Starting phenix.real_space_refine on Fri Jul 26 22:32:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3y_36867/07_2024/8k3y_36867.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3y_36867/07_2024/8k3y_36867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3y_36867/07_2024/8k3y_36867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3y_36867/07_2024/8k3y_36867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3y_36867/07_2024/8k3y_36867.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3y_36867/07_2024/8k3y_36867.cif" } resolution = 4.42 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= 0.002 sd= 0.032 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 120 5.16 5 C 21815 2.51 5 N 6081 2.21 5 O 6565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B GLU 517": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C GLU 591": "OE1" <-> "OE2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E GLU 236": "OE1" <-> "OE2" Residue "E GLU 387": "OE1" <-> "OE2" Residue "E GLU 486": "OE1" <-> "OE2" Residue "E GLU 497": "OE1" <-> "OE2" Residue "F GLU 274": "OE1" <-> "OE2" Residue "F ARG 275": "NH1" <-> "NH2" Time to flip residues: 1.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 34589 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "F" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4136 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 32, 'TRANS': 498} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.15, per 1000 atoms: 0.52 Number of scatterers: 34589 At special positions: 0 Unit cell: (169.76, 196.285, 171.882, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 8 15.00 O 6565 8.00 N 6081 7.00 C 21815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 14.08 Conformation dependent library (CDL) restraints added in 6.5 seconds 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8154 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 41 sheets defined 47.6% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 30 through 39 removed outlier: 3.684A pdb=" N VAL A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 139 removed outlier: 3.707A pdb=" N VAL A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 157 through 169 removed outlier: 3.721A pdb=" N LEU A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 184 through 234 removed outlier: 3.743A pdb=" N ARG A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 removed outlier: 3.807A pdb=" N GLU A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.632A pdb=" N THR A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 4.064A pdb=" N GLU A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 360 through 372 removed outlier: 3.700A pdb=" N LEU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.640A pdb=" N ILE A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 461 through 465 removed outlier: 4.196A pdb=" N LYS A 464 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 465 " --> pdb=" O LEU A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 461 through 465' Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.604A pdb=" N LEU A 482 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.808A pdb=" N ARG A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 513 Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'A' and resid 630 through 646 removed outlier: 3.751A pdb=" N ALA A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 693 removed outlier: 4.175A pdb=" N THR A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 729 removed outlier: 3.697A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 761 through 766 removed outlier: 3.774A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 766' Processing helix chain 'B' and resid 30 through 39 removed outlier: 3.561A pdb=" N VAL B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 137 removed outlier: 3.877A pdb=" N VAL B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 136 " --> pdb=" O PHE B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 152 removed outlier: 3.979A pdb=" N GLN B 148 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 149 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 150 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 152 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.828A pdb=" N ASP B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.918A pdb=" N LYS B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 241 removed outlier: 3.855A pdb=" N LYS B 207 " --> pdb=" O PHE B 203 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN B 234 " --> pdb=" O MET B 230 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 removed outlier: 3.953A pdb=" N GLU B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 280 through 293 removed outlier: 4.207A pdb=" N THR B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 removed outlier: 3.673A pdb=" N LEU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 removed outlier: 4.479A pdb=" N LYS B 323 " --> pdb=" O TYR B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 4.491A pdb=" N TYR B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 403 through 413 Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.776A pdb=" N LYS B 426 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 444 removed outlier: 4.353A pdb=" N ALA B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 505 through 515 Processing helix chain 'B' and resid 523 through 534 Processing helix chain 'B' and resid 540 through 560 removed outlier: 3.833A pdb=" N GLU B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 Processing helix chain 'B' and resid 584 through 588 Processing helix chain 'B' and resid 630 through 647 Processing helix chain 'B' and resid 679 through 693 removed outlier: 3.594A pdb=" N MET B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 688 " --> pdb=" O ALA B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 728 Processing helix chain 'B' and resid 738 through 744 removed outlier: 4.839A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 770 Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.703A pdb=" N ARG C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 139 removed outlier: 3.815A pdb=" N ALA C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 143 removed outlier: 3.755A pdb=" N ARG C 143 " --> pdb=" O LYS C 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.773A pdb=" N LEU C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA C 151 " --> pdb=" O TYR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 169 removed outlier: 3.903A pdb=" N ILE C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR C 167 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 169 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 Processing helix chain 'C' and resid 184 through 238 removed outlier: 3.511A pdb=" N GLN C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 257 removed outlier: 4.215A pdb=" N