Starting phenix.real_space_refine on Mon Apr 15 10:58:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3y_36867/04_2024/8k3y_36867_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3y_36867/04_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_36867/04_2024/8k3y_36867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3y_36867/04_2024/8k3y_36867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3y_36867/04_2024/8k3y_36867_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3y_36867/04_2024/8k3y_36867_updated.pdb" } 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 19.06, per 1000 atoms: 0.55 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: 14.92 Conformation dependent library (CDL) restraints added in 6.7 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... running ksdssp... Secondary structure from input PDB file: 170 helices and 37 sheets defined 41.0% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.93 Creating SS restraints... Processing helix chain 'A' and resid 31 through 40 removed outlier: 3.558A pdb=" N GLY A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 142 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) removed outlier: 3.638A pdb=" N LYS A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N SER A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU A 142 " --> pdb=" O ASN A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 150 No H-bonds generated for 'chain 'A' and resid 147 through 150' Processing helix chain 'A' and resid 158 through 168 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 185 through 233 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) Processing helix chain 'A' and resid 244 through 254 removed outlier: 4.287A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.823A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 317 removed outlier: 4.064A pdb=" N GLU A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 336 Processing helix chain 'A' and resid 361 through 371 removed outlier: 3.765A pdb=" N GLY A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 No H-bonds generated for 'chain 'A' and resid 387 through 390' Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.717A pdb=" N MET A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 495 through 504 removed outlier: 3.808A pdb=" N ARG A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 512 Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'A' and resid 541 through 558 Processing helix chain 'A' and resid 571 through 577 Proline residue: A 575 - end of helix Processing helix chain 'A' and resid 631 through 645 Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 718 through 727 Processing helix chain 'A' and resid 737 through 744 removed outlier: 4.828A pdb=" N ALA A 741 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 764 No H-bonds generated for 'chain 'A' and resid 762 through 764' Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 118 through 138 removed outlier: 3.548A pdb=" N VAL B 136 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 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) Processing helix chain 'B' and resid 158 through 167 removed outlier: 3.828A pdb=" N ASP B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 185 through 240 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 246 through 254 removed outlier: 3.953A pdb=" N GLU B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 309 through 318 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 324 removed outlier: 4.479A pdb=" N LYS B 323 " --> pdb=" O TYR B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 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 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 404 through 412 Processing helix chain 'B' and resid 435 through 443 Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'B' and resid 541 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 577 Processing helix chain 'B' and resid 585 through 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 631 through 646 Processing helix chain 'B' and resid 680 through 692 removed outlier: 3.737A pdb=" N ALA B 688 " --> pdb=" O ALA B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 763 through 769 Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.703A pdb=" N ARG C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 33' Processing helix chain 'C' and resid 118 through 138 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 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 158 through 168 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) Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 185 through 237 removed outlier: 3.511A pdb=" N GLN C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 256 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 282 through 295 Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.565A pdb=" N ASP C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 337 Processing helix chain 'C' and resid 361 through 372 Processing helix chain 'C' and resid 381 through 383 No H-bonds generated for 'chain 'C' and resid 381 through 383' Processing helix chain 'C' and resid 387 through 390 No H-bonds generated for 'chain 'C' and resid 387 through 390' Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 445 through 448 No H-bonds generated for 'chain 'C' and resid 445 through 448' Processing helix chain 'C' and resid 479 through 482 No H-bonds generated for 'chain 'C' and resid 479 through 482' Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 506 through 513 Processing helix chain 'C' and resid 524 through 533 Processing helix chain 'C' and resid 541 through 559 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 571 through 577 Proline residue: C 575 - end of helix No H-bonds generated for 'chain 'C' and