287 (t) cc_final: 0.9050 (p) REVERT: C 344 LEU cc_start: 0.7796 (tp) cc_final: 0.7301 (tp) REVERT: C 380 MET cc_start: 0.9091 (mmm) cc_final: 0.8248 (tpt) REVERT: C 406 MET cc_start: 0.8570 (ppp) cc_final: 0.7987 (ppp) REVERT: C 743 PHE cc_start: 0.8772 (m-80) cc_final: 0.8431 (t80) REVERT: D 319 PHE cc_start: 0.9104 (m-80) cc_final: 0.8823 (m-10) REVERT: D 335 MET cc_start: 0.8108 (mmp) cc_final: 0.7635 (mmm) REVERT: D 344 LEU cc_start: 0.7861 (tp) cc_final: 0.7432 (tp) REVERT: D 437 LEU cc_start: 0.8540 (mt) cc_final: 0.8330 (tt) REVERT: D 743 PHE cc_start: 0.8756 (m-80) cc_final: 0.8452 (t80) outliers start: 17 outliers final: 13 residues processed: 171 average time/residue: 0.4350 time to fit residues: 125.4335 Evaluate side-chains 159 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 3.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 613 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 9.9990 chunk 268 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 239 optimal weight: 4.9990 chunk 357 optimal weight: 7.9990 chunk 378 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 339 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 634 HIS ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 33580 Z= 0.296 Angle : 0.600 8.091 45424 Z= 0.311 Chirality : 0.040 0.180 5088 Planarity : 0.004 0.042 5644 Dihedral : 10.674 150.131 4908 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.85 % Allowed : 8.82 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.14), residues: 3916 helix: 2.17 (0.10), residues: 2616 sheet: -0.88 (0.37), residues: 172 loop : -0.38 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 327 HIS 0.011 0.001 HIS B 326 PHE 0.020 0.002 PHE A 379 TYR 0.021 0.001 TYR D 118 ARG 0.005 0.001 ARG H 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 4.063 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: B 335 MET cc_start: 0.8200 (mmp) cc_final: 0.7754 (mmm) REVERT: B 336 THR cc_start: 0.9352 (t) cc_final: 0.9130 (p) REVERT: B 344 LEU cc_start: 0.7816 (tp) cc_final: 0.7331 (tp) REVERT: B 380 MET cc_start: 0.9092 (mmm) cc_final: 0.7898 (tpp) REVERT: B 437 LEU cc_start: 0.8593 (mt) cc_final: 0.8381 (tt) REVERT: B 619 MET cc_start: 0.8340 (tmm) cc_final: 0.7960 (tmm) REVERT: B 743 PHE cc_start: 0.8825 (m-80) cc_final: 0.8511 (t80) REVERT: F 243 MET cc_start: 0.8031 (tpp) cc_final: 0.7551 (tpp) REVERT: G 243 MET cc_start: 0.8186 (tpp) cc_final: 0.7797 (tpp) REVERT: H 243 MET cc_start: 0.8043 (tpp) cc_final: 0.7755 (tpp) REVERT: A 49 LYS cc_start: 0.9274 (tttt) cc_final: 0.9024 (ttpt) REVERT: A 324 ARG cc_start: 0.8221 (mtt180) cc_final: 0.7684 (mtm180) REVERT: A 335 MET cc_start: 0.8154 (mmp) cc_final: 0.7763 (mmm) REVERT: A 336 THR cc_start: 0.9289 (t) cc_final: 0.9056 (p) REVERT: A 344 LEU cc_start: 0.7878 (tp) cc_final: 0.7406 (tp) REVERT: A 380 MET cc_start: 0.9050 (mmm) cc_final: 0.7977 (tpp) REVERT: A 619 MET cc_start: 0.8367 (tmm) cc_final: 0.8017 (tmm) REVERT: A 743 PHE cc_start: 0.8818 (m-80) cc_final: 0.8435 (t80) REVERT: C 319 PHE cc_start: 0.9123 (m-80) cc_final: 0.8917 (m-10) REVERT: C 335 MET cc_start: 0.8194 (mmp) cc_final: 0.7785 (mmp) REVERT: C 336 THR cc_start: 0.9298 (t) cc_final: 0.9074 (p) REVERT: C 344 LEU cc_start: 0.7996 (tp) cc_final: 0.7494 (tp) REVERT: C 380 MET cc_start: 0.9100 (mmm) cc_final: 0.8746 (tpp) REVERT: C 406 MET cc_start: 0.8424 (ppp) cc_final: 0.7888 (ppp) REVERT: C 603 