GLY C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.565A pdb=" N ASP C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.659A pdb=" N ILE C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 371 Processing helix chain 'C' and resid 380 through 384 removed outlier: 4.050A pdb=" N GLY C 383 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 391 Processing helix chain 'C' and resid 403 through 411 removed outlier: 3.685A pdb=" N HIS C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 444 through 449 removed outlier: 4.291A pdb=" N ASN C 449 " --> pdb=" O PRO C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 514 Processing helix chain 'C' and resid 523 through 534 Processing helix chain 'C' and resid 540 through 560 removed outlier: 3.580A pdb=" N GLU C 546 " --> pdb=" O GLY C 542 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS C 556 " --> pdb=" O ARG C 552 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 578 Processing helix chain 'C' and resid 586 through 590 Processing helix chain 'C' and resid 630 through 647 Processing helix chain 'C' and resid 675 through 680 removed outlier: 4.394A pdb=" N ALA C 679 " --> pdb=" O GLY C 676 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY C 680 " --> pdb=" O PRO C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.847A pdb=" N LEU C 723 " --> pdb=" O LYS C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 removed outlier: 4.181A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 747 through 752 Processing helix chain 'C' and resid 761 through 770 removed outlier: 3.731A pdb=" N LEU C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 39 removed outlier: 3.622A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 140 Processing helix chain 'D' and resid 141 through 143 No H-bonds generated for 'chain 'D' and resid 141 through 143' Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 157 through 169 removed outlier: 3.531A pdb=" N LEU D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 185 through 233 Processing helix chain 'D' and resid 239 through 256 removed outlier: 3.501A pdb=" N LEU D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.664A pdb=" N LYS D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.613A pdb=" N THR D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TRP D 292 " --> pdb=" O THR D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 325 through 339 removed outlier: 3.777A pdb=" N TYR D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 373 removed outlier: 3.643A pdb=" N GLY D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 412 removed outlier: 3.776A pdb=" N HIS D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 removed outlier: 3.629A pdb=" N MET D 427 " --> pdb=" O ILE D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 444 removed outlier: 3.602A pdb=" N ALA D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 465 removed outlier: 3.965A pdb=" N LYS D 464 " --> pdb=" O ASP D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.803A pdb=" N THR D 476 " --> pdb=" O THR D 473 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 477 " --> pdb=" O LEU D 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 473 through 477' Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.582A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 560 Processing helix chain 'D' and resid 630 through 647 Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 717 through 727 removed outlier: 4.140A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 744 Processing helix chain 'D' and resid 747 through 753 removed outlier: 3.544A pdb=" N LEU D 751 " --> pdb=" O PRO D 747 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY D 753 " --> pdb=" O GLU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 770 removed outlier: 3.648A pdb=" N GLU D 767 " --> pdb=" O GLY D 763 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR D 768 " --> pdb=" O GLU D 764 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 38 removed outlier: 3.747A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET E 38 " --> pdb=" O VAL E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 41 No H-bonds generated for 'chain 'E' and resid 39 through 41' Processing helix chain 'E' and resid 58 through 60 No H-bonds generated for 'chain 'E' and resid 58 through 60' Processing helix chain 'E' and resid 117 through 138 Processing helix chain 'E' and resid 145 through 152 removed outlier: 3.623A pdb=" N VAL E 152 " --> pdb=" O GLN E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 169 removed outlier: 3.661A pdb=" N ASP E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR E 164 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 4.109A pdb=" N GLU E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 237 Processing helix chain 'E' and resid 237 through 257 Processing helix chain 'E' and resid 259 through 273 Processing helix chain 'E' and resid 280 through 295 removed outlier: 3.696A pdb=" N THR E 294 " --> pdb=" O LEU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 320 removed outlier: 4.357A pdb=" N ASP E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR E 320 " --> pdb=" O ASP E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 337 removed outlier: 4.160A pdb=" N ILE E 329 " --> pdb=" O VAL E 325 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 372 Processing helix chain 'E' and resid 386 through 391 removed outlier: 3.741A pdb=" N ILE E 390 " --> pdb=" O ASP E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 412 removed outlier: 3.660A pdb=" N GLN E 411 " --> pdb=" O HIS E 407 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 436 through 444 removed outlier: 3.575A pdb=" N LEU E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU E 441 " --> pdb=" O SER E 437 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 465 removed outlier: 3.529A pdb=" N LYS E 464 " --> pdb=" O ASP E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 483 removed outlier: 4.271A pdb=" N ASP E 483 " --> pdb=" O PRO E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 505 through 514 Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 540 through 556 Processing helix chain 'E' and resid 573 through 578 Processing helix chain 'E' and resid 630 through 646 Processing helix chain 'E' and resid 679 through 693 Processing helix chain 'E' and resid 717 through 728 removed outlier: 3.709A pdb=" N ALA E 728 " --> pdb=" O ALA E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 744 removed outlier: 3.685A pdb=" N GLU E 744 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 752 removed outlier: 3.738A pdb=" N LEU E 751 " --> pdb=" O PRO E 747 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 767 removed outlier: 4.214A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 252 removed outlier: 3.703A pdb=" N ARG F 250 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 273 