Starting phenix.real_space_refine on Tue Aug 26 11:23:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9avv_43924/08_2025/9avv_43924_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9avv_43924/08_2025/9avv_43924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9avv_43924/08_2025/9avv_43924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9avv_43924/08_2025/9avv_43924.map" model { file = "/net/cci-nas-00/data/ceres_data/9avv_43924/08_2025/9avv_43924_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9avv_43924/08_2025/9avv_43924_neut_trim.cif" } resolution = 2.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.052 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 98 5.16 5 C 11790 2.51 5 N 2852 2.21 5 O 3428 1.98 5 H 17490 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35666 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 6487 Classifications: {'peptide': 400} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 379} Chain breaks: 1 Chain: "E" Number of atoms: 6670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 6670 Classifications: {'peptide': 410} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 382} Chain breaks: 2 Chain: "C" Number of atoms: 6501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 6501 Classifications: {'peptide': 401} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 379} Chain breaks: 1 Chain: "D" Number of atoms: 6949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 6949 Classifications: {'peptide': 429} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 398} Chain breaks: 1 Chain: "B" Number of atoms: 6440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 6440 Classifications: {'peptide': 408} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 384} Chain breaks: 1 Chain: "F" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 942 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "G" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 951 Classifications: {'peptide': 62} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "J" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N POV A 501 " occ=0.75 ... (33 atoms not shown) pdb=" P POV A 501 " occ=0.75 residue: pdb=" N POV A 502 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV A 502 " occ=0.75 residue: pdb=" N POV E 601 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV E 601 " occ=0.75 residue: pdb=" N POV E 602 " occ=0.75 ... (33 atoms not shown) pdb=" P POV E 602 " occ=0.75 residue: pdb=" N POV E 603 " occ=0.75 ... (33 atoms not shown) pdb=" P POV E 603 " occ=0.75 residue: pdb=" N POV C 501 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV C 501 " occ=0.75 residue: pdb=" N POV C 502 " occ=0.75 ... (30 atoms not shown) pdb=" P POV C 502 " occ=0.75 residue: pdb=" N POV B 501 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV B 501 " occ=0.75 Time building chain proxies: 5.68, per 1000 atoms: 0.16 Number of scatterers: 35666 At special positions: 0 Unit cell: (99.11, 129.965, 175.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 98 16.00 P 8 15.00 O 3428 8.00 N 2852 7.00 C 11790 6.00 H 17490 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 152 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 162 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 490 " distance=2.02 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 22 " distance=2.03 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 39 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 52 " distance=2.04 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 17 " distance=2.04 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 22 " distance=2.04 Simple disulfide: pdb=" SG CYS G 17 " - pdb=" SG CYS G 39 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 52 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 58 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 5 " - " MAN J 6 " " MAN J 7 " - " MAN J 8 " " MAN J 9 " - " MAN J 10 " " MAN L 4 " - " MAN L 5 " " MAN L 5 " - " MAN L 6 " " MAN L 8 " - " MAN L 9 " " MAN L 10 " - " MAN L 11 " ALPHA1-3 " BMA J 3 " - " MAN J 9 " " MAN J 4 " - " MAN J 5 " " BMA L 3 " - " MAN L 4 " " MAN L 7 " - " MAN L 8 " " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " ALPHA1-6 " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 7 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 7 " " MAN L 7 " - " MAN L 10 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG B 502 " - " ASN B 86 " " NAG D 601 " - " ASN D 96 " " NAG J 1 " - " ASN A 161 " " NAG K 1 " - " ASN E 165 " " NAG L 1 " - " ASN C 161 " " NAG M 1 " - " ASN D 163 " " NAG N 1 " - " ASN B 161 " Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 885.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4156 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 23 sheets defined 41.4% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 Processing helix chain 'A' and resid 88 through 93 removed outlier: 4.171A pdb=" N GLY A 93 " --> pdb=" O ASP A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 238 through 248 Processing helix chain 'A' and resid 249 through 255 removed outlier: 3.792A pdb=" N VAL A 252 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 261 through 284 removed outlier: 3.851A pdb=" N LEU A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 320 Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 389 through 456 removed outlier: 3.694A pdb=" N ALA A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 432 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 442 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ARG A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'E' and resid 107 through 109 No H-bonds generated for 'chain 'E' and resid 107 through 109' Processing helix chain 'E' and resid 246 through 253 Processing helix chain 'E' and resid 253 through 266 Processing helix chain 'E' and resid 267 through 270 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 276 through 296 removed outlier: 4.136A pdb=" N PHE E 283 " --> pdb=" O GLY E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 335 Processing helix chain 'E' and resid 344 through 353 removed outlier: 3.611A pdb=" N ILE E 352 " --> pdb=" O ARG E 348 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS E 353 " --> pdb=" O GLN