Starting phenix.real_space_refine on Wed Feb 14 12:16:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/02_2024/8hgo_34744.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/02_2024/8hgo_34744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/02_2024/8hgo_34744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/02_2024/8hgo_34744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/02_2024/8hgo_34744.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/02_2024/8hgo_34744.pdb" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 4 Type Number sf(0) Gaussians S 109 5.16 5 C 5714 2.51 5 N 1636 2.21 5 O 1768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B ARG 558": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 531": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9227 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4345 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 35, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 4391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4391 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 26, 'TRANS': 541} Chain: "C" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ASN A 182 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 182 " occ=0.00 residue: pdb=" N HIS A 183 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS A 183 " occ=0.00 residue: pdb=" N LEU A 184 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 184 " occ=0.00 residue: pdb=" N GLY A 203 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 203 " occ=0.00 residue: pdb=" N CYS A 329 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 329 " occ=0.00 residue: pdb=" N GLU A 330 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 330 " occ=0.00 residue: pdb=" N GLY A 331 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 331 " occ=0.00 residue: pdb=" N PRO A 332 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 332 " occ=0.00 residue: pdb=" N CYS A 333 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 333 " occ=0.00 Time building chain proxies: 5.61, per 1000 atoms: 0.61 Number of scatterers: 9227 At special positions: 0 Unit cell: (78.11, 131.61, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 109 16.00 O 1768 8.00 N 1636 7.00 C 5714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.02 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 504 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 260 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 337 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 506 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 523 " distance=2.04 Simple disulfide: pdb=" SG CYS A 526 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 539 " - pdb=" SG CYS A 555 " distance=2.04 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 31 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 42 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-3 " NAG D 2 " - " BMA D 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A 801 " - " ASN A 56 " " NAG A 802 " - " ASN A 175 " " NAG D 1 " - " ASN A 352 " " NAG E 1 " - " ASN B 259 " Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 1.9 seconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 21 sheets defined 11.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.825A pdb=" N GLN B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.965A pdb=" N GLN B 75 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 4.076A pdb=" N ILE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.566A pdb=" N ASP B 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N CYS B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 212' Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.534A pdb=" N PHE B 364 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.865A pdb=" N VAL B 399 " --> pdb=" O GLN B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 removed outlier: 3.601A pdb=" N GLN B 426 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.063A pdb=" N GLY B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.787A pdb=" N GLY B 518 " --> pdb=" O CYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 removed outlier: 3.586A pdb=" N GLN B 583 " --> pdb=" O GLU B 580 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS B 584 " --> pdb=" O ALA B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 