removed outlier: 3.502A pdb=" N THR F 264 " --> pdb=" O GLU F 260 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 293 removed outlier: 3.718A pdb=" N ASP F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 319 removed outlier: 3.513A pdb=" N GLN F 313 " --> pdb=" O ASN F 309 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU F 315 " --> pdb=" O THR F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 335 Processing helix chain 'F' and resid 360 through 372 removed outlier: 3.850A pdb=" N LEU F 364 " --> pdb=" O GLY F 360 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY F 365 " --> pdb=" O LYS F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 391 Processing helix chain 'F' and resid 403 through 409 Processing helix chain 'F' and resid 435 through 444 removed outlier: 3.728A pdb=" N MET F 439 " --> pdb=" O PRO F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 450 removed outlier: 4.248A pdb=" N ASN F 449 " --> pdb=" O PRO F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 483 Processing helix chain 'F' and resid 494 through 505 Processing helix chain 'F' and resid 506 through 515 removed outlier: 3.589A pdb=" N GLN F 510 " --> pdb=" O LEU F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.639A pdb=" N GLU F 533 " --> pdb=" O ARG F 529 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 560 removed outlier: 3.766A pdb=" N ARG F 545 " --> pdb=" O ARG F 541 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU F 546 " --> pdb=" O GLY F 542 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU F 547 " --> pdb=" O LEU F 543 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU F 560 " --> pdb=" O LYS F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 647 removed outlier: 3.637A pdb=" N LYS F 634 " --> pdb=" O GLY F 630 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA F 639 " --> pdb=" O GLU F 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 652 removed outlier: 3.733A pdb=" N TYR F 651 " --> pdb=" O THR F 648 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY F 652 " --> pdb=" O GLN F 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 648 through 652' Processing helix chain 'F' and resid 679 through 693 Processing helix chain 'F' and resid 717 through 728 removed outlier: 3.913A pdb=" N LYS F 721 " --> pdb=" O GLY F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 736 through 746 removed outlier: 3.933A pdb=" N GLU F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 754 removed outlier: 4.043A pdb=" N GLY F 753 " --> pdb=" O VAL F 750 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU F 754 " --> pdb=" O LEU F 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 750 through 754' Processing helix chain 'F' and resid 761 through 766 removed outlier: 4.142A pdb=" N VAL F 765 " --> pdb=" O ASP F 761 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU F 766 " --> pdb=" O VAL F 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 761 through 766' Processing helix chain 'F' and resid 767 through 770 removed outlier: 3.885A pdb=" N LEU F 770 " --> pdb=" O GLU F 767 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 767 through 770' Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 22 removed outlier: 6.354A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE A 45 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 5 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 105 " --> pdb=" O LEU A 5 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 378 removed outlier: 3.753A pdb=" N ILE A 419 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 468 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 522 removed outlier: 5.829A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 596 through 597 removed outlier: 3.980A pdb=" N GLU A 613 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS A 666 " --> pdb=" O GLU A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 600 through 603 Processing sheet with id=AA8, first strand: chain 'A' and resid 732 through 734 removed outlier: 3.700A pdb=" N ILE A 733 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 757 " --> pdb=" O ILE A 733 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.721A pdb=" N ALA B 105 " --> pdb=" O LEU B 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 23 through 25 removed outlier: 7.793A pdb=" N GLN B 83 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA B 74 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N MET B 85 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN B 68 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG B 91 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY B 66 " --> pdb=" O ARG B 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 5.831A pdb=" N HIS B 377 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE B 419 " --> pdb=" O ILE B 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 520 through 522 Processing sheet with id=AB4, first strand: chain 'B' and resid 596 through 601 removed outlier: 3.666A pdb=" N GLU B 613 " --> pdb=" O HIS B 666 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS B 666 " --> pdb=" O GLU B 613 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS B 622 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL B 665 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.698A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL B 759 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU B 735 " --> pdb=" O VAL B 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 21 through 25 removed outlier: 3.700A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C 23 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 84 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLN C 83 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA C 74 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N MET C 85 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS C 72 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG C 89 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLN C 68 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG C 91 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY C 66 " --> pdb=" O ARG C 91 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN C 93 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR C 64 " --> pdb=" O GLN C 93 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N THR C 95 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 11.396A pdb=" N LEU C 62 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP C 65 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA C 48 " --> pdb=" O TRP C 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 21 through 25 removed outlier: 3.700A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C 23 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 84 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG C 106 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR C 97 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ARG C 104 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 350 through 354 Processing sheet with id=AB9, first strand: chain 'C' and resid 376 through 377 removed outlier: 3.659A pdb=" N HIS C 377 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU C 420 " --> pdb=" O HIS C 377 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 520 through 522 removed outlier: 5.981A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 593 through 594 Processing sheet with id=AC3, first strand: chain 'C' and resid 598 through 600 Processing sheet with id=AC4, first strand: chain 'C' and resid 613 through 618 removed outlier: 8.390A pdb=" N SER C 624 " --> pdb=" O VAL C 661 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU C 663 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR C 626 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL C 665 " --> pdb=" O THR C 626 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC6, first strand: chain 'D' and resid 21 through 22 removed outlier: 4.487A pdb=" N THR D 21 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL D 86 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N MET D 85 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS D 72 " --> pdb=" O MET D 85 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 70 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLN D 68 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG D 91 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY D 66 " --> pdb=" O ARG D 91 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 379 through 380 removed outlier: 3.822A pdb=" N ASP D 422 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU D 351 " --> pdb=" O THR D 469 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 520 through 522 Processing sheet with id=AC9, first strand: chain 'D' and resid 600 through 602 Processing sheet with id=AD1, first strand: chain 'D' and resid 613 through 618 Processing sheet with id=AD2, first strand: chain 'D' and resid 700 through 701 removed outlier: 7.112A pdb=" N ALA D 701 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 20 through 25 removed outlier: 7.666A pdb=" N VAL E 86 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS E 72 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ALA E 88 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL E 70 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA E 90 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN E 68 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ALA E 48 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TRP E 65 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU E 46 " --> pdb=" O TRP E 65 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL E 67 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE E 44 " --> pdb=" O VAL E 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 96 through 98 Processing sheet with id=AD5, first strand: chain 'E' and resid 352 through 354 removed outlier: 6.717A pdb=" N VAL E 352 " --> pdb=" O ILE E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 375 through 376 removed outlier: 6.257A pdb=" N LYS E 375 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU E 420 " --> pdb=" O LYS E 375 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 520 through 522 Processing sheet with id=AD8, first strand: chain 'E' and resid 601 through 602 Processing sheet with id=AD9, first strand: chain 'E' and resid 613 through 615 removed outlier: 3.778A pdb=" N VAL E 667 " --> pdb=" O THR E 626 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN E 628 " --> pdb=" O VAL E 667 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP E 669 " --> pdb=" O GLN E 628 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 700 through 702 removed outlier: 3.587A pdb=" N VAL E 734 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE E 733 " --> pdb=" O LYS E 757 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL E 759 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU E 735 " --> pdb=" O VAL E 759 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 351 through 352 removed outlier: 7.373A pdb=" N LEU F 351 " --> pdb=" O THR F 469 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE F 419 " --> pdb=" O ILE F 468 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR F 470 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU F 421 " --> pdb=" O THR F 470 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N HIS F 377 " --> pdb=" O LEU F 420 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASP F 422 " --> pdb=" O HIS F 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'F' and resid 601 through 602 Processing sheet with id=AE4, first strand: chain 'F' and resid 613 through 618 removed outlier: 3.924A pdb=" N THR F 626 " --> pdb=" O VAL F 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 732 through 735 removed outlier: 3.576A pdb=" N LYS F 757 " --> pdb=" O ILE F 733 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU F 735 " --> pdb=" O LYS F 757 " (cutoff:3.500A) 1414 hydrogen bonds defined for protein. 4086 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: 12.65 Time building geometry restraints manager: 15.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11143 1.34 - 1.46: 6819 1.46 - 1.58: 17000 1.58 - 1.71: 12 1.71 - 1.83: 240 Bond restraints: 35214 Sorted by residual: bond pdb=" N ILE A 350 " pdb=" CA ILE A 350 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.09e-02 8.42e+03 1.16e+01 bond pdb=" N VAL A 614 " pdb=" CA VAL A 614 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.19e-02 7.06e+03 9.06e+00 bond pdb=" N ILE A 379 " pdb=" CA ILE A 379 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.22e-02 6.72e+03 8.38e+00 bond pdb=" N ARG A 374 " pdb=" CA ARG A 374 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.21e-02 6.83e+03 8.14e+00 bond pdb=" N VAL E 458 " pdb=" CA VAL E 458 " ideal model delta sigma weight residual 1.465 1.494 -0.029 1.02e-02 9.61e+03 8.11e+00 ... (remaining 35209 not shown) Histogram of bond angle deviations from ideal: 95.42 - 103.61: 605 103.61 - 111.80: 15897 111.80 - 119.98: 16105 119.98 - 128.17: 14845 128.17 - 136.35: 287 Bond angle restraints: 47739 Sorted by residual: angle pdb=" N GLU E 760 " pdb=" CA GLU E 760 " pdb=" C GLU E 760 " ideal model delta sigma weight residual 114.75 105.08 9.67 1.26e+00 6.30e-01 5.89e+01 angle pdb=" N VAL C 296 " pdb=" CA VAL C 296 " pdb=" C VAL C 296 " ideal model delta sigma weight residual 108.95 102.68 6.27 9.80e-01 1.04e+00 4.09e+01 angle pdb=" N LYS C 300 " pdb=" CA LYS C 300 " pdb=" C LYS C 300 " ideal model delta sigma weight residual 110.52 101.84 8.68 1.48e+00 4.57e-01 3.44e+01 angle pdb=" N LEU E 443 " pdb=" CA LEU E 443 " pdb=" C LEU E 443 " ideal model delta sigma weight residual 110.97 117.03 -6.06 1.09e+00 8.42e-01 3.09e+01 angle