E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 360 removed outlier: 3.639A pdb=" N TYR E 358 " --> pdb=" O LYS E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 496 removed outlier: 3.817A pdb=" N GLU E 439 " --> pdb=" O PRO E 435 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL E 440 " --> pdb=" O GLU E 436 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP E 464 " --> pdb=" O LEU E 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 32 Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 231 through 238 Processing helix chain 'C' and resid 238 through 251 removed outlier: 3.996A pdb=" N GLY C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 261 through 284 removed outlier: 3.968A pdb=" N LEU C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 320 Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 339 through 344 Processing helix chain 'C' and resid 389 through 456 removed outlier: 3.766A pdb=" N SER C 394 " --> pdb=" O PRO C 390 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP C 419 " --> pdb=" O ALA C 415 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 445 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE C 446 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ARG C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 34 Processing helix chain 'D' and resid 90 through 95 removed outlier: 4.164A pdb=" N GLY D 95 " --> pdb=" O GLU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 262 through 268 Processing helix chain 'D' and resid 275 through 296 removed outlier: 3.515A pdb=" N LEU D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 334 Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 352 through 359 removed outlier: 3.633A pdb=" N GLU D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 493 removed outlier: 3.631A pdb=" N GLU D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) Proline residue: D 436 - end of helix Proline residue: D 478 - end of helix removed outlier: 3.798A pdb=" N GLN D 490 " --> pdb=" O TRP D 486 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY D 491 " --> pdb=" O ILE D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 513 Processing helix chain 'B' and resid 23 through 33 Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.553A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY B 93 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 240 through 247 Processing helix chain 'B' and resid 247 through 257 removed outlier: 3.528A pdb=" N LEU B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.559A pdb=" N ALA B 261 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 292 removed outlier: 3.615A pdb=" N VAL B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 330 Processing helix chain 'B' and resid 339 through 353 Proline residue: B 351 - end of helix Processing helix chain 'B' and resid 418 through 479 removed outlier: 3.521A pdb=" N CYS B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 477 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.238A pdb=" N HIS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY A 134 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.238A pdb=" N HIS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY A 134 " --> pdb=" O ASP A 82 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 69 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A 63 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 71 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG A 75 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU A 57 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS A 77 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU A 55 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLN A 79 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL A 53 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N VAL A 81 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL A 51 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N TYR A 83 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 12.921A pdb=" N VAL A 49 " --> pdb=" O TYR A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 112 removed outlier: 4.763A pdb=" N THR A 168 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 219 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 200 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLN A 228 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ILE A 198 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 101 through 105 removed outlier: 4.064A pdb=" N SER E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY E 138 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 101 through 105 removed outlier: 4.064A pdb=" N SER E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY E 138 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU E 73 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU E 67 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER E 75 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TYR E 79 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU E 61 " --> pdb=" O TYR E 79 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP E 81 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU E 59 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU E 83 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE E 57 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N THR E 85 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL E 55 " --> pdb=" O THR E 85 " (cutoff:3.500A) removed outlier: 11.238A pdb=" N TYR E 87 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 13.338A pdb=" N VAL E 53 " --> pdb=" O TYR E 87 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 114 through 116 removed outlier: 3.535A pdb=" N HIS E 213 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG E 243 " --> pdb=" O ILE E 211 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE E 211 " --> pdb=" O ARG E 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 101 removed outlier: 4.123A pdb=" N HIS C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 101 removed outlier: 4.123A pdb=" N HIS C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 69 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL C 63 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C 71 