resid 571 through 577' Processing helix chain 'C' and resid 587 through 589 No H-bonds generated for 'chain 'C' and resid 587 through 589' Processing helix chain 'C' and resid 631 through 646 Processing helix chain 'C' and resid 676 through 679 removed outlier: 4.394A pdb=" N ALA C 679 " --> pdb=" O GLY C 676 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 676 through 679' Processing helix chain 'C' and resid 682 through 691 Processing helix chain 'C' and resid 718 through 727 removed outlier: 3.847A pdb=" N LEU C 723 " --> pdb=" O LYS C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 740 Processing helix chain 'C' and resid 748 through 753 removed outlier: 4.750A pdb=" N GLY C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 769 Processing helix chain 'D' and resid 28 through 38 removed outlier: 3.519A pdb=" N LYS D 31 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET D 38 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 142 removed outlier: 4.132A pdb=" N SER D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 151 No H-bonds generated for 'chain 'D' and resid 148 through 151' Processing helix chain 'D' and resid 158 through 168 removed outlier: 3.804A pdb=" N ASP D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 186 through 232 Processing helix chain 'D' and resid 240 through 255 removed outlier: 6.033A pdb=" N ASP D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 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 282 through 294 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 308 through 315 Processing helix chain 'D' and resid 326 through 338 removed outlier: 3.777A pdb=" N TYR D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 372 Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 424 through 426 No H-bonds generated for 'chain 'D' and resid 424 through 426' Processing helix chain 'D' and resid 435 through 443 Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 474 through 476 No H-bonds generated for 'chain 'D' and resid 474 through 476' Processing helix chain 'D' and resid 479 through 481 No H-bonds generated for 'chain 'D' and resid 479 through 481' Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 506 through 513 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 543 through 559 Processing helix chain 'D' and resid 631 through 646 Processing helix chain 'D' and resid 680 through 692 Processing helix chain 'D' and resid 718 through 726 Processing helix chain 'D' and resid 737 through 744 removed outlier: 3.929A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 753 removed outlier: 4.112A pdb=" N GLY D 753 " --> pdb=" O GLU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 769 removed outlier: 4.060A pdb=" N TYR D 768 " --> pdb=" O GLU D 764 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 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) removed outlier: 4.053A pdb=" N GLY E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 118 through 137 Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'E' and resid 158 through 168 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 181 removed outlier: 3.544A pdb=" N GLU E 178 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 180 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU E 181 " --> pdb=" O GLU E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 236 Processing helix chain 'E' and resid 238 through 256 Processing helix chain 'E' and resid 260 through 272 Processing helix chain 'E' and resid 281 through 294 removed outlier: 3.696A pdb=" N THR E 294 " --> pdb=" O LEU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 319 removed outlier: 4.357A pdb=" N ASP E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 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 361 through 371 Processing helix chain 'E' and resid 387 through 390 No H-bonds generated for 'chain 'E' and resid 387 through 390' Processing helix chain 'E' and resid 404 through 411 removed outlier: 3.660A pdb=" N GLN E 411 " --> pdb=" O HIS E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 426 No H-bonds generated for 'chain 'E' and resid 424 through 426' Processing helix chain 'E' and resid 435 through 443 removed outlier: 3.867A pdb=" N ALA E 438 " --> pdb=" O PRO E 435 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU E 440 " --> pdb=" O SER E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 464 No H-bonds generated for 'chain 'E' and resid 462 through 464' Processing helix chain 'E' and resid 479 through 482 Processing helix chain 'E' and resid 495 through 504 Processing helix chain 'E' and resid 506 through 513 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 541 through 555 Processing helix chain 'E' and resid 574 through 577 No H-bonds generated for 'chain 'E' and resid 574 through 577' Processing helix chain 'E' and resid 631 through 646 Processing helix chain 'E' and resid 680 through 692 Processing helix chain 'E' and resid 718 through 727 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 748 through 751 No H-bonds generated for 'chain 'E' and resid 748 through 751' Processing helix chain 'E' and resid 762 through 766 Processing helix chain 'E' and resid 771 through 773 No H-bonds generated for 'chain 'E' and resid 771 through 773' Processing helix chain 'F' and resid 245 through 251 removed outlier: 3.703A pdb=" N ARG F 250 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 272 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 281 through 292 removed outlier: 3.718A pdb=" N ASP F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 318 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 325 through 334 Processing helix chain 'F' and resid 361 through 371 removed outlier: 3.701A pdb=" N GLY F 365 " --> pdb=" O LYS F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 