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8929 (t) REVERT: C 619 MET cc_start: 0.8373 (tmm) cc_final: 0.7869 (tmm) REVERT: C 743 PHE cc_start: 0.8869 (m-80) cc_final: 0.8513 (t80) REVERT: D 319 PHE cc_start: 0.9140 (m-80) cc_final: 0.8913 (m-10) REVERT: D 335 MET cc_start: 0.8162 (mmp) cc_final: 0.7744 (mmm) REVERT: D 344 LEU cc_start: 0.8005 (tp) cc_final: 0.7505 (tp) REVERT: D 380 MET cc_start: 0.9124 (mmm) cc_final: 0.7943 (tpp) REVERT: D 743 PHE cc_start: 0.8851 (m-80) cc_final: 0.8501 (t80) outliers start: 30 outliers final: 11 residues processed: 183 average time/residue: 0.4232 time to fit residues: 131.8483 Evaluate side-chains 160 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 4.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 613 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 282 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 4.9990 chunk 340 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 634 HIS A 297 HIS ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN D 297 HIS ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33580 Z= 0.184 Angle : 0.511 8.074 45424 Z= 0.263 Chirality : 0.037 0.175 5088 Planarity : 0.003 0.037 5644 Dihedral : 10.327 143.260 4908 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.42 % Allowed : 9.81 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.14), residues: 3916 helix: 2.34 (0.10), residues: 2628 sheet: -0.39 (0.39), residues: 160 loop : -0.23 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 327 HIS 0.004 0.001 HIS B 634 PHE 0.030 0.001 PHE C 341 TYR 0.016 0.001 TYR D 524 ARG 0.003 0.000 ARG H 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 3.749 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: B 131 MET cc_start: 0.7288 (tpp) cc_final: 0.7050 (tpt) REVERT: B 335 MET cc_start: 0.8171 (mmp) cc_final: 0.7763 (mmm) REVERT: B 336 THR cc_start: 0.9321 (t) cc_final: 0.9095 (p) REVERT: B 344 LEU cc_start: 0.7756 (tp) cc_final: 0.7191 (tp) REVERT: B 380 MET cc_start: 0.9133 (mmm) cc_final: 0.8050 (tpp) REVERT: B 437 LEU cc_start: 0.8533 (mt) cc_final: 0.8318 (tt) REVERT: B 619 MET cc_start: 0.8233 (tmm) cc_final: 0.7819 (tmm) REVERT: B 743 PHE cc_start: 0.8795 (m-80) cc_final: 0.8448 (t80) REVERT: F 243 MET cc_start: 0.7623 (tpp) cc_final: 0.6947 (tpp) REVERT: G 243 MET cc_start: 0.8139 (tpp) cc_final: 0.7182 (tpp) REVERT: H 243 MET cc_start: 0.8102 (tpp) cc_final: 0.7185 (tpp) REVERT: A 335 MET cc_start: 0.8187 (mmp) cc_final: 0.7833 (mmm) REVERT: A 336 THR cc_start: 0.9268 (t) cc_final: 0.9035 (p) REVERT: A 344 LEU cc_start: 0.7639 (tp) cc_final: 0.7079 (tp) REVERT: A 380 MET cc_start: 0.9066 (mmm) cc_final: 0.8045 (tpp) REVERT: A 442 MET cc_start: 0.8736 (ttm) cc_final: 0.8521 (ttm) REVERT: A 619 MET cc_start: 0.8138 (tmm) cc_final: 0.7836 (tmm) REVERT: A 743 PHE cc_start: 0.8797 (m-80) cc_final: 0.8534 (t80) REVERT: C 335 MET cc_start: 0.8127 (mmp) cc_final: 0.7705 (mmp) REVERT: C 336 THR cc_start: 0.9259 (t) cc_final: 0.9028 (p) REVERT: C 344 LEU cc_start: 0.7722 (tp) cc_final: 0.7157 (tp) REVERT: C 380 MET cc_start: 0.9074 (mmm) cc_final: 0.7914 (tpp) REVERT: C 613 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8753 (mm) REVERT: C 619 MET cc_start: 0.8184 (tmm) cc_final: 0.7650 (tmm) REVERT: D 335 MET cc_start: 0.8117 (mmp) cc_final: 0.7712 (mmm) REVERT: D 336 THR cc_start: 0.9318 (t) cc_final: 0.9089 (p) REVERT: D 344 LEU cc_start: 0.7760 (tp) cc_final: 0.7207 (tp) REVERT: D 380 MET cc_start: 0.9124 (mmm) cc_final: 0.8007 (tpp) REVERT: D 524 TYR cc_start: 0.8648 (t80) cc_final: 0.8306 (t80) REVERT: D 619 MET cc_start: 0.8263 (tmm) cc_final: 0.7889 (tmm) outliers start: 15 outliers final: 9 residues processed: 173 average time/residue: 0.4227 time to fit residues: 124.8924 Evaluate side-chains 161 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 613 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 2.9990 chunk 341 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 379 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 125 optimal weight: 0.5980 chunk 199 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN C 247 GLN ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33580 Z= 0.195 Angle : 0.514 8.246 45424 Z= 0.263 Chirality : 0.038 0.134 5088 Planarity : 0.003 0.036 5644 Dihedral : 9.789 143.448 4908 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.51 % Allowed : 10.51 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.14), residues: 3916 helix: 2.44 (0.10), residues: 2624 sheet: -0.59 (0.38), residues: 172 loop : -0.11 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 327 HIS 0.003 0.001 HIS D 594 PHE 0.027 0.001 PHE B 341 TYR 0.014 0.001 TYR D 524 ARG 0.003 0.000 ARG B 730 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 3.872 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: B 86 MET cc_start: 0.8835 (ttm) cc_final: 0.8555 (mmt) REVERT: B 335 MET cc_start: 0.8185 (mmp) cc_final: 0.7787 (mmm) REVERT: B 336 THR cc_start: 0.9319 (t) cc_final: 0.9084 (p) REVERT: B 344 LEU cc_start: 0.7561 (tp) cc_final: 0.6978 (tp) REVERT: B 380 MET cc_start: 0.9113 (mmm) cc_final: 0.7921 (tpp) REVERT: B 437 LEU cc_start: 0.8553 (mt) cc_final: 0.8328 (tt) REVERT: B 619 MET cc_start: 0.8190 (tmm) cc_final: 0.7263 (tmm) REVERT: B 623 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.9035 (ttp) REVERT: F 243 MET cc_start: 0.7630 (tpp) cc_final: 0.7091 (tpp) REVERT: G 243 MET cc_start: 0.7871 (tpp) cc_final: 0.7421 (tpp) REVERT: H 243 MET cc_start: 0.7913 (tpp) cc_final: 0.7283 (tpp) REVERT: A 335 MET cc_start: 0.8226 (mmp) cc_final: 0.7861 (mmm) REVERT: A 336 THR cc_start: 0.9272 (t) cc_final: 0.9025 (p) REVERT: A 344 LEU cc_start: 0.7600 (tp) cc_final: 0.6993 (tp) REVERT: A 380 MET cc_start: 0.9078 (mmm) cc_final: 0.8063 (tpp) REVERT: A 619 MET cc_start: 0.8160 (tmm) cc_final: 0.7840 (tmm) REVERT: C 335 MET cc_start: 0.7961 (mmp) cc_final: 0.7560 (mmp) REVERT: C 336 THR cc_start: 0.9271 (t) cc_final: 0.9037 (p) REVERT: C 344 LEU cc_start: 0.7626 (tp) cc_final: 0.7056 (tp) REVERT: C 380 MET cc_start: 0.9094 (mmm) cc_final: 0.7911 (tpp) REVERT: C 613 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8737 (mm) REVERT: C 619 MET cc_start: 0.8131 (tmm) cc_final: 0.7573 (tmm) REVERT: C 743 PHE cc_start: 0.8816 (m-80) cc_final: 0.8508 (t80) REVERT: D 335 MET cc_start: 0.8180 (mmp) cc_final: 0.7762 (mmm) REVERT: D 336 THR cc_start: 0.9328 (t) cc_final: 0.9093 (p) REVERT: D 344 LEU cc_start: 0.7559 (tp) cc_final: 0.7032 (tp) REVERT: D 380 MET cc_start: 0.9107 (mmm) cc_final: 0.8016 (tpp) REVERT: D 619 MET cc_start: 0.8282 (tmm) cc_final: 0.7891 (tmm) REVERT: D 743 PHE cc_start: 0.8787 (m-80) cc_final: 0.8435 (t80) outliers start: 18 outliers final: 8 residues processed: 172 average time/residue: 0.4211 time to fit residues: 123.2577 Evaluate side-chains 162 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 152 time to evaluate : 4.