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG C 75 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU C 57 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS C 77 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU C 55 " --> pdb=" O LYS C 77 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLN C 79 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL C 53 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N VAL C 81 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL C 51 " --> pdb=" O VAL C 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 112 removed outlier: 4.763A pdb=" N THR C 168 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU C 219 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N THR C 216 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE C 209 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR C 218 " --> pdb=" O TRP C 207 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP C 207 " --> pdb=" O TYR C 218 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP C 220 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS C 205 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR C 222 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY C 203 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS C 224 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER C 201 " --> pdb=" O HIS C 224 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL C 226 " --> pdb=" O LYS C 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 100 through 103 Processing sheet with id=AB3, first strand: chain 'D' and resid 100 through 103 removed outlier: 3.514A pdb=" N SER D 64 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN D 75 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU D 62 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N TRP D 77 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER D 60 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU D 79 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR D 58 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY D 81 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ALA D 56 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N THR D 83 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N SER D 54 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL D 51 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N SER D 181 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE D 53 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 112 through 114 removed outlier: 5.413A pdb=" N SER D 170 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLN D 233 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE D 240 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 112 through 114 removed outlier: 5.413A pdb=" N SER D 170 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLN D 233 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 184 through 187 Processing sheet with id=AB7, first strand: chain 'B' and resid 98 through 101 removed outlier: 4.400A pdb=" N GLY B 134 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 98 through 101 removed outlier: 4.400A pdb=" N GLY B 134 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR B 69 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER B 62 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR B 71 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU B 60 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER B 73 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN B 81 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR B 50 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL B 49 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL B 179 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE B 51 " --> pdb=" O VAL B 179 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 110 through 112 removed outlier: 4.916A pdb=" N SER B 168 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR B 228 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 235 " --> pdb=" O ASP B 208 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 110 through 112 removed outlier: 4.916A pdb=" N SER B 168 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR B 228 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 1 through 4 Processing sheet with id=AC3, first strand: chain 'F' and resid 33 through 39 Processing sheet with id=AC4, first strand: chain 'G' and resid 1 through 4 Processing sheet with id=AC5, first strand: chain 'G' and resid 32 through 39 965 hydrogen bonds defined for protein. 2751 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: 7.88 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 17465 1.04 - 1.24: 1988 1.24 - 1.44: 5880 1.44 - 1.64: 10628 1.64 - 1.83: 147 Bond restraints: 36108 Sorted by residual: bond pdb=" NZ LYS D 40 " pdb=" HZ2 LYS D 40 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS D 40 " pdb=" HZ3 LYS D 40 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS A 296 " pdb=" HZ2 LYS A 296 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS G 43 " pdb=" HZ2 LYS G 43 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS C 199 " pdb=" HZ3 LYS C 199 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 36103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.06: 65129 12.06 - 24.12: 1 24.12 - 36.19: 1 36.19 - 48.25: 0 48.25 - 60.31: 2 Bond angle restraints: 65133 Sorted by residual: angle pdb=" CA ALA D 426 " pdb=" N ALA D 426 " pdb=" H ALA D 426 " ideal model delta sigma weight residual 114.00 174.31 -60.31 3.00e+00 1.11e-01 4.04e+02 angle pdb=" CA ALA B 417 " pdb=" N ALA B 417 " pdb=" H ALA B 417 " ideal model delta sigma weight residual 114.00 170.51 -56.51 3.00e+00 1.11e-01 3.55e+02 angle pdb=" CA LEU A 386 " pdb=" N LEU A 386 " pdb=" H LEU A 386 " ideal model delta sigma weight residual 114.00 150.08 -36.08 3.00e+00 1.11e-01 1.45e+02 angle pdb=" CA ARG E 232 " pdb=" N ARG E 232 " pdb=" H ARG E 232 " ideal model delta sigma weight residual 114.00 93.00 21.00 3.00e+00 1.11e-01 4.90e+01 angle pdb=" N PHE A 345 " pdb=" CA PHE A 345 " pdb=" C PHE A 345 " ideal model delta sigma weight residual 112.38 104.75 7.63 1.22e+00 6.72e-01 3.91e+01 ... (remaining 65128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.30: 16844 32.30 - 64.59: 727 64.59 - 96.89: 91 96.89 - 129.19: 22 129.19 - 161.49: 1 Dihedral angle restraints: 17685 sinusoidal: 9997 harmonic: 7688 Sorted by residual: dihedral pdb=" CD ARG E 233 " pdb=" NE ARG E 233 " pdb=" CZ ARG E 233 " pdb=" NH1 ARG E 233 " ideal model delta sinusoidal sigma weight residual 0.00 81.15 -81.15 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CD ARG B 167 " pdb=" NE ARG B 167 " pdb=" CZ ARG B 167 " pdb=" NH1 ARG B 167 " ideal model delta sinusoidal sigma weight residual 0.00 53.35 -53.35 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CA LYS A 96 " pdb=" C LYS A 96 " pdb=" N LYS A 97 " pdb=" CA LYS A 97 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 17682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 2998 0.231 - 0.462: 10 0.462 - 0.693: 1 0.693 - 0.924: 0 0.924 - 1.155: 3 Chirality restraints: 3012 Sorted by residual: chirality pdb=" C1 MAN J 4 " pdb=" O6 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 2.01 0.39 2.00e-02 2.50e+03 3.79e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.49e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-02 2.50e+03 2.66e+02 ... (remaining 3009 not shown) Planarity restraints: 5123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 96 " -0.164 2.00e-02 2.50e+03 2.18e-01 7.13e+02 pdb=" CG ASN D 96 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN D 96 " 0.067 2.00e-02 2.50e+03 pdb=" ND2 ASN D 96 " 0.165 2.00e-02 2.50e+03 pdb="HD21 ASN D 96 " 0.278 2.00e-02 2.50e+03 pdb=" C1 NAG D 601 " -0.384 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 233 " 1.113 9.50e-02 1.11e+02 3.72e-01 1.47e+02 pdb=" NE ARG E 233 " -0.040 2.00e-02 2.50e+03 pdb=" CZ ARG E 233 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG E 233 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 233 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG E 233 " -0.025 2.00e-02 2.50e+03 pdb="HH12 ARG E 233 " 0.021 2.00e-02 2.50e+03 pdb="HH21 ARG E 233 " -0.022 2.00e-02 2.50e+03 pdb="HH22 ARG E 233 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.127 2.00e-02 2.50e+03 1.07e-01 1.44e+02 pdb=" C7 NAG M 2 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.173 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.102 2.00e-02 2.50e+03 ... (remaining 5120 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 403 2.05 - 2.69: 52620 2.69 - 3.33: 102662 3.33 - 3.96: 140324 3.96 - 4.60: 213203 Nonbonded interactions: 509212 Sorted by model distance: nonbonded pdb="HD21 ASN D 96 " pdb=" O5 NAG D 601 " model vdw 1.417 1.960 nonbonded pdb="HD21 ASN A 161 " pdb=" O5 NAG J 1 " model vdw 1.522 1.960 nonbonded pdb="HG21 ILE C 340 " pdb="HD11 ILE C 429 " model vdw 1.540 2.440 nonbonded pdb=" HH TYR E 39 " pdb=" H TRP E 110 " model vdw 1.546 2.100 nonbonded pdb=" HG SER A 268 " pdb="HG21 ILE E 282 " model vdw 1.589 2.270 ... (remaining 509207 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 456 or (resid 501 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or n \ ame O21 or name O22 or name O31 or name O32 or name P )) or (resid 502 and (name \ N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or nam \ e C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38 or name O11 or name O12 or name O13 or name O14 or name \ O21 or name O22 or name O31 or name O32 or name P )))) selection = (chain 'C' and (resid 21 through 349 or resid 386 through 456 or (resid 501 and \ (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 or name C27 or name C28 or name C3 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name O12 or \ name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P ) \ ) or resid 502)) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 0 through 60) } ncs_group { reference = (chain 'J' and (resid 1 or resid 4 through 10)) selection = (chain 'L' and (resid 2 or resid 5 through 11)) } ncs_group { reference = chain 'K' selection = chain 'N' } 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.420 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: 0.240 Extract box with map and model: 0.370 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.640 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.007 0.240 18670 Z= 0.346 Angle : 1.046 31.705 25489 Z= 0.511 Chirality : 0.067 1.155 3012 Planarity : 0.015 0.479 3085 Dihedral : 18.750 161.487 7454 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.60 % Allowed : 20.02 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.18), residues: 2145 helix: 1.39 (0.18), residues: 773 sheet: 0.34 (0.23), residues: 480 loop : -0.34 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 470 TYR 0.019 0.002 TYR B 307 PHE 0.020 0.002 PHE D 431 TRP 0.014 0.002 TRP B 447 HIS 0.018 0.002 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00659 (18618) covalent geometry : angle 0.95874 (25348) SS BOND : bond 0.00540 ( 15) SS BOND : angle 2.38348 ( 30) hydrogen bonds : bond 0.12695 ( 879) hydrogen bonds : angle 5.55541 ( 2751) link_ALPHA1-2 : bond 0.00355 ( 7) link_ALPHA1-2 : angle 2.23530 ( 21) link_ALPHA1-3 : bond 0.01115 ( 6) link_ALPHA1-3 : angle 2.73618 ( 18) link_ALPHA1-6 : bond 0.00621 ( 7) link_ALPHA1-6 : angle 2.87263 ( 21) link_BETA1-4 : bond 0.00811 ( 10) link_BETA1-4 : angle 3.16076 ( 30) link_NAG-ASN : bond 0.15349 ( 7) link_NAG-ASN : angle 13.31596 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 249 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 278 MET cc_start: 0.8520 (mmp) cc_final: 0.7989 (mmp) REVERT: E 460 LEU cc_start: 0.8597 (mp) cc_final: 0.8337 (mt) REVERT: E 502 ASP cc_start: 0.8285 (t0) cc_final: 0.7995 (t0) REVERT: C 22 GLU cc_start: 0.7481 (mp0) cc_final: 0.6974 (tm-30) REVERT: C 133 THR cc_start: 0.8401 (m) cc_final: 0.8112 (p) REVERT: D 61 ASN cc_start: 0.8626 (p0) cc_final: 0.8395 (m-40) REVERT: D 463 ARG cc_start: 0.7574 (mtp-110) cc_final: 0.7204 (mtp180) REVERT: D 474 PHE cc_start: 0.7529 (m-10) cc_final: 0.7308 (m-80) REVERT: F 49 LYS cc_start: 0.7776 (tttm) cc_final: 0.7524 (tttp) REVERT: G 2 ILE cc_start: 0.8455 (mt) cc_final: 0.8083 (mp) outliers start: 12 outliers final: 5 residues processed: 256 average time/residue: 1.4789 time to fit residues: 418.9388 Evaluate side-chains 231 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 226 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain G residue 59 