390 No H-bonds generated for 'chain 'F' and resid 387 through 390' Processing helix chain 'F' and resid 404 through 408 Processing helix chain 'F' and resid 436 through 443 Processing helix chain 'F' and resid 446 through 449 No H-bonds generated for 'chain 'F' and resid 446 through 449' Processing helix chain 'F' and resid 479 through 482 No H-bonds generated for 'chain 'F' and resid 479 through 482' Processing helix chain 'F' and resid 495 through 504 Processing helix chain 'F' and resid 507 through 514 Processing helix chain 'F' and resid 524 through 534 removed outlier: 3.639A pdb=" N GLU F 533 " --> pdb=" O ARG F 529 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 559 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) Processing helix chain 'F' and resid 572 through 576 removed outlier: 3.986A pdb=" N THR F 576 " --> pdb=" O SER F 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 572 through 576' Processing helix chain 'F' and resid 631 through 646 removed outlier: 3.712A pdb=" N ALA F 639 " --> pdb=" O GLU F 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 651 No H-bonds generated for 'chain 'F' and resid 649 through 651' Processing helix chain 'F' and resid 680 through 692 Processing helix chain 'F' and resid 718 through 727 Processing helix chain 'F' and resid 737 through 745 removed outlier: 3.933A pdb=" N GLU F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 753 No H-bonds generated for 'chain 'F' and resid 751 through 753' Processing helix chain 'F' and resid 762 through 769 removed outlier: 3.754A pdb=" N LEU F 766 " --> pdb=" O VAL F 762 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU F 767 " --> pdb=" O GLY F 763 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TYR F 768 " --> pdb=" O GLU F 764 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU F 769 " --> pdb=" O VAL F 765 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 762 through 769' Processing sheet with id= A, first strand: chain 'A' and resid 7 through 10 removed outlier: 8.464A pdb=" N ILE A 8 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE A 45 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU A 10 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL A 47 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.986A pdb=" N ILE A 488 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 376 through 380 removed outlier: 6.450A pdb=" N VAL A 418 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE A 379 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU A 420 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE A 466 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU A 421 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 468 " --> pdb=" O LEU A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 520 through 522 removed outlier: 5.803A pdb=" N ARG A 567 " --> pdb=" O GLU A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 600 through 603 Processing sheet with id= F, first strand: chain 'A' and resid 612 through 614 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) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 732 through 734 removed outlier: 7.018A pdb=" N GLU A 755 " --> pdb=" O ILE A 733 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 23 through 25 removed outlier: 3.855A pdb=" N GLN B 83 " --> pdb=" O MET B 75 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 75 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 73 " --> pdb=" O MET B 85 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 43 through 47 removed outlier: 5.747A pdb=" N VAL B 70 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA B 88 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 376 through 379 removed outlier: 6.788A pdb=" N VAL B 418 " --> pdb=" O HIS B 377 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ILE B 379 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU B 420 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE B 466 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU B 421 " --> pdb=" O PHE B 466 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 468 " --> pdb=" O LEU B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 520 through 522 removed outlier: 5.503A pdb=" N ARG B 567 " --> pdb=" O GLU B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, 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= M, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.190A pdb=" N GLU B 755 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 735 " --> pdb=" O GLU B 755 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LYS B 757 " --> pdb=" O LEU B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, 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) Processing sheet with id= O, first strand: chain 'C' and resid 65 through 67 Processing sheet with id= P, first strand: chain 'C' and resid 485 through 489 removed outlier: 6.302A pdb=" N ILE C 350 " --> pdb=" O GLU C 486 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE C 488 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 352 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N PHE C 467 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N LEU C 353 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR C 469 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.328A pdb=" N ARG C 567 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 598 through 600 Processing sheet with id= S, first strand: chain 'C' and resid 613 through 618 Processing sheet with id= T, first strand: chain 'C' and resid 732 through 736 removed outlier: 6.098A pdb=" N GLU C 755 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU C 735 " --> pdb=" O GLU C 755 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS C 757 " --> pdb=" O LEU C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 