580 through 584' Processing helix chain 'A' and resid 43 through 55 Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.798A pdb=" N THR A 81 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.746A pdb=" N GLY A 197 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 198' Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.793A pdb=" N PHE A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 346' Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.934A pdb=" N LYS A 360 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.573A pdb=" N LEU A 392 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP A 393 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.888A pdb=" N PHE A 420 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 421 " --> pdb=" O HIS A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 421' Processing helix chain 'A' and resid 431 through 434 Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.516A pdb=" N LYS A 479 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 523 removed outlier: 4.427A pdb=" N CYS A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 26 removed outlier: 3.743A pdb=" N CYS B 26 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.411A pdb=" N LEU B 60 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ALA B 87 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU B 62 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 114 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLN B 156 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL B 116 " --> pdb=" O GLN B 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AA4, first strand: chain 'B' and resid 272 through 275 Processing sheet with id=AA5, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AA6, first strand: chain 'B' and resid 319 through 320 removed outlier: 3.695A pdb=" N GLU B 332 " --> pdb=" O GLN B 320 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AA8, first strand: chain 'B' and resid 374 through 376 removed outlier: 6.440A pdb=" N LEU B 374 " --> pdb=" O TYR B 411 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS B 469 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 553 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AB2, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.976A pdb=" N GLN A 40 " --> pdb=" O CYS C 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.670A pdb=" N LEU A 65 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ALA A 92 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 67 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 89 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU A 122 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 91 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 119 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER A 151 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 121 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 148 " --> pdb=" O SER A 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 236 through 240 removed outlier: 3.574A pdb=" N ALA A 237 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL A 250 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N GLY A 239 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS A 248 " --> pdb=" O GLY A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 254 through 256 removed outlier: 3.564A pdb=" N PHE A 254 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 261 " --> pdb=" O PHE A 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AB7, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AB8, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AB9, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.569A pdb=" N LEU A 369 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 405 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE A 462 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA A 439 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 461 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 548 through 549 removed outlier: 3.600A pdb=" N PHE A 549 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 556 " --> pdb=" O PHE A 549 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 585 through 587 Processing sheet with id=AC3, first strand: chain 'C' and resid 37 through 38 97 hydrogen bonds defined for protein. 