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN E 452 GLN E 465 GLN D 231 ASN B 115 ASN B 271 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.153029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116638 restraints weight = 48494.500| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.56 r_work: 0.3300 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18670 Z= 0.140 Angle : 0.882 38.900 25489 Z= 0.370 Chirality : 0.047 0.484 3012 Planarity : 0.007 0.206 3085 Dihedral : 13.246 147.194 3283 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.36 % Allowed : 17.96 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.18), residues: 2145 helix: 2.18 (0.18), residues: 774 sheet: 0.32 (0.22), residues: 489 loop : -0.08 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 167 TYR 0.011 0.001 TYR B 307 PHE 0.022 0.002 PHE A 345 TRP 0.010 0.001 TRP D 196 HIS 0.005 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00299 (18618) covalent geometry : angle 0.60358 (25348) SS BOND : bond 0.00315 ( 15) SS BOND : angle 1.34898 ( 30) hydrogen bonds : bond 0.05142 ( 879) hydrogen bonds : angle 4.42738 ( 2751) link_ALPHA1-2 : bond 0.00125 ( 7) link_ALPHA1-2 : angle 1.97790 ( 21) link_ALPHA1-3 : bond 0.00538 ( 6) link_ALPHA1-3 : angle 1.84256 ( 18) link_ALPHA1-6 : bond 0.00526 ( 7) link_ALPHA1-6 : angle 1.84345 ( 21) link_BETA1-4 : bond 0.00656 ( 10) link_BETA1-4 : angle 2.59037 ( 30) link_NAG-ASN : bond 0.00618 ( 7) link_NAG-ASN : angle 21.93791 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8472 (tp) cc_final: 0.8204 (tm) REVERT: E 195 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: C 22 GLU cc_start: 0.7505 (mp0) cc_final: 0.6842 (tm-30) REVERT: C 133 THR cc_start: 0.8382 (m) cc_final: 0.8146 (p) REVERT: C 435 MET cc_start: 0.8085 (mmt) cc_final: 0.7015 (mmt) REVERT: D 61 ASN cc_start: 0.8596 (p0) cc_final: 0.8173 (m-40) REVERT: D 101 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8485 (mtm180) REVERT: D 206 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: D 335 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7730 (mtt180) REVERT: D 474 PHE cc_start: 0.7431 (m-10) cc_final: 0.7173 (m-80) REVERT: D 495 GLN cc_start: 0.7903 (mt0) cc_final: 0.7699 (tt0) REVERT: B 174 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: B 336 HIS cc_start: 0.5710 (m-70) cc_final: 0.5352 (m-70) REVERT: F 49 LYS cc_start: 0.7600 (tttm) cc_final: 0.7257 (tttp) outliers start: 27 outliers final: 8 residues processed: 244 average time/residue: 1.4428 time to fit residues: 391.8359 Evaluate side-chains 224 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 101 ARG Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain F residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 139 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN C 179 ASN C 237 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN G 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.149466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113127 restraints weight = 48185.760| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.51 r_work: 0.3249 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18670 Z= 0.151 Angle : 0.877 39.362 25489 Z= 0.367 Chirality : 0.048 0.495 3012 Planarity : 0.005 0.064 3085 Dihedral : 12.341 135.175 3279 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.31 % Allowed : 16.15 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.18), residues: 2145 helix: 2.40 (0.18), residues: 779 sheet: 0.38 (0.23), residues: 474 loop : 0.05 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 233 TYR 0.013 0.002 TYR D 454 PHE 0.019 0.002 PHE E 291 TRP 0.013 0.001 TRP D 196 HIS 0.005 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00333 (18618) covalent geometry : angle 0.58810 (25348) SS BOND : bond 0.00382 ( 15) SS BOND : angle 1.21816 ( 30) hydrogen bonds : bond 0.05018 ( 879) hydrogen bonds : angle 4.28981 ( 2751) link_ALPHA1-2 : bond 0.00226 ( 7) link_ALPHA1-2 : angle 2.11957 ( 21) link_ALPHA1-3 : bond 0.00540 ( 6) link_ALPHA1-3 : angle 1.72084 ( 18) link_ALPHA1-6 : bond 0.00700 ( 7) link_ALPHA1-6 : angle 1.89115 ( 21) link_BETA1-4 : bond 0.00523 ( 10) link_BETA1-4 : angle 2.41009 ( 30) link_NAG-ASN : bond 0.00357 ( 7) link_NAG-ASN : angle 22.27064 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8474 (tp) cc_final: 0.8171 (tm) REVERT: A 436 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7910 (mp) REVERT: E 195 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: E 460 LEU cc_start: 0.8368 (mt) cc_final: 0.8051 (mt) REVERT: C 22 GLU cc_start: 0.7487 (mp0) cc_final: 0.6817 (tm-30) REVERT: C 133 THR cc_start: 0.8479 (m) cc_final: 0.8237 (p) REVERT: D 206 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: D 335 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7700 (mtt180) REVERT: D 474 PHE cc_start: 0.7362 (m-10) cc_final: 0.7143 (m-10) REVERT: D 480 MET cc_start: 0.8296 (ttt) cc_final: 0.8023 (ttt) REVERT: B 152 VAL cc_start: 0.8806 (p) cc_final: 0.8543 (m) REVERT: B 174 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7303 (mp0) outliers start: 26 outliers final: 10 residues processed: 237 average time/residue: 1.4379 time to fit residues: 377.4668 Evaluate side-chains 226 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain G residue 54 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN B 271 GLN B 292 GLN F 10 GLN G 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.111314 restraints weight = 48081.016| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.52 r_work: 0.3223 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18670 Z= 0.167 Angle : 0.878 39.092 25489 Z= 0.371 Chirality : 0.048 0.507 3012 Planarity : 0.005 0.056 3085 Dihedral : 12.046 146.132 3279 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.76 % Allowed : 14.44 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.18), residues: 2145 helix: 2.49 (0.18), residues: 777 sheet: 0.31 (0.23), residues: 470 loop : 0.07 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 215 TYR 0.014 0.002 TYR D 454 PHE 0.021 0.002 PHE E 291 TRP 0.013 0.001 TRP D 196 HIS 0.008 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00368 (18618) covalent geometry : angle 0.59164 (25348) SS BOND : bond 0.00446 ( 15) SS BOND : angle 1.23536 ( 30) hydrogen bonds : bond 