21 through 23 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: 3.888A pdb=" N VAL D 84 " --> pdb=" O VAL D 23 " (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= V, first strand: chain 'D' and resid 350 through 355 Processing sheet with id= W, first strand: chain 'D' and resid 418 through 421 removed outlier: 6.939A pdb=" N PHE D 466 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU D 421 " --> pdb=" O PHE D 466 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE D 468 " --> pdb=" O LEU D 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 520 through 522 removed outlier: 5.777A pdb=" N ARG D 567 " --> pdb=" O GLU D 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 600 through 602 Processing sheet with id= Z, first strand: chain 'D' and resid 612 through 618 removed outlier: 4.243A pdb=" N VAL D 667 " --> pdb=" O THR D 626 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 732 through 736 removed outlier: 5.940A pdb=" N GLU D 755 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU D 735 " --> pdb=" O GLU D 755 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 20 through 25 removed outlier: 3.506A pdb=" N GLU E 87 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLN E 68 " --> pdb=" O ARG E 89 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG E 91 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY E 66 " --> pdb=" O ARG E 91 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 96 through 98 Processing sheet with id= AD, first strand: chain 'E' and resid 352 through 355 Processing sheet with id= AE, first strand: chain 'E' and resid 375 through 378 removed outlier: 4.019A pdb=" N LEU E 420 " --> pdb=" O HIS E 377 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 520 through 522 removed outlier: 5.561A pdb=" N ARG E 567 " --> pdb=" O GLU E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'E' and resid 613 through 615 Processing sheet with id= AH, first strand: chain 'E' and resid 700 through 702 removed outlier: 6.587A pdb=" N LYS E 732 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU E 755 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU E 735 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LYS E 757 " --> pdb=" O LEU E 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 376 through 378 removed outlier: 6.230A pdb=" N VAL F 418 " --> pdb=" O HIS F 377 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE F 468 " --> pdb=" O LEU F 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 613 through 618 Processing sheet with id= AK, first strand: chain 'F' and resid 732 through 735 removed outlier: 6.461A pdb=" N GLU F 755 " --> pdb=" O ILE F 733 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU F 735 " --> pdb=" O GLU F 755 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS F 757 " --> pdb=" O LEU F 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK 1163 hydrogen bonds defined for protein. 3375 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: 12.31 Time building geometry restraints manager: 15.89 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: 6140 2.77 - 3.30: 36110 3.30 - 3.83: 66915 3.83 - 4.37: 78620 4.37 - 4.90: 121480 Nonbonded interactions: 309265 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 309260 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: 2.120 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: 8.830 Check model and map are aligned: 0.450 Set scattering table: 0.320 Process input model: 92.480 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.310 ------------------------------------------------------------------------------- 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 : 3.916 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: 0.4703 time to fit residues: 146.8807 Evaluate side-chains 155 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 3.962 ------------------------------------------------------------------------------- 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: 5.9990 chunk 113 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 177 optimal weight: 20.0000 chunk 343 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 397 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 ASN ** D 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 647 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.1002 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= 0.197 Angle : 0.668 10.440 47739 Z= 0.336 Chirality : 0.043 0.187 5435 Planarity : 0.006 0.082 6200 Dihedral : 9.215 170.339 4874 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 26.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.03 % Allowed : 4.72 % Favored : 95.25 % 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: -2.23 (0.12), residues: 4384 helix: -0.96 (0.11), residues: 1853 sheet: -2.03 (0.26), residues: 365 loop : -1.80 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 563 HIS 0.009 0.001 HIS D 664 PHE 0.026 0.002 PHE A 467 TYR 0.025 0.002 TYR C 455 ARG 0.006 0.000 ARG C 536 *********************** 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 179 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 3.993 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 702 MET cc_start: 0.2692 (tpp) cc_final: 0.2446 (mmm) REVERT: B 38 MET cc_start: 0.2965 (mtt) cc_final: 0.2602 (mtt) REVERT: B 424 ILE cc_start: 0.9299 (mp) cc_final: 0.8821 (mp) REVERT: B 485 MET cc_start: 0.6654 (pmm) cc_final: 0.6445 (pmm) REVERT: C 132 PHE cc_start: 0.8501 (m-80) cc_final: 0.8146 (m-80) REVERT: C 258 MET cc_start: 0.3479 (mmt) cc_final: 0.3257 (mmt) REVERT: C 401 MET cc_start: 0.8220 (mmp) cc_final: 0.8001 (tpp) REVERT: D 75 MET cc_start: 0.1356 (pmm) cc_final: 0.0806 (pmm) REVERT: D 631 GLU cc_start: 0.9704 (pm20) cc_final: 0.9295 (tp30) REVERT: D 702 MET cc_start: 