pdb=" N GLU D 295 " pdb=" CA GLU D 295 " pdb=" C GLU D 295 " ideal model delta sigma weight residual 111.33 104.64 6.69 1.21e+00 6.83e-01 3.06e+01 ... (remaining 47734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.74: 21289 33.74 - 67.48: 398 67.48 - 101.21: 36 101.21 - 134.95: 3 134.95 - 168.69: 6 Dihedral angle restraints: 21732 sinusoidal: 9063 harmonic: 12669 Sorted by residual: dihedral pdb=" O1B ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " pdb=" PA ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 108.69 -168.69 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C2' ADP C 801 " pdb=" C1' ADP C 801 " pdb=" N9 ADP C 801 " pdb=" C4 ADP C 801 " ideal model delta sinusoidal sigma weight residual 91.55 -76.03 167.58 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C2' ADP B 801 " pdb=" C1' ADP B 801 " pdb=" N9 ADP B 801 " pdb=" C4 ADP B 801 " ideal model delta sinusoidal sigma weight residual 91.55 -68.70 160.25 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 21729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 5088 0.120 - 0.240: 321 0.240 - 0.360: 23 0.360 - 0.480: 1 0.480 - 0.599: 2 Chirality restraints: 5435 Sorted by residual: chirality pdb=" CB ILE E 253 " pdb=" CA ILE E 253 " pdb=" CG1 ILE E 253 " pdb=" CG2 ILE E 253 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.60 2.00e-01 2.50e+01 8.98e+00 chirality pdb=" CB ILE E 379 " pdb=" CA ILE E 379 " pdb=" CG1 ILE E 379 " pdb=" CG2 ILE E 379 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.57 2.00e-01 2.50e+01 8.12e+00 chirality pdb=" CB ILE D 612 " pdb=" CA ILE D 612 " pdb=" CG1 ILE D 612 " pdb=" CG2 ILE D 612 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 5432 not shown) Planarity restraints: 6200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 563 " -0.029 2.00e-02 2.50e+03 2.90e-02 2.10e+01 pdb=" CG TRP C 563 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP C 563 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP C 563 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 563 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 563 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 563 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 563 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 563 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP C 563 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 773 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO D 774 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO D 774 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO D 774 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 768 " -0.016 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C TYR A 768 " 0.059 2.00e-02 2.50e+03 pdb=" O TYR A 768 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU A 769 " -0.020 2.00e-02 2.50e+03 ... (remaining 6197 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 6078 2.77 - 3.30: 35919 3.30 - 3.83: 66592 3.83 - 4.37: 78275 4.37 - 4.90: 121421 Nonbonded interactions: 308285 Sorted by model distance: nonbonded pdb=" O LEU E 290 " pdb=" OG1 THR E 294 " model vdw 2.232 2.440 nonbonded pdb=" OD1 ASP F 422 " pdb=" OG1 THR F 470 " model vdw 2.243 2.440 nonbonded pdb=" O LEU C 351 " pdb=" OG1 THR C 469 " model vdw 2.248 2.440 nonbonded pdb=" O GLN E 510 " pdb=" OG SER E 514 " model vdw 2.249 2.440 nonbonded pdb=" O THR B 682 " pdb=" OG1 THR B 685 " model vdw 2.258 2.440 ... (remaining 308280 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' and resid 2 through 774) selection = (chain 'C' and resid 2 through 774) selection = (chain 'D' and resid 2 through 774) selection = (chain 'E' and resid 2 through 774) } 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=0.00 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.470 Check model and map are aligned: 0.260 Set scattering table: 0.340 Process input model: 90.950 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.160 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 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 : 0.006 0.070 35214 Z= 0.404 Angle : 1.148 14.001 47739 Z= 0.619 Chirality : 0.065 0.599 5435 Planarity : 0.008 0.113 6200 Dihedral : 14.644 168.690 13578 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.89 % Favored : 93.09 % Rotamer: Outliers : 0.05 % Allowed : 1.08 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % 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: -3.10 (0.11), residues: 4384 helix: -1.94 (0.10), residues: 1823 sheet: -2.11 (0.25), residues: 397 loop : -2.09 (0.12), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP C 563 HIS 0.012 0.002 HIS B 664 PHE 0.045 0.003 PHE B 466 TYR 0.057 0.003 TYR C 455 ARG 0.015 0.001 ARG D 694 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 3.907 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 38 MET cc_start: 0.2954 (mtt) cc_final: 0.2566 (mtt) REVERT: B 424 ILE cc_start: 0.9166 (mp) cc_final: 0.8587 (mp) REVERT: C 132 PHE cc_start: 0.8555 (m-80) cc_final: 0.8233 (m-80) REVERT: D 260 GLU cc_start: 0.9715 (mm-30) cc_final: 0.9505 (mm-30) REVERT: D 702 MET cc_start: 0.6009 (ptm) cc_final: 0.5436 (tmm) REVERT: E 258 MET cc_start: 0.7687 (mmp) cc_final: 0.6844 (mmp) REVERT: E 427 MET cc_start: 0.7201 (mmt) cc_final: 0.6620 (mmt) REVERT: E 698 MET cc_start: 0.8063 (mmp) cc_final: 0.7667 (mmp) REVERT: F 427 MET cc_start: 0.4534 (tpt) cc_final: 0.4064 (tpt) REVERT: F 439 MET cc_start: 0.7979 (mpp) cc_final: 0.7676 (mpp) REVERT: F 633 MET cc_start: 0.9164 (mmp) cc_final: 0.8723 (mmm) REVERT: F 693 ARG cc_start: 0.8647 (mmp-170) cc_final: 0.8390 (mmm160) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.4668 time to fit residues: 145.5247 Evaluate side-chains 155 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 4.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 10.0000 chunk 331 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 177 optimal weight: 20.0000 chunk 343 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 255 optimal weight: 6.9990 chunk 397 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 229 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 HIS D 313 GLN D 373 ASN E 277 GLN F 647 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35214 Z= 0.236 Angle : 0.715 10.638 47739 Z= 0.363 Chirality : 0.044 0.185 5435 Planarity : 0.006 0.085 6200 Dihedral : 9.295 171.358 4874 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 31.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.05 % Allowed : 5.45 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % 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: -2.30 (0.12), residues: 4384 helix: -1.03 (0.11), residues: 1902 sheet: -1.93 (0.25), residues: 405 loop : -1.86 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 563 HIS 0.011 0.001 HIS D 664 PHE 0.027 0.002 PHE A 467 TYR 0.025 0.002 TYR C 455 ARG 0.016 0.001 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 3.