186 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: 2.92 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3127 1.34 - 1.46: 2001 1.46 - 1.58: 4168 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 9420 Sorted by residual: bond pdb=" C5 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.418 1.473 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" C PRO B 593 " pdb=" N PRO B 594 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.51e+00 bond pdb=" C LYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.17e+00 bond pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.417 1.462 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" C1 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.399 1.443 -0.044 2.00e-02 2.50e+03 4.86e+00 ... (remaining 9415 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.16: 369 107.16 - 113.87: 5176 113.87 - 120.58: 3500 120.58 - 127.29: 3628 127.29 - 134.00: 96 Bond angle restraints: 12769 Sorted by residual: angle pdb=" N LEU A 509 " pdb=" CA LEU A 509 " pdb=" C LEU A 509 " ideal model delta sigma weight residual 110.80 121.59 -10.79 2.13e+00 2.20e-01 2.57e+01 angle pdb=" N ARG A 334 " pdb=" CA ARG A 334 " pdb=" C ARG A 334 " ideal model delta sigma weight residual 110.97 115.32 -4.35 1.09e+00 8.42e-01 1.59e+01 angle pdb=" C ALA B 324 " pdb=" N GLU B 325 " pdb=" CA GLU B 325 " ideal model delta sigma weight residual 122.08 127.78 -5.70 1.47e+00 4.63e-01 1.50e+01 angle pdb=" C GLU A 204 " pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 angle pdb=" N PRO B 593 " pdb=" CA PRO B 593 " pdb=" C PRO B 593 " ideal model delta sigma weight residual 110.70 114.91 -4.21 1.22e+00 6.72e-01 1.19e+01 ... (remaining 12764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 5723 22.60 - 45.20: 152 45.20 - 67.79: 35 67.79 - 90.39: 18 90.39 - 112.99: 8 Dihedral angle restraints: 5936 sinusoidal: 2554 harmonic: 3382 Sorted by residual: dihedral pdb=" CB CYS B 299 " pdb=" SG CYS B 299 " pdb=" SG CYS B 311 " pdb=" CB CYS B 311 " ideal model delta sinusoidal sigma weight residual 93.00 -176.55 -90.45 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS A 219 " pdb=" SG CYS A 219 " pdb=" SG CYS A 231 " pdb=" CB CYS A 231 " ideal model delta sinusoidal sigma weight residual 93.00 -179.51 -87.49 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 190 " pdb=" SG CYS A 190 " pdb=" SG CYS A 199 " pdb=" CB CYS A 199 " ideal model delta sinusoidal sigma weight residual -86.00 -168.44 82.44 1 1.00e+01 1.00e-02 8.34e+01 ... (remaining 5933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1224 0.076 - 0.152: 190 0.152 - 0.228: 6 0.228 - 0.304: 2 0.304 - 0.380: 3 Chirality restraints: 1425 Sorted by residual: chirality pdb=" C2 NAG A 802 " pdb=" C1 NAG A 802 " pdb=" C3 NAG A 802 " pdb=" N2 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA LEU A 509 " pdb=" N LEU A 509 " pdb=" C LEU A 509 " pdb=" CB LEU A 509 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 175 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1422 not shown) Planarity restraints: 1683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 519 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A 520 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 520 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 511 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 512 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 372 " -0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO A 373 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.028 5.00e-02 4.00e+02 ... (remaining 1680 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2411 2.81 - 3.33: 7501 3.33 - 3.85: 14605 3.85 - 4.38: 16494 4.38 - 4.90: 28622 Nonbonded interactions: 69633 Sorted by model distance: nonbonded pdb=" OH TYR B 163 " pdb=" O HIS B 193 " model vdw 2.284 2.440 nonbonded pdb=" ND1 HIS A 507 " pdb=" O ALA A 508 " model vdw 2.315 2.520 nonbonded pdb=" OG SER B 38 " pdb=" OG1 THR B 41 " model vdw 2.324 2.440 nonbonded pdb=" OE2 GLU A 66 " pdb=" OH TYR A 88 " model vdw 2.349 2.440 nonbonded pdb=" O VAL B 356 " pdb=" OG SER B 380 " model vdw 2.365 2.440 ... (remaining 69628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 3.350 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: 0.010 Extract box with map and model: 11.600 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 