0.6307 (ptm) cc_final: 0.6059 (tmm) REVERT: E 258 MET cc_start: 0.7933 (mmp) cc_final: 0.7214 (mmp) REVERT: E 427 MET cc_start: 0.7481 (mmt) cc_final: 0.7102 (mmt) REVERT: E 633 MET cc_start: 0.9388 (mmt) cc_final: 0.9148 (mmt) REVERT: F 427 MET cc_start: 0.5421 (tpt) cc_final: 0.5007 (tpt) REVERT: F 439 MET cc_start: 0.7919 (mpp) cc_final: 0.7401 (mpp) REVERT: F 633 MET cc_start: 0.8966 (mmp) cc_final: 0.8519 (mmm) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.4484 time to fit residues: 139.3739 Evaluate side-chains 154 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 4.257 ------------------------------------------------------------------------------- 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: 0.0470 chunk 123 optimal weight: 10.0000 chunk 331 optimal weight: 6.9990 chunk 270 optimal weight: 40.0000 chunk 109 optimal weight: 9.9990 chunk 398 optimal weight: 0.9990 chunk 430 optimal weight: 30.0000 chunk 354 optimal weight: 7.9990 chunk 395 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 319 optimal weight: 0.4980 overall best weight: 3.3084 ------------------------------------------------------------------------------- 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN D 229 GLN ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 647 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35214 Z= 0.188 Angle : 0.644 12.352 47739 Z= 0.320 Chirality : 0.043 0.167 5435 Planarity : 0.005 0.080 6200 Dihedral : 8.903 172.315 4874 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 27.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: -1.86 (0.12), residues: 4384 helix: -0.54 (0.12), residues: 1855 sheet: -2.04 (0.26), residues: 382 loop : -1.66 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 563 HIS 0.006 0.001 HIS B 664 PHE 0.028 0.002 PHE A 467 TYR 0.020 0.001 TYR C 455 ARG 0.006 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 176 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 3.995 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: B 38 MET cc_start: 0.2679 (mtt) cc_final: 0.2278 (mtt) REVERT: B 424 ILE cc_start: 0.9301 (mp) cc_final: 0.8872 (mp) REVERT: B 485 MET cc_start: 0.6494 (pmm) cc_final: 0.6251 (pmm) REVERT: C 132 PHE cc_start: 0.8360 (m-80) cc_final: 0.7974 (m-80) REVERT: C 401 MET cc_start: 0.8094 (mmp) cc_final: 0.7693 (tpp) REVERT: D 75 MET cc_start: 0.1383 (pmm) cc_final: 0.0898 (pmm) REVERT: D 631 GLU cc_start: 0.9730 (pm20) cc_final: 0.9316 (tp30) REVERT: E 258 MET cc_start: 0.7983 (mmp) cc_final: 0.7109 (mmp) REVERT: E 427 MET cc_start: 0.7630 (mmt) cc_final: 0.7283 (mmt) REVERT: E 683 MET cc_start: 0.9613 (pmm) cc_final: 0.9397 (pmm) REVERT: F 427 MET cc_start: 0.5306 (tpt) cc_final: 0.4915 (tpt) REVERT: F 439 MET cc_start: 0.7847 (mpp) cc_final: 0.7322 (mpp) REVERT: F 633 MET cc_start: 0.8924 (mmp) cc_final: 0.8489 (mmm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.4459 time to fit residues: 135.7494 Evaluate side-chains 153 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.951 ------------------------------------------------------------------------------- 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: 4.9990 chunk 299 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 190 optimal weight: 8.9990 chunk 267 optimal weight: 5.9990 chunk 399 optimal weight: 3.9990 chunk 423 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 chunk 379 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN B 83 GLN ** B 313 GLN ** 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 C 666 HIS ** D 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 647 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35214 Z= 0.272 Angle : 0.718 11.731 47739 Z= 0.359 Chirality : 0.044 0.164 5435 Planarity : 0.005 0.065 6200 Dihedral : 8.941 175.263 4874 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 36.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.03 % Allowed : 4.88 % Favored : 95.09 % 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: -1.80 (0.12), residues: 4384 helix: -0.46 (0.12), residues: 1867 sheet: -2.14 (0.25), residues: 386 loop : -1.63 (0.13), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 563 HIS 0.013 0.002 HIS B 664 PHE 0.035 0.002 PHE A 467 TYR 0.032 0.002 TYR C 455 ARG 0.008 0.001 ARG C 512 *********************** 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 179 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 4.336 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 496 MET cc_start: 0.9702 (mpp) cc_final: 0.9501 (mpp) REVERT: B 38 MET cc_start: 0.2623 (mtt) cc_final: 0.2228 (mtt) REVERT: B 424 ILE cc_start: 0.9424 (mp) cc_final: 0.9061 (mp) REVERT: B 477 ILE cc_start: 0.9322 (pt) cc_final: 0.8744 (mm) REVERT: B 479 ARG cc_start: 0.9305 (mmp-170) cc_final: 0.8978 (mmp80) REVERT: B 485 MET cc_start: 0.6598 (pmm) cc_final: 0.6395 (pmm) REVERT: C 132 PHE cc_start: 0.8390 (m-80) cc_final: 0.7973 (m-80) REVERT: C 401 MET cc_start: 0.8091 (mmp) cc_final: 0.7487 (tpp) REVERT: D 75 MET cc_start: 0.0239 (pmm) cc_final: -0.0311 (pmm) REVERT: D 631 GLU cc_start: 0.9783 (pm20) cc_final: 0.9383 (tp30) REVERT: E 258 MET cc_start: 0.8229 (mmp) cc_final: 0.7418 (mmp) REVERT: E 427 MET cc_start: 0.7984 (mmt) cc_final: 0.7684 (mmt) REVERT: E 496 MET cc_start: 0.9029 (ptp) cc_final: 0.8800 (ptp) REVERT: E 683 MET cc_start: 0.9617 (pmm) cc_final: 0.9373 (pmm) REVERT: F 427 MET cc_start: 0.5841 (tpt) cc_final: 0.5511 (tpt) REVERT: F 439 MET cc_start: 0.7932 (mpp) cc_final: 0.7386 (mpp) REVERT: F 633 MET cc_start: 0.8930 (mmp) cc_final: 0.8496 (mmm) outliers start: 1 outliers final: 1 residues processed: 179 average time/residue: 0.4795 time to fit residues: 145.4994 Evaluate side-chains 156 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 4.183 ------------------------------------------------------------------------------- 