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 MET cc_start: 0.2630 (tpp) cc_final: 0.2396 (mmm) REVERT: B 38 MET cc_start: 0.2866 (mtt) cc_final: 0.2500 (mtt) REVERT: B 424 ILE cc_start: 0.9130 (mp) cc_final: 0.8742 (mp) REVERT: B 485 MET cc_start: 0.6663 (pmm) cc_final: 0.6418 (pmm) REVERT: C 132 PHE cc_start: 0.8505 (m-80) cc_final: 0.8281 (m-80) REVERT: C 258 MET cc_start: 0.3554 (mmt) cc_final: 0.3187 (mmt) REVERT: C 401 MET cc_start: 0.8148 (mmp) cc_final: 0.7899 (tpp) REVERT: D 75 MET cc_start: 0.1408 (pmm) cc_final: 0.0742 (pmm) REVERT: D 260 GLU cc_start: 0.9704 (mm-30) cc_final: 0.9403 (tp30) REVERT: E 258 MET cc_start: 0.7949 (mmp) cc_final: 0.7197 (mmp) REVERT: E 427 MET cc_start: 0.7497 (mmt) cc_final: 0.7144 (mmt) REVERT: F 427 MET cc_start: 0.5577 (tpt) cc_final: 0.5193 (tpt) REVERT: F 439 MET cc_start: 0.7807 (mpp) cc_final: 0.7273 (mpp) REVERT: F 633 MET cc_start: 0.8983 (mmp) cc_final: 0.8647 (mmm) REVERT: F 647 HIS cc_start: 0.8963 (t70) cc_final: 0.8354 (t70) REVERT: F 683 MET cc_start: 0.8958 (mpp) cc_final: 0.7968 (ptt) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.4485 time to fit residues: 138.9442 Evaluate side-chains 153 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 331 optimal weight: 10.0000 chunk 270 optimal weight: 40.0000 chunk 109 optimal weight: 5.9990 chunk 398 optimal weight: 2.9990 chunk 430 optimal weight: 50.0000 chunk 354 optimal weight: 0.4980 chunk 395 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 319 optimal weight: 9.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 GLN A 664 HIS ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35214 Z= 0.200 Angle : 0.670 12.936 47739 Z= 0.333 Chirality : 0.044 0.243 5435 Planarity : 0.005 0.075 6200 Dihedral : 8.957 172.477 4874 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 28.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % 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: -1.90 (0.12), residues: 4384 helix: -0.55 (0.12), residues: 1895 sheet: -1.92 (0.25), residues: 412 loop : -1.74 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 563 HIS 0.006 0.001 HIS B 664 PHE 0.034 0.002 PHE A 467 TYR 0.026 0.002 TYR E 505 ARG 0.007 0.000 ARG A 645 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 4.122 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: A 258 MET cc_start: 0.1937 (ptt) cc_final: 0.1686 (ptt) REVERT: B 38 MET cc_start: 0.2667 (mtt) cc_final: 0.2270 (mtt) REVERT: B 258 MET cc_start: 0.3499 (mpp) cc_final: 0.3260 (mmm) REVERT: B 485 MET cc_start: 0.6527 (pmm) cc_final: 0.6273 (pmm) REVERT: C 132 PHE cc_start: 0.8475 (m-80) cc_final: 0.8109 (m-80) REVERT: C 401 MET cc_start: 0.8081 (mmp) cc_final: 0.7686 (tpp) REVERT: D 702 MET cc_start: 0.6235 (ptm) cc_final: 0.5861 (ptm) REVERT: E 258 MET cc_start: 0.8125 (mmp) cc_final: 0.7321 (mmp) REVERT: E 427 MET cc_start: 0.7693 (mmt) cc_final: 0.7405 (mmt) REVERT: F 427 MET cc_start: 0.5250 (tpt) cc_final: 0.4895 (tpt) REVERT: F 439 MET cc_start: 0.7871 (mpp) cc_final: 0.7533 (mpp) REVERT: F 633 MET cc_start: 0.8921 (mmp) cc_final: 0.8561 (mmm) REVERT: F 647 HIS cc_start: 0.8897 (t70) cc_final: 0.8280 (t70) REVERT: F 683 MET cc_start: 0.8903 (mpp) cc_final: 0.7932 (ptt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.4563 time to fit residues: 139.5870 Evaluate side-chains 156 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 0.0010 chunk 299 optimal weight: 0.7980 chunk 206 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 267 optimal weight: 0.9990 chunk 399 optimal weight: 9.9990 chunk 423 optimal weight: 20.0000 chunk 208 optimal weight: 7.9990 chunk 379 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 HIS C 504 GLN ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35214 Z= 0.171 Angle : 0.640 10.758 47739 Z= 0.316 Chirality : 0.044 0.213 5435 Planarity : 0.005 0.060 6200 Dihedral : 8.710 173.109 4874 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % 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: -1.67 (0.12), residues: 4384 helix: -0.32 (0.12), residues: 1902 sheet: -1.84 (0.26), residues: 392 loop : -1.67 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 563 HIS 0.005 0.001 HIS C 377 PHE 0.029 0.001 PHE A 467 TYR 0.030 0.001 TYR C 455 ARG 0.004 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.2185 (ptt) cc_final: 0.1930 (ptt) REVERT: B 38 MET cc_start: 0.2927 (mtt) cc_final: 0.2575 (mtt) REVERT: B 485 MET cc_start: 0.6332 (pmm) cc_final: 0.6115 (pmm) REVERT: C 132 PHE cc_start: 0.8471 (m-80) cc_final: 0.8095 (m-80) REVERT: C 401 MET cc_start: 0.7939 (mmp) cc_final: 0.7468 (tpp) REVERT: C 543 LEU cc_start: 0.9695 (tp) cc_final: 0.9385 (pp) REVERT: D 75 MET cc_start: 0.1898 (pmm) cc_final: 0.1532 (pmm) REVERT: D 401 MET cc_start: 0.9597 (tpt) cc_final: 0.9089 (pmm) REVERT: D 702 MET cc_start: 0.5909 (ptm) cc_final: 0.5624 (ptm) REVERT: E 258 MET cc_start: 0.8080 (mmp) cc_final: 0.7227 (mmp) REVERT: E 427 MET cc_start: 0.7803 (mmt) cc_final: 0.7522 (mmt) REVERT: E 633 MET cc_start: 0.9351 (mmt) cc_final: 0.9044 (mmt) REVERT: F 427 MET cc_start: 0.5058 (tpt) cc_final: 0.4754 (tpt) REVERT: F 439 MET cc_start: 0.7840 (mpp) cc_final: 0.7533 (mpp) REVERT: F 633 MET cc_start: 0.8901 (mmp) cc_final: 0.8551 (mmm) REVERT: F 647 HIS cc_start: 0.8879 (t70) cc_final: 0.8304 (t-90) REVERT: F 683 MET cc_start: 0.8942 (mpp) cc_final: 0.7778 (ptt) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.4469 time to fit residues: 138.3406 Evaluate side-chains 162 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 8.9990 chunk 240 optimal weight: 40.0000 chunk 6 optimal weight: 50.0000 chunk 315 optimal weight: 50.0000 chunk 174 optimal weight: 40.0000 chunk 361 optimal weight: 0.0060 chunk 292 optimal weight: 20.0000 chunk 0 optimal weight: 60.0000 chunk 216 optimal weight: 5.9990 chunk 380 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 overall best weight: 6.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 475 GLN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35214 Z= 0.294 Angle : 0.747 11.668 47739 Z= 0.375 Chirality : 0.045 0.261 5435 Planarity : 0.005 0.062 6200 Dihedral : 8.880 176.190 4874 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 38.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % 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: -1.67 (0.12), residues: 4384 helix: -0.25 (0.12), residues: 1884 sheet: -1.94 (0.25), residues: 416 loop : -1.69 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 431 HIS 0.015 0.002 HIS B 664 PHE 0.035 0.002 PHE A 467 TYR 0.032 0.002 TYR C 455 ARG 0.009 0.001 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 4.