28.760 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9420 Z= 0.239 Angle : 0.711 10.795 12769 Z= 0.397 Chirality : 0.054 0.380 1425 Planarity : 0.007 0.053 1679 Dihedral : 10.134 112.989 3621 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.03 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.20), residues: 1170 helix: -3.97 (0.38), residues: 41 sheet: -2.80 (0.49), residues: 91 loop : -2.68 (0.16), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 452 HIS 0.015 0.001 HIS B 48 PHE 0.019 0.002 PHE A 404 TYR 0.014 0.001 TYR B 554 ARG 0.004 0.000 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7294 (t70) cc_final: 0.6925 (t70) REVERT: B 89 ASN cc_start: 0.7573 (m-40) cc_final: 0.7250 (m110) REVERT: B 103 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7373 (mtp85) REVERT: B 112 TYR cc_start: 0.6756 (m-80) cc_final: 0.6533 (m-80) REVERT: B 164 GLN cc_start: 0.6589 (pm20) cc_final: 0.6193 (pm20) REVERT: B 183 LEU cc_start: 0.8231 (mp) cc_final: 0.7844 (tp) REVERT: B 228 LYS cc_start: 0.7510 (mtpt) cc_final: 0.7278 (mtpt) REVERT: B 405 GLU cc_start: 0.6892 (tt0) cc_final: 0.6636 (tt0) REVERT: B 434 ARG cc_start: 0.8286 (mtt90) cc_final: 0.7945 (mtt180) REVERT: B 460 GLU cc_start: 0.6684 (tt0) cc_final: 0.6187 (tt0) REVERT: B 467 LEU cc_start: 0.8448 (tp) cc_final: 0.7783 (tp) REVERT: B 541 VAL cc_start: 0.7565 (m) cc_final: 0.7159 (p) REVERT: B 561 LEU cc_start: 0.7389 (mt) cc_final: 0.7124 (mt) REVERT: A 45 GLU cc_start: 0.7186 (mp0) cc_final: 0.6738 (mp0) REVERT: A 46 ASP cc_start: 0.7642 (t70) cc_final: 0.7218 (t0) REVERT: A 152 ASN cc_start: 0.7274 (m110) cc_final: 0.6942 (m110) REVERT: A 160 GLU cc_start: 0.7180 (pm20) cc_final: 0.6471 (pm20) REVERT: A 234 ASN cc_start: 0.7890 (t0) cc_final: 0.7649 (t0) REVERT: A 268 MET cc_start: 0.5860 (mtm) cc_final: 0.5359 (mtm) REVERT: A 277 MET cc_start: 0.5040 (mtt) cc_final: 0.4820 (mtt) REVERT: A 292 VAL cc_start: 0.7916 (m) cc_final: 0.7545 (p) REVERT: A 293 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7713 (mtpp) REVERT: A 294 LYS cc_start: 0.7981 (tttt) cc_final: 0.7751 (tttt) REVERT: A 325 LYS cc_start: 0.7243 (mttt) cc_final: 0.6891 (mtmm) REVERT: A 360 LYS cc_start: 0.7592 (tttt) cc_final: 0.7361 (tttt) REVERT: A 425 ILE cc_start: 0.8526 (tt) cc_final: 0.7990 (tt) REVERT: A 430 THR cc_start: 0.7999 (m) cc_final: 0.7331 (p) REVERT: A 431 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7855 (mtmm) REVERT: A 593 LYS cc_start: 0.6587 (tptp) cc_final: 0.6324 (tptp) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2923 time to fit residues: 110.2735 Evaluate side-chains 231 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.0020 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 90 optimal weight: 0.0970 chunk 35 optimal weight: 0.0980 chunk 55 optimal weight: 0.6980 chunk 67 optimal weight: 0.0980 chunk 105 optimal weight: 0.0970 overall best weight: 0.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 302 ASN B 438 ASN A 47 HIS A 64 ASN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 110 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN A 233 HIS A 235 GLN A 486 GLN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN A 559 HIS A 565 GLN A 584 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 9420 Z= 0.168 Angle : 0.624 9.770 12769 Z= 0.313 Chirality : 0.046 0.247 1425 Planarity : 0.005 0.041 1679 Dihedral : 9.140 93.580 1433 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.27 % Allowed : 7.22 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.22), residues: 1170 helix: -3.34 (0.51), residues: 63 sheet: -2.58 (0.51), residues: 89 loop : -2.35 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 452 HIS 0.009 0.001 HIS B 469 PHE 0.025 0.001 PHE A 549 TYR 0.018 0.001 TYR B 64 ARG 0.007 0.001 ARG B 499 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 261 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7298 (t70) cc_final: 0.6888 (t70) REVERT: B 93 GLN cc_start: 0.6923 (pp30) cc_final: 0.6623 (pp30) REVERT: B 147 GLU cc_start: 0.6663 (tp30) cc_final: 0.6376 (tp30) REVERT: B 156 GLN cc_start: 0.7566 (mt0) cc_final: 0.7149 (mt0) REVERT: B 183 LEU cc_start: 0.8292 (mp) cc_final: 0.7924 (tp) REVERT: B 228 LYS cc_start: 0.7541 (mtpt) cc_final: 0.7218 (mtpt) REVERT: B 403 LEU cc_start: 0.6680 (tp) cc_final: 