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 613 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 276 optimal weight: 7.9990 chunk 214 optimal weight: 9.9990 chunk 319 optimal weight: 0.4980 chunk 211 optimal weight: 4.9990 chunk 377 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 230 optimal weight: 4.9990 chunk 174 optimal weight: 0.3980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33580 Z= 0.210 Angle : 0.526 8.941 45424 Z= 0.268 Chirality : 0.038 0.167 5088 Planarity : 0.003 0.037 5644 Dihedral : 9.711 143.749 4908 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.62 % Allowed : 10.85 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.14), residues: 3916 helix: 2.44 (0.10), residues: 2624 sheet: -0.55 (0.38), residues: 172 loop : -0.06 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.003 0.001 HIS D 594 PHE 0.032 0.001 PHE B 341 TYR 0.016 0.001 TYR D 118 ARG 0.006 0.000 ARG G 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 4.016 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: B 335 MET cc_start: 0.8234 (mmp) cc_final: 0.7733 (mmm) REVERT: B 336 THR cc_start: 0.9318 (t) cc_final: 0.9081 (p) REVERT: B 344 LEU cc_start: 0.7464 (tp) cc_final: 0.6895 (tp) REVERT: B 380 MET cc_start: 0.9116 (mmm) cc_final: 0.7999 (tpp) REVERT: B 437 LEU cc_start: 0.8619 (mt) cc_final: 0.8380 (tt) REVERT: B 619 MET cc_start: 0.8198 (tmm) cc_final: 0.7753 (tmm) REVERT: B 743 PHE cc_start: 0.8836 (m-80) cc_final: 0.8445 (t80) REVERT: F 243 MET cc_start: 0.7572 (tpp) cc_final: 0.6974 (tpp) REVERT: E 247 MET cc_start: 0.8796 (tpt) cc_final: 0.7973 (tmm) REVERT: G 243 MET cc_start: 0.7938 (tpp) cc_final: 0.7437 (tpp) REVERT: H 243 MET cc_start: 0.7633 (tpp) cc_final: 0.7168 (tpp) REVERT: A 335 MET cc_start: 0.8207 (mmp) cc_final: 0.7850 (mmm) REVERT: A 336 THR cc_start: 0.9250 (t) cc_final: 0.9001 (p) REVERT: A 344 LEU cc_start: 0.7570 (tp) cc_final: 0.6985 (tp) REVERT: A 380 MET cc_start: 0.9083 (mmm) cc_final: 0.8049 (tpp) REVERT: A 619 MET cc_start: 0.8149 (tmm) cc_final: 0.7803 (tmm) REVERT: A 743 PHE cc_start: 0.8787 (m-80) cc_final: 0.8417 (t80) REVERT: C 144 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8793 (p) REVERT: C 147 MET cc_start: 0.8427 (ptp) cc_final: 0.8219 (ptt) REVERT: C 335 MET cc_start: 0.8005 (mmp) cc_final: 0.7579 (mmp) REVERT: C 336 THR cc_start: 0.9277 (t) cc_final: 0.9040 (p) REVERT: C 344 LEU cc_start: 0.7506 (tp) cc_final: 0.6933 (tp) REVERT: C 380 MET cc_start: 0.9101 (mmm) cc_final: 0.7946 (tpp) REVERT: C 406 MET cc_start: 0.8689 (ppp) cc_final: 0.8443 (ppp) REVERT: C 613 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8699 (mm) REVERT: C 619 MET cc_start: 0.8059 (tmm) cc_final: 0.7581 (tmm) REVERT: C 743 PHE cc_start: 0.8888 (m-80) cc_final: 0.8530 (t80) REVERT: D 144 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8713 (p) REVERT: D 335 MET cc_start: 0.8007 (mmp) cc_final: 0.7529 (mmm) REVERT: D 336 THR cc_start: 0.9315 (t) cc_final: 0.9083 (p) REVERT: D 344 LEU cc_start: 0.7628 (tp) cc_final: 0.7054 (tp) REVERT: D 380 MET cc_start: 0.9104 (mmm) cc_final: 0.7963 (tpp) REVERT: D 619 MET cc_start: 0.8270 (tmm) cc_final: 0.7864 (tmm) REVERT: D 743 PHE cc_start: 0.8832 (m-80) cc_final: 0.8482 (t80) outliers start: 22 outliers final: 9 residues processed: 178 average time/residue: 0.4338 time to fit residues: 132.4139 Evaluate side-chains 162 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 3.