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 633 MET cc_start: 0.8040 (mmp) cc_final: 0.7700 (mpp) REVERT: B 38 MET cc_start: 0.2637 (mtt) cc_final: 0.2331 (mtt) REVERT: B 485 MET cc_start: 0.6826 (pmm) cc_final: 0.6529 (pmm) REVERT: C 132 PHE cc_start: 0.8326 (m-80) cc_final: 0.7960 (m-80) REVERT: D 75 MET cc_start: 0.1127 (pmm) cc_final: 0.0855 (pmm) REVERT: D 260 GLU cc_start: 0.9734 (mm-30) cc_final: 0.9463 (tp30) REVERT: E 38 MET cc_start: 0.5803 (mpp) cc_final: 0.4895 (pmm) REVERT: E 258 MET cc_start: 0.8396 (mmp) cc_final: 0.8045 (mmp) REVERT: E 427 MET cc_start: 0.7984 (mmt) cc_final: 0.7723 (mmt) REVERT: F 258 MET cc_start: 0.5109 (mmt) cc_final: 0.4371 (mmt) REVERT: F 427 MET cc_start: 0.5847 (tpt) cc_final: 0.5529 (tpt) REVERT: F 439 MET cc_start: 0.8071 (mpp) cc_final: 0.7729 (mpp) REVERT: F 633 MET cc_start: 0.8955 (mmp) cc_final: 0.8589 (mmm) REVERT: F 647 HIS cc_start: 0.8919 (t70) cc_final: 0.8261 (t70) REVERT: F 683 MET cc_start: 0.8942 (mpp) cc_final: 0.7758 (ptt) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.4531 time to fit residues: 136.0623 Evaluate side-chains 151 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 4.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 0.3980 chunk 381 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 104 optimal weight: 20.0000 chunk 423 optimal weight: 9.9990 chunk 351 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 140 optimal weight: 0.9980 chunk 222 optimal weight: 7.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35214 Z= 0.224 Angle : 0.687 11.188 47739 Z= 0.340 Chirality : 0.045 0.374 5435 Planarity : 0.005 0.059 6200 Dihedral : 8.786 177.942 4874 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 32.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.03 % Allowed : 2.20 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % 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: -1.63 (0.12), residues: 4384 helix: -0.22 (0.12), residues: 1909 sheet: -1.90 (0.25), residues: 407 loop : -1.70 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 563 HIS 0.008 0.001 HIS B 664 PHE 0.030 0.002 PHE A 467 TYR 0.029 0.002 TYR C 455 ARG 0.009 0.000 ARG D 694 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 3.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.8786 (mmp) cc_final: 0.8268 (mmp) REVERT: A 633 MET cc_start: 0.7902 (mmp) cc_final: 0.7674 (mpp) REVERT: B 38 MET cc_start: 0.2843 (mtt) cc_final: 0.2548 (mtt) REVERT: B 479 ARG cc_start: 0.9268 (mmp-170) cc_final: 0.9023 (mmp80) REVERT: B 485 MET cc_start: 0.6831 (pmm) cc_final: 0.6534 (pmm) REVERT: C 132 PHE cc_start: 0.8280 (m-80) cc_final: 0.7860 (m-80) REVERT: D 75 MET cc_start: 0.1130 (pmm) cc_final: 0.0701 (pmm) REVERT: D 260 GLU cc_start: 0.9708 (mm-30) cc_final: 0.9439 (tp30) REVERT: D 401 MET cc_start: 0.9629 (tpt) cc_final: 0.9131 (pmm) REVERT: E 38 MET cc_start: 0.5837 (mpp) cc_final: 0.4906 (pmm) REVERT: E 258 MET cc_start: 0.8353 (mmp) cc_final: 0.7966 (mmp) REVERT: E 427 MET cc_start: 0.7996 (mmt) cc_final: 0.7756 (mmt) REVERT: F 258 MET cc_start: 0.4962 (mmt) cc_final: 0.4098 (mmt) REVERT: F 427 MET cc_start: 0.5499 (tpt) cc_final: 0.5081 (tpt) REVERT: F 439 MET cc_start: 0.7960 (mpp) cc_final: 0.7632 (mpp) REVERT: F 633 MET cc_start: 0.8933 (mmp) cc_final: 0.8551 (mmm) REVERT: F 647 HIS cc_start: 0.8923 (t70) cc_final: 0.8293 (t-90) REVERT: F 683 MET cc_start: 0.8944 (mpp) cc_final: 0.7757 (ptt) outliers start: 1 outliers final: 1 residues processed: 184 average time/residue: 0.4797 time to fit residues: 150.7492 Evaluate side-chains 156 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 4.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 0.3980 chunk 47 optimal weight: 30.0000 chunk 241 optimal weight: 50.0000 chunk 309 optimal weight: 40.0000 chunk 239 optimal weight: 50.0000 chunk 356 optimal weight: 8.9990 chunk 236 optimal weight: 50.0000 chunk 422 optimal weight: 0.8980 chunk 264 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 68 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN C 666 HIS ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35214 Z= 0.229 Angle : 0.690 11.178 47739 Z= 0.341 Chirality : 0.045 0.237 5435 Planarity : 0.005 0.059 6200 Dihedral : 8.712 178.541 4874 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 33.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % 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: -1.54 (0.13), residues: 4384 helix: -0.11 (0.12), residues: 1903 sheet: -1.85 (0.25), residues: 413 loop : -1.68 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP E 292 HIS 0.009 0.001 HIS B 664 PHE 0.030 0.002 PHE A 467 TYR 0.026 0.002 TYR C 455 ARG 0.007 0.000 ARG E 582 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 3.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.2635 (ptt) cc_final: 0.2252 (ptt) REVERT: A 409 MET cc_start: 0.8874 (mmp) cc_final: 0.8316 (mmp) REVERT: B 38 MET cc_start: 0.2731 (mtt) cc_final: 0.2452 (mtt) REVERT: B 479 ARG cc_start: 0.9277 (mmp-170) cc_final: 0.9068 (mmp80) REVERT: C 132 PHE cc_start: 0.8234 (m-80) cc_final: 0.7844 (m-80) REVERT: D 260 GLU cc_start: 0.9703 (mm-30) cc_final: 0.9437 (tp30) REVERT: D 401 MET cc_start: 0.9619 (tpt) cc_final: 0.9139 (pmm) REVERT: E 258 MET cc_start: 0.8269 (mmp) cc_final: 0.7833 (mmp) REVERT: E 427 MET cc_start: 0.8061 (mmt) cc_final: 0.7812 (mmt) REVERT: E 633 MET cc_start: 0.9360 (mmt) cc_final: 0.9077 (mmt) REVERT: F 258 MET cc_start: 0.5133 (mmt) cc_final: 0.4198 (mmt) REVERT: F 427 MET cc_start: 0.5385 (tpt) cc_final: 0.4961 (tpt) REVERT: F 439 MET cc_start: 0.8019 (mpp) cc_final: 0.7694 (mpp) REVERT: F 633 MET cc_start: 0.8936 (mmp) cc_final: 0.8551 (mmm) REVERT: F 647 HIS cc_start: 0.8924 (t70) cc_final: 0.8302 (t-90) REVERT: F 683 MET cc_start: 0.8972 (mpp) cc_final: 0.7818 (ptt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.4564 time to fit residues: 135.8592 Evaluate side-chains 153 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 4.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 20.0000 chunk 168 optimal weight: 50.0000 chunk 252 optimal weight: 30.0000 chunk 127 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 81 optimal weight: 50.0000 chunk 268 optimal weight: 3.9990 chunk 287 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 331 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35214 Z= 0.206 Angle : 0.682 11.364 47739 Z= 0.335 Chirality : 0.044 0.222 5435 Planarity : 0.005 0.058 6200 Dihedral : 8.652 176.449 4874 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 31.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % 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: -1.46 (0.13), residues: 4384 helix: -0.04 (0.12), residues: 1905 sheet: -1.77 (0.26), residues: 406 loop : -1.66 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 292 HIS 0.009 0.001 HIS B 454 PHE 0.027 0.002 PHE A 467 TYR 0.025 0.002 TYR C 455 ARG 0.009 0.000 ARG D 552 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 4.