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: 0.7980 chunk 240 optimal weight: 30.0000 chunk 6 optimal weight: 40.0000 chunk 315 optimal weight: 40.0000 chunk 174 optimal weight: 40.0000 chunk 361 optimal weight: 20.0000 chunk 292 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 216 optimal weight: 6.9990 chunk 380 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 overall best weight: 7.7590 ------------------------------------------------------------------------------- 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 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 GLN ** 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 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 647 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35214 Z= 0.335 Angle : 0.800 12.513 47739 Z= 0.402 Chirality : 0.047 0.272 5435 Planarity : 0.006 0.073 6200 Dihedral : 9.137 176.198 4874 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 44.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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: -1.97 (0.12), residues: 4384 helix: -0.55 (0.12), residues: 1867 sheet: -2.18 (0.24), residues: 412 loop : -1.78 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 431 HIS 0.014 0.002 HIS E 666 PHE 0.041 0.003 PHE A 467 TYR 0.030 0.002 TYR C 455 ARG 0.012 0.001 ARG D 694 *********************** 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 172 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 4.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.1128 (ptt) cc_final: 0.0887 (ptt) REVERT: A 496 MET cc_start: 0.9711 (mpp) cc_final: 0.9498 (mpp) REVERT: B 38 MET cc_start: 0.3110 (mtt) cc_final: 0.2740 (mtt) REVERT: B 424 ILE cc_start: 0.9476 (mp) cc_final: 0.9168 (mp) REVERT: B 477 ILE cc_start: 0.9278 (pt) cc_final: 0.8853 (mm) REVERT: B 479 ARG cc_start: 0.9327 (mmp-170) cc_final: 0.9029 (mmp80) REVERT: B 485 MET cc_start: 0.6911 (pmm) cc_final: 0.6643 (pmm) REVERT: B 698 MET cc_start: 0.8241 (ttt) cc_final: 0.7953 (ttt) REVERT: C 132 PHE cc_start: 0.8247 (m-80) cc_final: 0.7795 (m-80) REVERT: C 401 MET cc_start: 0.8110 (mmp) cc_final: 0.7374 (tpp) REVERT: D 401 MET cc_start: 0.9589 (tpt) cc_final: 0.9010 (pmm) REVERT: D 698 MET cc_start: 0.7745 (mmm) cc_final: 0.7450 (mmm) REVERT: D 702 MET cc_start: 0.5864 (tmm) cc_final: 0.5634 (tmm) REVERT: E 38 MET cc_start: 0.5421 (mpp) cc_final: 0.4506 (pmm) REVERT: E 258 MET cc_start: 0.8308 (mmp) cc_final: 0.7910 (mmp) REVERT: E 427 MET cc_start: 0.8110 (mmt) cc_final: 0.7881 (mmt) REVERT: E 683 MET cc_start: 0.9495 (pmm) cc_final: 0.9259 (pmm) REVERT: F 427 MET cc_start: 0.6332 (tpt) cc_final: 0.5987 (tpt) REVERT: F 439 MET cc_start: 0.8099 (mpp) cc_final: 0.7699 (mpp) REVERT: F 633 MET cc_start: 0.8938 (mmp) cc_final: 0.8517 (mmm) REVERT: F 647 HIS cc_start: 0.9048 (t70) cc_final: 0.8427 (t70) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.4837 time to fit residues: 140.5485 Evaluate side-chains 150 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 4.264 ------------------------------------------------------------------------------- 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: 9.9990 chunk 381 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 248 optimal weight: 40.0000 chunk 104 optimal weight: 20.0000 chunk 423 optimal weight: 40.0000 chunk 351 optimal weight: 0.6980 chunk 196 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN C 666 HIS ** C 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.2474 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= 0.214 Angle : 0.690 11.206 47739 Z= 0.340 Chirality : 0.045 0.391 5435 Planarity : 0.005 0.063 6200 Dihedral : 8.880 176.719 4874 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 33.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.03 % Allowed : 1.95 % Favored : 98.02 % 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: -1.74 (0.12), residues: 4384 helix: -0.30 (0.12), residues: 1842 sheet: -2.18 (0.24), residues: 418 loop : -1.66 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 563 HIS 0.008 0.001 HIS B 454 PHE 0.027 0.002 PHE A 467 TYR 0.026 0.002 TYR C 455 ARG 0.013 0.000 ARG A 378 *********************** 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 179 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 4.173 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: 0.1814 (ptt) cc_final: 0.1487 (ptt) REVERT: A 409 MET cc_start: 0.8949 (mmp) cc_final: 0.8345 (mmp) REVERT: A 496 MET cc_start: 0.9679 (mpp) cc_final: 0.9429 (mpp) REVERT: B 38 MET cc_start: 0.3091 (mtt) cc_final: 0.2725 (mtt) REVERT: B 424 ILE cc_start: 0.9435 (mp) cc_final: 0.9091 (mp) REVERT: B 477 ILE cc_start: 0.9248 (pt) cc_final: 0.8859 (mm) REVERT: B 479 ARG cc_start: 0.9288 (mmp-170) cc_final: 0.8984 (mmp80) REVERT: B 485 MET cc_start: 0.6844 (pmm) cc_final: 0.6525 (pmm) REVERT: C 132 PHE cc_start: 0.8236 (m-80) cc_final: 0.7823 (m-80) REVERT: D 75 MET cc_start: 0.0596 (pmm) cc_final: -0.0051 (pmm) REVERT: D 401 MET cc_start: 0.9578 (tpt) cc_final: 0.9058 (pmm) REVERT: D 698 MET cc_start: 0.7691 (mmm) cc_final: 0.7388 (mmm) REVERT: D 702 MET cc_start: 0.5810 (tmm) cc_final: 0.5576 (tmm) REVERT: E 38 MET cc_start: 0.5351 (mpp) cc_final: 0.4717 (pmm) REVERT: E 258 MET cc_start: 0.8230 (mmp) cc_final: 0.7821 (mmp) REVERT: E 427 MET cc_start: 0.8079 (mmt) cc_final: 0.7814 (mmt) REVERT: E 683 MET cc_start: 0.9488 (pmm) cc_final: 0.9242 (pmm) REVERT: F 427 MET cc_start: 0.5773 (tpt) cc_final: 0.5490 (tpt) REVERT: F 439 MET cc_start: 0.8008 (mpp) cc_final: 0.7648 (mpp) REVERT: F 633 MET cc_start: 0.8892 (mmp) cc_final: 0.8428 (mmm) REVERT: F 647 HIS cc_start: 0.9129 (t70) cc_final: 0.8517 (t70) outliers start: 1 outliers final: 1 residues processed: 179 average time/residue: 0.4914 time to fit residues: 149.1915 Evaluate side-chains 159 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 4.055 ------------------------------------------------------------------------------- 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: 0.6980 chunk 47 optimal weight: 10.0000 chunk 241 optimal weight: 50.0000 chunk 309 optimal weight: 50.0000 chunk 239 optimal weight: 8.9990 chunk 356 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 chunk 422 optimal weight: 9.9990 chunk 264 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35214 Z= 0.258 Angle : 0.714 11.486 47739 Z= 0.355 Chirality : 0.045 0.214 5435 Planarity : 0.005 0.062 6200 Dihedral : 8.842 178.893 4874 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 37.