0.6344 (tp) REVERT: B 405 GLU cc_start: 0.6966 (tt0) cc_final: 0.6758 (tt0) REVERT: B 430 VAL cc_start: 0.8468 (p) cc_final: 0.8242 (t) REVERT: B 561 LEU cc_start: 0.7359 (mt) cc_final: 0.7083 (mt) REVERT: A 45 GLU cc_start: 0.7244 (mp0) cc_final: 0.6790 (mp0) REVERT: A 46 ASP cc_start: 0.7689 (t70) cc_final: 0.7313 (t0) REVERT: A 80 LYS cc_start: 0.8347 (mttp) cc_final: 0.8090 (mttp) REVERT: A 152 ASN cc_start: 0.7300 (m110) cc_final: 0.6930 (m110) REVERT: A 198 SER cc_start: 0.8090 (m) cc_final: 0.7405 (p) REVERT: A 235 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7639 (mm110) REVERT: A 254 PHE cc_start: 0.7736 (m-10) cc_final: 0.7485 (m-10) REVERT: A 255 ARG cc_start: 0.6296 (ttt-90) cc_final: 0.5871 (tmt-80) REVERT: A 268 MET cc_start: 0.5719 (mtm) cc_final: 0.5227 (mtm) REVERT: A 277 MET cc_start: 0.5041 (mtt) cc_final: 0.4796 (mtt) REVERT: A 292 VAL cc_start: 0.7972 (m) cc_final: 0.7461 (p) REVERT: A 294 LYS cc_start: 0.8015 (tttt) cc_final: 0.7783 (tttt) REVERT: A 325 LYS cc_start: 0.7214 (mttt) cc_final: 0.6834 (mtmt) REVERT: A 347 ASP cc_start: 0.6339 (t0) cc_final: 0.5854 (t0) REVERT: A 430 THR cc_start: 0.8009 (m) cc_final: 0.7373 (p) REVERT: A 480 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7723 (tt) REVERT: A 578 ASN cc_start: 0.6527 (m-40) cc_final: 0.6259 (m-40) REVERT: A 593 LYS cc_start: 0.6529 (tptp) cc_final: 0.6309 (tptp) REVERT: C 38 ILE cc_start: 0.8309 (tt) cc_final: 0.7963 (pt) outliers start: 13 outliers final: 8 residues processed: 263 average time/residue: 0.2484 time to fit residues: 86.6003 Evaluate side-chains 252 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 243 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 480 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 0.0770 chunk 114 optimal weight: 0.0270 chunk 93 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 84 optimal weight: 0.2980 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 438 ASN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 HIS ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 233 HIS A 493 ASN A 552 ASN C 16 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9420 Z= 0.206 Angle : 0.611 9.709 12769 Z= 0.308 Chirality : 0.048 0.272 1425 Planarity : 0.004 0.039 1679 Dihedral : 8.084 83.563 1433 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.73 % Allowed : 8.78 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.22), residues: 1170 helix: -3.08 (0.54), residues: 69 sheet: -2.33 (0.51), residues: 94 loop : -2.10 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 49 HIS 0.005 0.001 HIS A 233 PHE 0.018 0.001 PHE A 549 TYR 0.018 0.002 TYR B 64 ARG 0.010 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 260 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 THR cc_start: 0.7928 (m) cc_final: 0.7695 (m) REVERT: B 30 ASP cc_start: 0.7418 (t70) cc_final: 0.6745 (t70) REVERT: B 93 GLN cc_start: 0.6951 (pp30) cc_final: 0.6623 (pp30) REVERT: B 109 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6329 (mm-30) REVERT: B 112 TYR cc_start: 0.6908 (m-80) cc_final: 0.6500 (m-80) REVERT: B 147 GLU cc_start: 0.6754 (tp30) cc_final: 0.6442 (tp30) REVERT: B 156 GLN cc_start: 0.7670 (mt0) cc_final: 0.7338 (mt0) REVERT: B 164 GLN cc_start: 0.6691 (pm20) cc_final: 0.6244 (pm20) REVERT: B 183 LEU cc_start: 0.8279 (mp) cc_final: 0.7827 (tp) REVERT: B 228 LYS cc_start: 0.7637 (mtpt) cc_final: 0.7325 (mtmm) REVERT: B 284 ASN cc_start: 0.7223 (t0) cc_final: 0.6839 (t0) REVERT: B 403 LEU cc_start: 0.6915 (tp) cc_final: 0.6654 (tp) REVERT: B 405 GLU cc_start: 0.6975 (tt0) cc_final: 0.6745 (tt0) REVERT: B 538 GLN cc_start: 0.6388 (OUTLIER) cc_final: 0.6121 (pm20) REVERT: B 568 GLN cc_start: 0.6569 (tm-30) cc_final: 0.6166 (tm-30) REVERT: A 45 GLU cc_start: 0.7235 (mp0) cc_final: 0.6860 (mp0) REVERT: A 46 ASP cc_start: 0.7824 (t70) cc_final: 0.7472 (t0) REVERT: A 67 ILE cc_start: 0.8331 (mt) cc_final: 0.8086 (mt) REVERT: A 152 ASN cc_start: 0.7293 (m110) cc_final: 0.6924 (m110) REVERT: A 198 SER cc_start: 0.8171 (m) cc_final: 0.7507 (p) REVERT: A 252 ARG cc_start: 0.7441 (mtp85) cc_final: 0.7122 (mtp85) REVERT: A 254 PHE cc_start: 0.7723 (m-10) cc_final: 0.7477 (m-10) REVERT: A 255 ARG cc_start: 0.6351 (ttt-90) cc_final: 0.6138 (tmt-80) REVERT: A 256 ASP cc_start: 0.7128 (t70) cc_final: 0.6703 (t70) REVERT: A 268 