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 144 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 225 optimal weight: 0.0170 chunk 113 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33580 Z= 0.201 Angle : 0.530 11.111 45424 Z= 0.269 Chirality : 0.038 0.218 5088 Planarity : 0.003 0.037 5644 Dihedral : 9.649 144.111 4908 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.51 % Allowed : 10.96 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.14), residues: 3916 helix: 2.45 (0.10), residues: 2624 sheet: -0.51 (0.38), residues: 172 loop : 0.00 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 327 HIS 0.005 0.001 HIS G 244 PHE 0.031 0.001 PHE A 341 TYR 0.013 0.001 TYR D 524 ARG 0.003 0.000 ARG E 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 4.282 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: B 335 MET cc_start: 0.8126 (mmp) cc_final: 0.7660 (mmm) REVERT: B 336 THR cc_start: 0.9318 (t) cc_final: 0.9089 (p) REVERT: B 380 MET cc_start: 0.9134 (mmm) cc_final: 0.7994 (tpp) REVERT: B 437 LEU cc_start: 0.8609 (mt) cc_final: 0.8384 (tt) REVERT: B 619 MET cc_start: 0.8168 (tmm) cc_final: 0.7688 (tmm) REVERT: B 743 PHE cc_start: 0.8816 (m-80) cc_final: 0.8393 (t80) REVERT: F 243 MET cc_start: 0.7562 (tpp) cc_final: 0.6910 (tpp) REVERT: E 247 MET cc_start: 0.8764 (tpt) cc_final: 0.7989 (tmm) REVERT: G 243 MET cc_start: 0.7839 (tpp) cc_final: 0.7229 (tpp) REVERT: G 247 MET cc_start: 0.8032 (mtm) cc_final: 0.7642 (mtm) REVERT: H 243 MET cc_start: 0.7658 (tpp) cc_final: 0.7039 (tpp) REVERT: A 335 MET cc_start: 0.8219 (mmp) cc_final: 0.7862 (mmm) REVERT: A 336 THR cc_start: 0.9248 (t) cc_final: 0.9007 (p) REVERT: A 380 MET cc_start: 0.9087 (mmm) cc_final: 0.8077 (tpp) REVERT: A 619 MET cc_start: 0.8144 (tmm) cc_final: 0.7796 (tmm) REVERT: A 743 PHE cc_start: 0.8801 (m-80) cc_final: 0.8369 (t80) REVERT: C 324 ARG cc_start: 0.8399 (mtt180) cc_final: 0.7743 (mtm180) REVERT: C 335 MET cc_start: 0.8047 (mmp) cc_final: 0.7628 (mmp) REVERT: C 336 THR cc_start: 0.9250 (t) cc_final: 0.9031 (p) REVERT: C 344 LEU cc_start: 0.7468 (tp) cc_final: 0.6909 (tp) REVERT: C 380 MET cc_start: 0.9082 (mmm) cc_final: 0.7900 (tpp) REVERT: C 613 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8689 (mm) REVERT: C 619 MET cc_start: 0.8089 (tmm) cc_final: 0.7541 (tmm) REVERT: C 743 PHE cc_start: 0.8881 (m-80) cc_final: 0.8478 (t80) REVERT: D 118 TYR cc_start: 0.6764 (t80) cc_final: 0.6562 (t80) REVERT: D 335 MET cc_start: 0.8006 (mmp) cc_final: 0.7508 (mmm) REVERT: D 336 THR cc_start: 0.9305 (t) cc_final: 0.9072 (p) REVERT: D 380 MET cc_start: 0.9109 (mmm) cc_final: 0.8001 (tpp) REVERT: D 513 MET cc_start: 0.8792 (mtm) cc_final: 0.7818 (mpp) REVERT: D 619 MET cc_start: 0.8264 (tmm) cc_final: 0.7841 (tmm) REVERT: D 743 PHE cc_start: 0.8858 (m-80) cc_final: 0.8497 (t80) outliers start: 18 outliers final: 14 residues processed: 162 average time/residue: 0.4096 time to fit residues: 113.9995 Evaluate side-chains 158 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 604 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 7.9990 chunk 361 optimal weight: 9.9990 chunk 330 optimal weight: 1.9990 chunk 352 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 276 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 318 optimal weight: 0.7980 chunk 332 optimal weight: 7.9990 chunk 350 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33580 Z= 