0.05100 ( 879) hydrogen bonds : angle 4.29737 ( 2751) link_ALPHA1-2 : bond 0.00267 ( 7) link_ALPHA1-2 : angle 2.31256 ( 21) link_ALPHA1-3 : bond 0.00535 ( 6) link_ALPHA1-3 : angle 1.83620 ( 18) link_ALPHA1-6 : bond 0.00814 ( 7) link_ALPHA1-6 : angle 1.87783 ( 21) link_BETA1-4 : bond 0.00554 ( 10) link_BETA1-4 : angle 2.34635 ( 30) link_NAG-ASN : bond 0.00413 ( 7) link_NAG-ASN : angle 22.17361 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8582 (tp) cc_final: 0.8284 (tm) REVERT: A 436 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8020 (mp) REVERT: E 454 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7267 (mt0) REVERT: C 22 GLU cc_start: 0.7496 (mp0) cc_final: 0.6845 (tm-30) REVERT: C 30 LYS cc_start: 0.8944 (tptm) cc_final: 0.8700 (tmtt) REVERT: C 333 ARG cc_start: 0.7285 (ttm110) cc_final: 0.6955 (ttm-80) REVERT: D 92 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8002 (mm-30) REVERT: D 206 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: D 335 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7603 (mtt180) REVERT: D 480 MET cc_start: 0.8438 (ttt) cc_final: 0.8075 (ttt) REVERT: B 174 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7365 (mp0) outliers start: 35 outliers final: 14 residues processed: 232 average time/residue: 1.4909 time to fit residues: 383.6938 Evaluate side-chains 221 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain F residue 21 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 156 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 171 optimal weight: 0.0570 chunk 169 optimal weight: 0.7980 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN B 271 GLN G 10 GLN G 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111129 restraints weight = 48440.919| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.44 r_work: 0.3219 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18670 Z= 0.167 Angle : 0.873 39.233 25489 Z= 0.368 Chirality : 0.048 0.504 3012 Planarity : 0.005 0.056 3085 Dihedral : 11.993 153.396 3279 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.76 % Allowed : 13.63 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.18), residues: 2145 helix: 2.53 (0.18), residues: 779 sheet: 0.25 (0.22), residues: 474 loop : 0.05 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 233 TYR 0.014 0.002 TYR D 454 PHE 0.020 0.002 PHE E 291 TRP 0.013 0.002 TRP D 196 HIS 0.003 0.001 HIS E 353 Details of bonding type rmsd covalent geometry : bond 0.00371 (18618) covalent geometry : angle 0.58528 (25348) SS BOND : bond 0.00417 ( 15) SS BOND : angle 1.22249 ( 30) hydrogen bonds : bond 0.05070 ( 879) hydrogen bonds : angle 4.26834 ( 2751) link_ALPHA1-2 : bond 0.00278 ( 7) link_ALPHA1-2 : angle 2.27846 ( 21) link_ALPHA1-3 : bond 0.00518 ( 6) link_ALPHA1-3 : angle 1.79777 ( 18) link_ALPHA1-6 : bond 0.00827 ( 7) link_ALPHA1-6 : angle 2.05345 ( 21) link_BETA1-4 : bond 0.00564 ( 10) link_BETA1-4 : angle 2.29999 ( 30) link_NAG-ASN : bond 0.00441 ( 7) link_NAG-ASN : angle 22.13124 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8591 (tp) cc_final: 0.8326 (tm) REVERT: A 436 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7995 (mp) REVERT: A 454 ASN cc_start: 0.4984 (OUTLIER) cc_final: 0.4067 (m-40) REVERT: E 454 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7229 (mt0) REVERT: C 286 SER cc_start: 0.8483 (m) cc_final: 0.8071 (p) REVERT: C 333 ARG cc_start: 0.7123 (ttm110) cc_final: 0.6859 (ttm-80) REVERT: D 92 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8054 (mm-30) REVERT: D 206 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: D 294 ILE cc_start: 0.8499 (mm) cc_final: 0.8181 (mt) REVERT: D 335 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7605 (mtt180) REVERT: D 469 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: D 480 MET cc_start: 0.8490 (ttt) cc_final: 0.8200 (ttt) REVERT: B 81 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: B 174 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: F 49 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7450 (tttm) outliers start: 35 outliers final: 17 residues processed: 231 average time/residue: 1.4634 time to fit residues: 376.1532 Evaluate side-chains 231 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 49 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 58 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN E 194 GLN B 271 GLN B 292 GLN G 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109827 restraints weight = 48472.979| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.45 r_work: 0.3199 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18670 Z= 0.195 Angle : 0.889 38.524 25489 Z= 0.381 Chirality : 0.049 0.544 3012 Planarity : 0.005 0.056 3085 Dihedral : 12.217 157.281 3279 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.91 % Allowed : 13.13 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.18), residues: 2145 helix: 2.44 (0.18), residues: 780 sheet: 0.29 (0.23), residues: 468 loop : 0.01 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 101 TYR 0.014 0.002 TYR D 454 PHE 0.022 0.002 PHE E 291 TRP 0.015 0.002 TRP D 196 HIS 0.005 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00440 (18618) covalent geometry : angle 0.61473 (25348) SS BOND : bond 0.00437 ( 15) SS BOND : angle 1.31802 ( 30) hydrogen bonds : bond 0.05328 ( 879) hydrogen bonds : angle 4.35063 ( 2751) link_ALPHA1-2 : bond 0.00420 ( 7) link_ALPHA1-2 : angle 2.49126 ( 21) link_ALPHA1-3 : bond 0.00455 ( 6) link_ALPHA1-3 : angle 1.92090 ( 18) link_ALPHA1-6 : bond 0.00887 ( 7) link_ALPHA1-6 : angle 2.22511 ( 21) link_BETA1-4 : bond 0.00662 ( 10) link_BETA1-4 : angle 2.43646 ( 30) link_NAG-ASN : bond 0.00519 ( 7) link_NAG-ASN : angle 21.87649 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8589 (tp) cc_final: 0.8314 (tm) REVERT: A 436 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8079 (mp) REVERT: A 454 ASN cc_start: 0.4994 (OUTLIER) cc_final: 0.4071 (m-40) REVERT: E 454 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7232 (mt0) REVERT: C 286 SER cc_start: 0.8464 (m) cc_final: 0.8051 (p) REVERT: C 333 ARG cc_start: 0.7094 (ttm110) cc_final: 0.6835 (ttm-80) REVERT: D 92 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8126 (mm-30) REVERT: D 206 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: D 294 ILE cc_start: 0.8626 (mm) cc_final: 0.8299 (mt) REVERT: D 335 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7560 (mtt180) REVERT: B 81 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: B 174 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: F 49 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7442 (tttm) REVERT: G 28 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.8039 (mtp85) outliers start: 38 outliers final: 15 residues processed: 227 average time/residue: 1.5583 time to fit residues: 393.6264 Evaluate side-chains 219 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain F residue 49 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 160 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN E 68 ASN B 271 GLN B 292 GLN G 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110566 restraints weight = 48258.132| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.44 r_work: 0.3205 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18670 Z= 0.180 Angle : 0.879 39.025 25489 Z= 0.373 Chirality : 0.048 0.518 3012 Planarity : 0.005 0.056 3085 Dihedral : 12.027 162.452 3277 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.61 % Allowed : 13.53 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.18), residues: 2145 helix: 2.47 (0.18), residues: 781 sheet: 0.29 (0.23), residues: 470 loop : 0.02 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 101 TYR 0.014 0.002 TYR D 454 PHE 0.020 0.002 PHE E 291 TRP 0.014 0.002 TRP D 196 HIS 0.007 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00400 (18618) covalent geometry : angle 0.59585 (25348) SS BOND : bond 0.00456 ( 15) SS BOND : angle 1.22817 ( 30) hydrogen bonds : bond 0.05173 ( 879) hydrogen bonds : angle 4.30970 ( 2751) link_ALPHA1-2 : bond 0.00345 ( 7) link_ALPHA1-2 : angle 2.38846 ( 21) link_ALPHA1-3 : bond 0.00479 ( 6) link_ALPHA1-3 : angle 1.78965 ( 18) link_ALPHA1-6 : bond 0.00854 ( 7) link_ALPHA1-6 : angle 2.24066 ( 21) link_BETA1-4 : bond 0.00602 ( 10) link_BETA1-4 : angle 2.33802 ( 30) link_NAG-ASN : bond 0.00471 ( 7) link_NAG-ASN : angle 22.03872 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8079 (mp) REVERT: E 454 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7227 (mt0) REVERT: C 22 GLU cc_start: 0.7553 (mp0) cc_final: 0.6932 (tm-30) REVERT: C 215 SER cc_start: 0.8060 (m) cc_final: 0.7760 (p) REVERT: C 286 SER cc_start: 0.8444 (m) cc_final: 0.8036 (p) REVERT: D 92 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8056 (mm-30) REVERT: D 206 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: D 294 ILE cc_start: 0.8619 (mm) cc_final: 0.8330 (mt) REVERT: D 335 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7547 (mtt180) REVERT: B 81 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8226 (mt0) REVERT: B 174 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: F 49 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7498 (tttm) outliers start: 32 outliers final: 15 residues processed: 218 average time/residue: 1.6941 time to fit residues: 409.7923 Evaluate side-chains 216 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain F residue 49 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 99 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 165 optimal weight: 0.0050 chunk 19 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN G 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.113615 restraints weight = 48748.817| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.52 r_work: 0.3280 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18670 Z= 0.137 Angle : 0.861 39.912 25489 Z= 0.358 Chirality : 0.046 0.467 3012 Planarity : 0.004 0.056 3085 Dihedral : 11.616 164.856 3277 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.56 % Allowed : 13.78 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.18), residues: 2145 helix: 2.65 (0.18), residues: 780 sheet: 0.27 (0.23), residues: 469 loop : 0.06 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 463 TYR 0.014 0.001 TYR D 454 PHE 0.017 0.002 PHE E 291 TRP 0.011 0.001 TRP D 196 HIS 0.007 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00299 (18618) covalent geometry : angle 0.55697 (25348) SS BOND : bond 0.00340 ( 15) SS BOND : angle 1.01728 ( 30) hydrogen bonds : bond 0.04757 ( 879) hydrogen bonds : angle 4.19113 ( 2751) link_ALPHA1-2 : bond 0.00183 ( 7) link_ALPHA1-2 : angle 2.17380 ( 21) link_ALPHA1-3 : bond 0.00510 ( 6) link_ALPHA1-3 : angle 1.63039 ( 18) link_ALPHA1-6 : bond 0.00788 ( 7) link_ALPHA1-6 : angle 2.09687 ( 21) link_BETA1-4 : bond 0.00482 ( 10) link_BETA1-4 : angle 2.20420 ( 30) link_NAG-ASN : bond 0.00326 ( 7) link_NAG-ASN : angle 22.46650 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8608 (tp) cc_final: 0.8346 (tm) REVERT: E 454 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7242 (mt0) REVERT: C 22 GLU cc_start: 0.7518 (mp0) cc_final: 0.6828 (tm-30) REVERT: C 215 SER cc_start: 0.8058 (m) cc_final: 0.7756 (p) REVERT: C 286 SER cc_start: 0.8398 (m) cc_final: 0.8031 (p) REVERT: D 92 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8057 (mm-30) REVERT: D 206 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: D 294 ILE cc_start: 0.8587 (mm) cc_final: 0.8289 (mt) REVERT: D 335 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7523 (mtt180) REVERT: B 81 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8185 (mt0) REVERT: B 174 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: F 49 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7460 (tttm) outliers start: 31 outliers final: 17 residues processed: 216 average time/residue: 1.3885 time to fit residues: 334.7998 Evaluate side-chains 218 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 49 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 161 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN G 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112535 restraints weight = 48384.604| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.51 r_work: 0.3260 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18670 Z= 0.177 Angle : 0.882 38.826 25489 Z= 0.374 Chirality : 0.048 0.523 3012 Planarity : 0.005 0.058 3085 Dihedral : 11.874 166.749 3277 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.36 % Allowed : 14.19 