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.2975 (ptt) cc_final: 0.2642 (ptt) REVERT: A 409 MET cc_start: 0.8912 (mmp) cc_final: 0.8327 (mmp) REVERT: B 38 MET cc_start: 0.2683 (mtt) cc_final: 0.2405 (mtt) REVERT: C 132 PHE cc_start: 0.8281 (m-80) cc_final: 0.7828 (m-80) REVERT: D 75 MET cc_start: 0.0713 (pmm) cc_final: 0.0142 (pmm) REVERT: D 260 GLU cc_start: 0.9693 (mm-30) cc_final: 0.9412 (tp30) REVERT: D 401 MET cc_start: 0.9596 (tpt) cc_final: 0.9171 (pmm) REVERT: E 258 MET cc_start: 0.8339 (mmp) cc_final: 0.7913 (mmp) REVERT: E 427 MET cc_start: 0.8139 (mmt) cc_final: 0.7891 (mmt) REVERT: F 258 MET cc_start: 0.5077 (mmt) cc_final: 0.4100 (mmt) REVERT: F 427 MET cc_start: 0.5140 (tpt) cc_final: 0.4720 (tpt) REVERT: F 439 MET cc_start: 0.8164 (mpp) cc_final: 0.7845 (mpp) REVERT: F 633 MET cc_start: 0.8909 (mmp) cc_final: 0.8520 (mmm) REVERT: F 647 HIS cc_start: 0.8918 (t70) cc_final: 0.8303 (t-90) REVERT: F 683 MET cc_start: 0.8965 (mpp) cc_final: 0.7830 (ptt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.4883 time to fit residues: 148.9562 Evaluate side-chains 155 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 4.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 3.9990 chunk 404 optimal weight: 5.9990 chunk 368 optimal weight: 7.9990 chunk 393 optimal weight: 3.9990 chunk 236 optimal weight: 30.0000 chunk 171 optimal weight: 30.0000 chunk 308 optimal weight: 50.0000 chunk 120 optimal weight: 10.0000 chunk 355 optimal weight: 6.9990 chunk 372 optimal weight: 0.9980 chunk 392 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35214 Z= 0.223 Angle : 0.693 11.014 47739 Z= 0.340 Chirality : 0.044 0.232 5435 Planarity : 0.005 0.128 6200 Dihedral : 8.610 176.323 4874 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 32.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % 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: -1.42 (0.13), residues: 4384 helix: -0.00 (0.12), residues: 1900 sheet: -1.71 (0.27), residues: 387 loop : -1.66 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 292 HIS 0.009 0.001 HIS E 666 PHE 0.023 0.002 PHE A 467 TYR 0.025 0.002 TYR C 455 ARG 0.008 0.001 ARG D 694 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 3.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.2291 (ptt) cc_final: 0.1955 (ptt) REVERT: B 38 MET cc_start: 0.2692 (mtt) cc_final: 0.2410 (mtt) REVERT: C 132 PHE cc_start: 0.8227 (m-80) cc_final: 0.7849 (m-80) REVERT: D 260 GLU cc_start: 0.9694 (mm-30) cc_final: 0.9407 (tp30) REVERT: D 401 MET cc_start: 0.9599 (tpt) cc_final: 0.9190 (pmm) REVERT: D 698 MET cc_start: 0.7582 (mmm) cc_final: 0.7213 (mmm) REVERT: E 258 MET cc_start: 0.8391 (mmp) cc_final: 0.7979 (mmp) REVERT: E 427 MET cc_start: 0.8183 (mmt) cc_final: 0.7946 (mmt) REVERT: E 633 MET cc_start: 0.9351 (mmt) cc_final: 0.9052 (mmt) REVERT: F 258 MET cc_start: 0.5079 (mmt) cc_final: 0.4056 (mmt) REVERT: F 427 MET cc_start: 0.5159 (tpt) cc_final: 0.4727 (tpt) REVERT: F 439 MET cc_start: 0.8128 (mpp) cc_final: 0.7790 (mpp) REVERT: F 633 MET cc_start: 0.8927 (mmp) cc_final: 0.8540 (mmm) REVERT: F 683 MET cc_start: 0.8984 (mpp) cc_final: 0.7860 (ptt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.4672 time to fit residues: 139.6459 Evaluate side-chains 152 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 20.0000 chunk 415 optimal weight: 40.0000 chunk 253 optimal weight: 30.0000 chunk 197 optimal weight: 8.9990 chunk 289 optimal weight: 8.9990 chunk 436 optimal weight: 5.9990 chunk 401 optimal weight: 7.9990 chunk 347 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 268 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 GLN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 HIS ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 35214 Z= 0.318 Angle : 0.795 12.128 47739 Z= 0.396 Chirality : 0.047 0.235 5435 Planarity : 0.006 0.088 6200 Dihedral : 8.835 178.001 4874 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 41.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % 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: -1.64 (0.12), residues: 4384 helix: -0.20 (0.12), residues: 1895 sheet: -1.66 (0.26), residues: 388 loop : -1.80 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 292 HIS 0.014 0.002 HIS B 664 PHE 0.027 0.002 PHE A 467 TYR 0.024 0.002 TYR C 455 ARG 0.012 0.001 ARG D 694 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 3.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.6261 (mmp) cc_final: 0.6033 (mmp) REVERT: A 258 MET cc_start: 0.2847 (ptt) cc_final: 0.2357 (ptt) REVERT: A 409 MET cc_start: 0.9071 (mmp) cc_final: 0.8572 (mmp) REVERT: A 633 MET cc_start: 0.8378 (mpp) cc_final: 0.8098 (mpp) REVERT: B 38 MET cc_start: 0.2771 (mtt) cc_final: 0.2500 (mtt) REVERT: C 132 PHE cc_start: 0.8234 (m-80) cc_final: 0.7787 (m-80) REVERT: D 75 MET cc_start: 0.1665 (pmm) cc_final: 0.1156 (pmm) REVERT: D 260 GLU cc_start: 0.9727 (mm-30) cc_final: 0.9457 (tp30) REVERT: D 698 MET cc_start: 0.7602 (mmm) cc_final: 0.7267 (mmm) REVERT: E 258 MET cc_start: 0.8409 (mmp) cc_final: 0.8000 (mmp) REVERT: E 427 MET cc_start: 0.8198 (mmt) cc_final: 0.7976 (mmt) REVERT: E 633 MET cc_start: 0.9378 (mmt) cc_final: 0.9170 (mmt) REVERT: F 258 MET cc_start: 0.5875 (mmt) cc_final: 0.4958 (mmt) REVERT: F 427 MET cc_start: 0.5893 (tpt) cc_final: 0.5571 (tpt) REVERT: F 439 MET cc_start: 0.8056 (mpp) cc_final: 0.7499 (mpp) REVERT: F 633 MET cc_start: 0.8973 (mmp) cc_final: 0.8600 (mmm) REVERT: F 683 MET cc_start: 0.9160 (mpp) cc_final: 0.8119 (ptt) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.4538 time to fit residues: 132.3472 Evaluate side-chains 153 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 9.9990 chunk 370 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 320 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 96 optimal weight: 50.0000 chunk 348 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 357 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 GLN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.099909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.058638 restraints weight = 447484.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.057510 restraints weight = 414169.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.056956 restraints weight = 362191.257| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35214 Z= 0.211 Angle : 0.699 11.458 47739 Z= 0.342 Chirality : 0.045 0.218 5435 Planarity : 0.005 0.087 6200 Dihedral : 8.653 177.834 4874 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 31.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % 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: -1.48 (0.13), residues: 4384 helix: -0.07 (0.12), residues: 1898 sheet: -1.73 (0.27), residues: 377 loop : -1.67 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 292 HIS 0.008 0.001 HIS B 454 PHE 0.023 0.002 PHE A 467 TYR 0.027 0.002 TYR C 455 ARG 0.008 0.000 ARG D 552 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7401.10 seconds wall clock time: 134 minutes 34.78 seconds (8074.78 seconds total)