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: -0.23 (0.12), residues: 1835 sheet: -2.14 (0.25), residues: 398 loop : -1.66 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 431 HIS 0.011 0.002 HIS B 664 PHE 0.032 0.002 PHE A 467 TYR 0.027 0.002 TYR D 455 ARG 0.008 0.001 ARG D 694 *********************** 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 171 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 4.138 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 409 MET cc_start: 0.9076 (mmp) cc_final: 0.8541 (mmp) REVERT: A 496 MET cc_start: 0.9666 (mpp) cc_final: 0.9415 (mpp) REVERT: B 38 MET cc_start: 0.2760 (mtt) cc_final: 0.2425 (mtt) REVERT: B 424 ILE cc_start: 0.9474 (mp) cc_final: 0.9138 (mp) REVERT: B 477 ILE cc_start: 0.9221 (pt) cc_final: 0.8810 (mm) REVERT: B 479 ARG cc_start: 0.9300 (mmp-170) cc_final: 0.9000 (mmp80) REVERT: B 485 MET cc_start: 0.6863 (pmm) cc_final: 0.6547 (pmm) REVERT: C 132 PHE cc_start: 0.8198 (m-80) cc_final: 0.7848 (m-80) REVERT: D 702 MET cc_start: 0.5702 (tmm) cc_final: 0.5460 (tmm) REVERT: E 38 MET cc_start: 0.5273 (mpp) cc_final: 0.4453 (pmm) REVERT: E 258 MET cc_start: 0.8321 (mmp) cc_final: 0.7897 (mmp) REVERT: E 427 MET cc_start: 0.8034 (mmt) cc_final: 0.7783 (mmt) REVERT: E 683 MET cc_start: 0.9516 (pmm) cc_final: 0.9238 (pmm) REVERT: F 439 MET cc_start: 0.8092 (mpp) cc_final: 0.7704 (mpp) REVERT: F 633 MET cc_start: 0.8907 (mmp) cc_final: 0.8448 (mmm) REVERT: F 647 HIS cc_start: 0.9164 (t70) cc_final: 0.8424 (t70) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.4889 time to fit residues: 140.5410 Evaluate side-chains 151 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 3.802 ------------------------------------------------------------------------------- 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: 0.7980 chunk 82 optimal weight: 50.0000 chunk 81 optimal weight: 50.0000 chunk 268 optimal weight: 10.0000 chunk 287 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 331 optimal weight: 3.9990 overall best weight: 6.1590 ------------------------------------------------------------------------------- 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 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 HIS ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35214 Z= 0.288 Angle : 0.755 12.648 47739 Z= 0.373 Chirality : 0.046 0.240 5435 Planarity : 0.005 0.062 6200 Dihedral : 8.895 179.706 4874 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 40.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -1.72 (0.12), residues: 4384 helix: -0.27 (0.12), residues: 1835 sheet: -2.16 (0.26), residues: 368 loop : -1.71 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.003 TRP E 292 HIS 0.012 0.002 HIS B 664 PHE 0.040 0.002 PHE A 467 TYR 0.028 0.002 TYR D 455 ARG 0.010 0.001 ARG D 694 *********************** 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 171 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 4.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.9097 (mmp) cc_final: 0.8622 (mmp) REVERT: A 496 MET cc_start: 0.9666 (mpp) cc_final: 0.9415 (mpp) REVERT: B 38 MET cc_start: 0.2689 (mtt) cc_final: 0.2365 (mtt) REVERT: B 424 ILE cc_start: 0.9498 (mp) cc_final: 0.9181 (mp) REVERT: B 477 ILE cc_start: 0.9170 (pt) cc_final: 0.8731 (mm) REVERT: B 479 ARG cc_start: 0.9309 (mmp-170) cc_final: 0.9014 (mmp80) REVERT: B 485 MET cc_start: 0.6840 (pmm) cc_final: 0.6561 (pmm) REVERT: C 132 PHE cc_start: 0.8203 (m-80) cc_final: 0.7827 (m-80) REVERT: D 698 MET cc_start: 0.7705 (mmm) cc_final: 0.7395 (mmm) REVERT: D 702 MET cc_start: 0.5727 (tmm) cc_final: 0.5488 (tmm) REVERT: E 38 MET cc_start: 0.5341 (mpp) cc_final: 0.4508 (pmm) REVERT: E 258 MET cc_start: 0.8144 (mmp) cc_final: 0.7803 (mmp) REVERT: E 427 MET cc_start: 0.8041 (mmt) cc_final: 0.7826 (mmt) REVERT: F 427 MET cc_start: 0.6396 (tpt) cc_final: 0.6103 (tpt) REVERT: F 439 MET cc_start: 0.8047 (mpp) cc_final: 0.7670 (mpp) REVERT: F 633 MET cc_start: 0.8901 (mmp) cc_final: 0.8441 (mmm) REVERT: F 647 HIS cc_start: 0.9109 (t70) cc_final: 0.8408 (t70) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.4917 time to fit residues: 142.1180 Evaluate side-chains 153 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 4.274 ------------------------------------------------------------------------------- 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: 9.9990 chunk 404 optimal weight: 0.0170 chunk 368 optimal weight: 8.9990 chunk 393 optimal weight: 6.9990 chunk 236 optimal weight: 40.0000 chunk 171 optimal weight: 50.0000 chunk 308 optimal weight: 40.0000 chunk 120 optimal weight: 10.0000 chunk 355 optimal weight: 6.9990 chunk 372 optimal weight: 10.0000 chunk 392 optimal weight: 8.9990 overall best weight: 6.4026 ------------------------------------------------------------------------------- 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 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 35214 Z= 0.298 Angle : 0.783 14.215 47739 Z= 0.388 Chirality : 0.047 0.216 5435 Planarity : 0.006 0.112 6200 Dihedral : 8.938 177.518 4874 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 42.