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.18), residues: 2145 helix: 2.53 (0.18), residues: 780 sheet: 0.27 (0.23), residues: 470 loop : 0.04 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 463 TYR 0.013 0.002 TYR B 154 PHE 0.021 0.002 PHE E 291 TRP 0.014 0.002 TRP D 196 HIS 0.006 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00397 (18618) covalent geometry : angle 0.59944 (25348) SS BOND : bond 0.00462 ( 15) SS BOND : angle 1.24581 ( 30) hydrogen bonds : bond 0.05106 ( 879) hydrogen bonds : angle 4.27767 ( 2751) link_ALPHA1-2 : bond 0.00328 ( 7) link_ALPHA1-2 : angle 2.42243 ( 21) link_ALPHA1-3 : bond 0.00429 ( 6) link_ALPHA1-3 : angle 1.78931 ( 18) link_ALPHA1-6 : bond 0.00897 ( 7) link_ALPHA1-6 : angle 2.31347 ( 21) link_BETA1-4 : bond 0.00605 ( 10) link_BETA1-4 : angle 2.30784 ( 30) link_NAG-ASN : bond 0.00466 ( 7) link_NAG-ASN : angle 22.05434 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8660 (tp) cc_final: 0.8411 (tm) REVERT: E 454 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7288 (mt0) REVERT: C 22 GLU cc_start: 0.7608 (mp0) cc_final: 0.6969 (tm-30) REVERT: C 286 SER cc_start: 0.8436 (m) cc_final: 0.8089 (p) REVERT: D 92 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8117 (mm-30) REVERT: D 206 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: D 294 ILE cc_start: 0.8652 (mm) cc_final: 0.8372 (mt) REVERT: D 335 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7581 (mtt180) REVERT: B 81 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8228 (mt0) REVERT: B 174 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: F 49 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7510 (tttm) outliers start: 27 outliers final: 17 residues processed: 215 average time/residue: 1.5775 time to fit residues: 378.5587 Evaluate side-chains 218 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 49 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 44 optimal weight: 0.4980 chunk 171 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 292 GLN G 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113708 restraints weight = 49070.222| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.51 r_work: 0.3280 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18670 Z= 0.144 Angle : 0.864 39.796 25489 Z= 0.360 Chirality : 0.046 0.477 3012 Planarity : 0.005 0.056 3085 Dihedral : 11.563 169.028 3277 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.26 % Allowed : 14.29 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.18), residues: 2145 helix: 2.65 (0.18), residues: 780 sheet: 0.28 (0.23), residues: 469 loop : 0.06 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 470 TYR 0.013 0.001 TYR D 454 PHE 0.017 0.002 PHE E 291 TRP 0.011 0.001 TRP D 196 HIS 0.004 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00317 (18618) covalent geometry : angle 0.56378 (25348) SS BOND : bond 0.00404 ( 15) SS BOND : angle 1.01032 ( 30) hydrogen bonds : bond 0.04782 ( 879) hydrogen bonds : angle 4.18824 ( 2751) link_ALPHA1-2 : bond 0.00198 ( 7) link_ALPHA1-2 : angle 2.22616 ( 21) link_ALPHA1-3 : bond 0.00493 ( 6) link_ALPHA1-3 : angle 1.63220 ( 18) link_ALPHA1-6 : bond 0.00842 ( 7) link_ALPHA1-6 : angle 2.17042 ( 21) link_BETA1-4 : bond 0.00502 ( 10) link_BETA1-4 : angle 2.21738 ( 30) link_NAG-ASN : bond 0.00333 ( 7) link_NAG-ASN : angle 22.41655 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8659 (tp) cc_final: 0.8413 (tm) REVERT: E 297 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7504 (p0) REVERT: E 454 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7283 (mt0) REVERT: C 22 GLU cc_start: 0.7592 (mp0) cc_final: 0.6905 (tm-30) REVERT: C 215 SER cc_start: 0.7999 (m) cc_final: 0.7735 (p) REVERT: C 286 SER cc_start: 0.8415 (m) cc_final: 0.8063 (p) REVERT: D 92 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8108 (mm-30) REVERT: D 206 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: D 294 ILE cc_start: 0.8625 (mm) cc_final: 0.8344 (mt) REVERT: D 335 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7563 (mtt180) REVERT: B 81 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8218 (mt0) REVERT: B 174 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: F 49 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7515 (tttm) outliers start: 25 outliers final: 17 residues processed: 210 average time/residue: 1.4617 time to fit residues: 342.8182 Evaluate side-chains 217 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 454 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 49 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 3 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 178 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 134 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS B 278 ASN B 292 GLN G 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.150008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114671 restraints weight = 48722.618| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.49 r_work: 0.3291 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18670 Z= 0.124 Angle : 0.856 40.212 25489 Z= 0.353 Chirality : 0.046 0.449 3012 Planarity : 0.004 0.063 3085 Dihedral : 11.253 169.710 3277 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.31 % Allowed : 14.39 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.18), residues: 2145 helix: 2.76 (0.18), residues: 778 sheet: 0.27 (0.23), residues: 469 loop : 0.08 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 470 TYR 0.013 0.001 TYR D 454 PHE 0.015 0.001 PHE E 291 TRP 0.009 0.001 TRP D 196 HIS 0.006 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00270 (18618) covalent geometry : angle 0.54474 (25348) SS BOND : bond 0.00319 ( 15) SS BOND : angle 0.91854 ( 30) hydrogen bonds : bond 0.04525 ( 879) hydrogen bonds : angle 4.11027 ( 2751) link_ALPHA1-2 : bond 0.00108 ( 7) link_ALPHA1-2 : angle 2.08764 ( 21) link_ALPHA1-3 : bond 0.00516 ( 6) link_ALPHA1-3 : angle 1.54952 ( 18) link_ALPHA1-6 : bond 0.00827 ( 7) link_ALPHA1-6 : angle 2.09853 ( 21) link_BETA1-4 : bond 0.00454 ( 10) link_BETA1-4 : angle 2.11333 ( 30) link_NAG-ASN : bond 0.00292 ( 7) link_NAG-ASN : angle 22.64509 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16285.66 seconds wall clock time: 275 minutes 15.53 seconds (16515.53 seconds total)