0.184 Angle : 0.532 11.131 45424 Z= 0.268 Chirality : 0.038 0.142 5088 Planarity : 0.003 0.037 5644 Dihedral : 9.576 144.563 4908 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.51 % Allowed : 11.19 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.14), residues: 3916 helix: 2.50 (0.10), residues: 2624 sheet: -0.49 (0.38), residues: 172 loop : 0.06 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 327 HIS 0.004 0.001 HIS D 326 PHE 0.026 0.001 PHE A 341 TYR 0.013 0.001 TYR D 524 ARG 0.003 0.000 ARG E 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 4.384 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: B 335 MET cc_start: 0.8078 (mmp) cc_final: 0.7536 (mmm) REVERT: B 336 THR cc_start: 0.9300 (t) cc_final: 0.9067 (p) REVERT: B 380 MET cc_start: 0.9145 (mmm) cc_final: 0.7990 (tpp) REVERT: B 437 LEU cc_start: 0.8645 (mt) cc_final: 0.8423 (tt) REVERT: B 541 TYR cc_start: 0.6706 (m-10) cc_final: 0.6494 (m-10) REVERT: B 619 MET cc_start: 0.8159 (tmm) cc_final: 0.7705 (tmm) REVERT: B 743 PHE cc_start: 0.8798 (m-80) cc_final: 0.8380 (t80) REVERT: F 243 MET cc_start: 0.7487 (tpp) cc_final: 0.7008 (tpp) REVERT: E 247 MET cc_start: 0.8834 (tpt) cc_final: 0.7971 (tmm) REVERT: G 243 MET cc_start: 0.7764 (tpp) cc_final: 0.7104 (tpp) REVERT: G 247 MET cc_start: 0.7959 (mtm) cc_final: 0.7641 (mtm) REVERT: H 243 MET cc_start: 0.7689 (tpp) cc_final: 0.7199 (tpp) REVERT: A 335 MET cc_start: 0.8214 (mmp) cc_final: 0.7857 (mmm) REVERT: A 336 THR cc_start: 0.9227 (t) cc_final: 0.8986 (p) REVERT: A 380 MET cc_start: 0.9094 (mmm) cc_final: 0.8102 (tpp) REVERT: A 619 MET cc_start: 0.8127 (tmm) cc_final: 0.7773 (tmm) REVERT: A 743 PHE cc_start: 0.8786 (m-80) cc_final: 0.8337 (t80) REVERT: C 335 MET cc_start: 0.8081 (mmp) cc_final: 0.7555 (mmp) REVERT: C 336 THR cc_start: 0.9239 (t) cc_final: 0.9033 (p) REVERT: C 343 MET cc_start: 0.8300 (ppp) cc_final: 0.8056 (ppp) REVERT: C 380 MET cc_start: 0.9064 (mmm) cc_final: 0.7872 (tpp) REVERT: C 613 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8699 (mm) REVERT: C 619 MET cc_start: 0.8146 (tmm) cc_final: 0.7642 (tmm) REVERT: C 743 PHE cc_start: 0.8880 (m-80) cc_final: 0.8475 (t80) REVERT: D 335 MET cc_start: 0.8039 (mmp) cc_final: 0.7541 (mmm) REVERT: D 336 THR cc_start: 0.9294 (t) cc_final: 0.9053 (p) REVERT: D 380 MET cc_start: 0.9131 (mmm) cc_final: 0.8027 (tpp) REVERT: D 619 MET cc_start: 0.8244 (tmm) cc_final: 0.7815 (tmm) REVERT: D 743 PHE cc_start: 0.8865 (m-80) cc_final: 0.8494 (t80) outliers start: 18 outliers final: 12 residues processed: 160 average time/residue: 0.4202 time to fit residues: 116.1700 Evaluate side-chains 154 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 604 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 2.9990 chunk 372 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 258 optimal weight: 6.9990 chunk 390 optimal weight: 5.9990 chunk 359 optimal weight: 2.9990 chunk 310 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33580 Z= 0.276 Angle : 0.598 11.643 45424 Z= 0.303 Chirality : 0.039 0.166 5088 Planarity : 0.004 0.040 5644 Dihedral : 9.635 145.480 4908 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.48 % Allowed : 11.27 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.14), residues: 3916 helix: 2.41 (0.10), residues: 2620 sheet: -0.61 (0.38), residues: 172 loop : -0.07 (0.20), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 327 HIS 0.005 0.001 HIS B 172 