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -1.79 (0.12), residues: 4384 helix: -0.32 (0.12), residues: 1829 sheet: -2.20 (0.26), residues: 381 loop : -1.75 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP E 292 HIS 0.013 0.002 HIS B 664 PHE 0.034 0.002 PHE A 467 TYR 0.026 0.002 TYR C 455 ARG 0.014 0.001 ARG A 582 *********************** 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 170 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 4.390 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 276 MET cc_start: 0.0065 (ptt) cc_final: -0.1054 (ppp) REVERT: A 409 MET cc_start: 0.9222 (mmp) cc_final: 0.8752 (mmp) REVERT: A 496 MET cc_start: 0.9662 (mpp) cc_final: 0.9413 (mpp) REVERT: B 38 MET cc_start: 0.2765 (mtt) cc_final: 0.2433 (mtt) REVERT: B 424 ILE cc_start: 0.9519 (mp) cc_final: 0.9213 (mp) REVERT: B 477 ILE cc_start: 0.9139 (pt) cc_final: 0.8866 (mm) REVERT: B 485 MET cc_start: 0.6901 (pmm) cc_final: 0.6641 (pmm) REVERT: C 132 PHE cc_start: 0.8313 (m-80) cc_final: 0.7873 (m-80) REVERT: D 698 MET cc_start: 0.7660 (mmm) cc_final: 0.7373 (mmm) REVERT: D 702 MET cc_start: 0.5922 (tmm) cc_final: 0.5662 (tmm) REVERT: E 38 MET cc_start: 0.5446 (mpp) cc_final: 0.4908 (pmm) REVERT: E 258 MET cc_start: 0.8195 (mmp) cc_final: 0.7847 (mmp) REVERT: E 427 MET cc_start: 0.8014 (mmt) cc_final: 0.7812 (mmt) REVERT: F 427 MET cc_start: 0.6729 (tpt) cc_final: 0.6490 (tpt) REVERT: F 439 MET cc_start: 0.8016 (mpp) cc_final: 0.7666 (mpp) REVERT: F 633 MET cc_start: 0.8857 (mmp) cc_final: 0.8425 (mmm) REVERT: F 647 HIS cc_start: 0.9130 (t70) cc_final: 0.8399 (t70) REVERT: F 687 ILE cc_start: 0.9119 (mm) cc_final: 0.8795 (pt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.4997 time to fit residues: 142.0905 Evaluate side-chains 150 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 4.146 ------------------------------------------------------------------------------- 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: 30.0000 chunk 253 optimal weight: 30.0000 chunk 197 optimal weight: 3.9990 chunk 289 optimal weight: 0.9990 chunk 436 optimal weight: 6.9990 chunk 401 optimal weight: 5.9990 chunk 347 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 268 optimal weight: 7.9990 chunk 213 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35214 Z= 0.223 Angle : 0.714 12.649 47739 Z= 0.348 Chirality : 0.046 0.228 5435 Planarity : 0.005 0.064 6200 Dihedral : 8.744 176.448 4874 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 34.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.66 (0.12), residues: 4384 helix: -0.18 (0.12), residues: 1837 sheet: -2.10 (0.26), residues: 376 loop : -1.71 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP E 292 HIS 0.008 0.001 HIS B 454 PHE 0.030 0.002 PHE A 467 TYR 0.025 0.002 TYR C 455 ARG 0.010 0.000 ARG A 374 ********************** 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 174 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 3.205 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: 0.2974 (pmm) cc_final: 0.2589 (pmm) REVERT: A 276 MET cc_start: 0.0092 (ptt) cc_final: -0.0818 (ppp) REVERT: A 409 MET cc_start: 0.9177 (mmp) cc_final: 0.8641 (mmp) REVERT: A 496 MET cc_start: 0.9646 (mpp) cc_final: 0.9358 (mpp) REVERT: B 38 MET cc_start: 0.2953 (mtt) cc_final: 0.2621 (mtt) REVERT: B 424 ILE cc_start: 0.9459 (mp) cc_final: 0.9185 (mp) REVERT: B 479 ARG cc_start: 0.9336 (mmp-170) cc_final: 0.9081 (mmp80) REVERT: B 485 MET cc_start: 0.6891 (pmm) cc_final: 0.6568 (pmm) REVERT: C 132 PHE cc_start: 0.8258 (m-80) cc_final: 0.7874 (m-80) REVERT: C 258 MET cc_start: 0.3496 (mmt) cc_final: 0.3174 (mmt) REVERT: D 698 MET cc_start: 0.7643 (mmm) cc_final: 0.7345 (mmm) REVERT: D 702 MET cc_start: 0.5668 (tmm) cc_final: 0.5414 (tmm) REVERT: E 38 MET cc_start: 0.5331 (mpp) cc_final: 0.4475 (pmm) REVERT: E 258 MET cc_start: 0.8098 (mmp) cc_final: 0.7712 (mmp) REVERT: E 427 MET cc_start: 0.7989 (mmt) cc_final: 0.7784 (mmt) REVERT: F 439 MET cc_start: 0.7996 (mpp) cc_final: 0.7683 (mpp) REVERT: F 633 MET cc_start: 0.8936 (mmp) cc_final: 0.8471 (mmm) REVERT: F 687 ILE cc_start: 0.9087 (mm) cc_final: 0.8793 (pt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.4954 time to fit residues: 145.8807 Evaluate side-chains 153 residues out of total 3687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.946 ------------------------------------------------------------------------------- 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: 5.9990 chunk 370 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 320 optimal weight: 10.0000 chunk 51 optimal weight: 0.0170 chunk 96 optimal weight: 50.0000 chunk 348 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 357 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.098870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.052825 restraints weight = 445904.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.053098 restraints weight = 345166.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.053099 restraints weight = 317483.733| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35214 Z= 0.218 Angle : 0.701 14.385 47739 Z= 0.341 Chirality : 0.045 0.201 5435 Planarity : 0.005 0.077 6200 Dihedral : 8.612 175.131 4874 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 34.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.58 (0.13), residues: 4384 helix: -0.09 (0.12), residues: 1843 sheet: -2.15 (0.26), residues: 383 loop : -1.68 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP E 292 HIS 0.008 0.001 HIS B 454 PHE 0.028 0.002 PHE A 467 TYR 0.028 0.002 TYR F 643 ARG 0.011 0.001 ARG D 552 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8034.57 seconds wall clock time: 148 minutes 26.25 seconds (8906.25 seconds total)