PHE 0.028 0.001 PHE C 341 TYR 0.015 0.001 TYR D 524 ARG 0.004 0.000 ARG F 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 3.817 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: B 335 MET cc_start: 0.8162 (mmp) cc_final: 0.7627 (mmm) REVERT: B 336 THR cc_start: 0.9316 (t) cc_final: 0.9096 (p) REVERT: B 380 MET cc_start: 0.9159 (mmm) cc_final: 0.7968 (tpp) REVERT: B 437 LEU cc_start: 0.8690 (mt) cc_final: 0.8474 (tt) REVERT: B 619 MET cc_start: 0.8217 (tmm) cc_final: 0.7741 (tmm) REVERT: B 743 PHE cc_start: 0.8843 (m-80) cc_final: 0.8399 (t80) REVERT: F 243 MET cc_start: 0.7572 (tpp) cc_final: 0.7025 (tpp) REVERT: E 247 MET cc_start: 0.8853 (tpt) cc_final: 0.8028 (tmm) REVERT: G 243 MET cc_start: 0.7804 (tpp) cc_final: 0.7226 (tpp) REVERT: G 247 MET cc_start: 0.7956 (mtm) cc_final: 0.7644 (mtm) REVERT: H 243 MET cc_start: 0.7693 (tpp) cc_final: 0.7259 (tpp) REVERT: A 335 MET cc_start: 0.8280 (mmp) cc_final: 0.7922 (mmm) REVERT: A 336 THR cc_start: 0.9257 (t) cc_final: 0.9026 (p) REVERT: A 380 MET cc_start: 0.9078 (mmm) cc_final: 0.7975 (tpp) REVERT: A 619 MET cc_start: 0.8181 (tmm) cc_final: 0.7824 (tmm) REVERT: A 743 PHE cc_start: 0.8800 (m-80) cc_final: 0.8379 (t80) REVERT: C 335 MET cc_start: 0.8114 (mmp) cc_final: 0.7588 (mmp) REVERT: C 336 THR cc_start: 0.9261 (t) cc_final: 0.9056 (p) REVERT: C 380 MET cc_start: 0.9112 (mmm) cc_final: 0.8398 (tpp) REVERT: C 613 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8693 (mm) REVERT: C 619 MET cc_start: 0.8176 (tmm) cc_final: 0.7685 (tmm) REVERT: C 743 PHE cc_start: 0.8921 (m-80) cc_final: 0.8468 (t80) REVERT: D 86 MET cc_start: 0.8741 (mmt) cc_final: 0.8267 (mmm) REVERT: D 335 MET cc_start: 0.8154 (mmp) cc_final: 0.7674 (mmm) REVERT: D 336 THR cc_start: 0.9318 (t) cc_final: 0.9091 (p) REVERT: D 380 MET cc_start: 0.9113 (mmm) cc_final: 0.7892 (tpp) REVERT: D 619 MET cc_start: 0.8282 (tmm) cc_final: 0.7851 (tmm) REVERT: D 743 PHE cc_start: 0.8926 (m-80) cc_final: 0.8518 (t80) outliers start: 17 outliers final: 14 residues processed: 155 average time/residue: 0.4353 time to fit residues: 116.4893 Evaluate side-chains 151 residues out of total 3548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 3.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 604 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 1.9990 chunk 331 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 311 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.061259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.049956 restraints weight = 190027.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.051488 restraints weight = 102449.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.052529 restraints weight = 68659.556| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33580 Z= 0.176 Angle : 0.539 11.783 45424 Z= 0.272 Chirality : 0.038 0.159 5088 Planarity : 0.003 0.037 5644 Dihedral : 9.506 145.821 4908 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.56 % Allowed : 11.22 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.14), residues: 3916 helix: 2.50 (0.10), residues: 2624 sheet: -0.54 (0.38), residues: 172 loop : 0.04 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 327 HIS 0.004 0.001 HIS D 326 PHE 0.023 0.001 PHE C 341 TYR 0.020 0.001 TYR D 118 ARG 0.004 0.000 ARG E 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4505.46 seconds wall clock time: 84 minutes 33.88 seconds (5073.88 seconds total)