MET cc_start: 0.5810 (mtm) cc_final: 0.5321 (mtm) REVERT: A 277 MET cc_start: 0.5201 (mtt) cc_final: 0.4911 (mtt) REVERT: A 292 VAL cc_start: 0.8096 (m) cc_final: 0.7695 (p) REVERT: A 294 LYS cc_start: 0.8077 (tttt) cc_final: 0.7825 (tttt) REVERT: A 316 TYR cc_start: 0.6437 (t80) cc_final: 0.6137 (t80) REVERT: A 325 LYS cc_start: 0.7301 (mttt) cc_final: 0.6856 (mtmt) REVERT: A 347 ASP cc_start: 0.6544 (t0) cc_final: 0.6067 (t0) REVERT: A 391 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6982 (mm-30) REVERT: A 430 THR cc_start: 0.8045 (m) cc_final: 0.7407 (p) REVERT: A 480 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7858 (tt) REVERT: A 489 LYS cc_start: 0.7787 (ttmm) cc_final: 0.7193 (mtpp) REVERT: A 578 ASN cc_start: 0.6745 (m-40) cc_final: 0.6439 (m-40) REVERT: A 593 LYS cc_start: 0.6542 (tptp) cc_final: 0.6332 (tptp) outliers start: 28 outliers final: 15 residues processed: 266 average time/residue: 0.2565 time to fit residues: 89.4924 Evaluate side-chains 246 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 229 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 480 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.0870 chunk 79 optimal weight: 0.4980 chunk 54 optimal weight: 0.0670 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 0.0970 chunk 112 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 overall best weight: 0.2494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN A 153 ASN A 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9420 Z= 0.200 Angle : 0.611 12.040 12769 Z= 0.305 Chirality : 0.048 0.465 1425 Planarity : 0.004 0.037 1679 Dihedral : 7.347 71.171 1433 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.24 % Allowed : 10.24 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.22), residues: 1170 helix: -2.92 (0.56), residues: 68 sheet: -2.14 (0.52), residues: 92 loop : -1.96 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 49 HIS 0.004 0.001 HIS A 507 PHE 0.032 0.002 PHE A 549 TYR 0.023 0.002 TYR B 163 ARG 0.007 0.001 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 254 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 THR cc_start: 0.7873 (m) cc_final: 0.7651 (m) REVERT: B 30 ASP cc_start: 0.7457 (t70) cc_final: 0.6816 (t70) REVERT: B 93 GLN cc_start: 0.6967 (pp30) cc_final: 0.6608 (pp30) REVERT: B 112 TYR cc_start: 0.6961 (m-80) cc_final: 0.6595 (m-80) REVERT: B 147 GLU cc_start: 0.6785 (tp30) cc_final: 0.6427 (tp30) REVERT: B 164 GLN cc_start: 0.6907 (pm20) cc_final: 0.6546 (pm20) REVERT: B 183 LEU cc_start: 0.8257 (mp) cc_final: 0.7851 (tp) REVERT: B 228 LYS cc_start: 0.7531 (mtpt) cc_final: 0.7178 (mtpt) REVERT: B 274 TYR cc_start: 0.7806 (t80) cc_final: 0.7462 (t80) REVERT: B 280 GLU cc_start: 0.6757 (pt0) cc_final: 0.6193 (pm20) REVERT: B 284 ASN cc_start: 0.7393 (t0) cc_final: 0.7035 (t0) REVERT: B 403 LEU cc_start: 0.6949 (tp) cc_final: 0.6723 (tp) REVERT: B 405 GLU cc_start: 0.6983 (tt0) cc_final: 0.6739 (tt0) REVERT: B 421 ASP cc_start: 0.6556 (p0) cc_final: 0.6226 (p0) REVERT: B 538 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.6094 (pm20) REVERT: A 45 GLU cc_start: 0.7222 (mp0) cc_final: 0.6913 (mp0) REVERT: A 46 ASP cc_start: 0.7849 (t70) cc_final: 0.7415 (t0) REVERT: A 80 LYS cc_start: 0.8358 (mttm) cc_final: 0.8147 (mttp) REVERT: A 148 VAL cc_start: 0.8218 (t) cc_final: 0.7830 (m) REVERT: A 198 SER cc_start: 0.8227 (m) cc_final: 0.7542 (p) REVERT: A 255 ARG cc_start: 0.6292 (ttt-90) cc_final: 0.6048 (tmt-80) REVERT: A 268 MET cc_start: 0.5871 (mtm) cc_final: 0.5372 (mtm) REVERT: A 277 MET cc_start: 0.5257 (mtt) cc_final: 0.4940 (mtt) REVERT: A 292 VAL cc_start: 0.8060 (m) cc_final: 0.7726 (p) REVERT: A 294 LYS cc_start: 0.8097 (tttt) cc_final: 0.7847 (tttt) REVERT: A 316 TYR cc_start: 0.6514 (t80) cc_final: 0.6018 (t80) REVERT: A 325 LYS cc_start: 0.7325 (mttt) cc_final: 0.6841 (mtmt) REVERT: A 347 ASP cc_start: 0.6606 (t0) cc_final: 0.6163 (t0) REVERT: A 391 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7082 (mm-30) REVERT: A 430 THR cc_start: 0.8040 (m) cc_final: 0.7388 (p) REVERT: A 578 ASN cc_start: 0.6891 (m-40) cc_final: 0.6686 (m-40) outliers start: 23 outliers final: 16 residues processed: 262 average time/residue: 0.2553 time to fit residues: 88.6312 Evaluate side-chains 248 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 231 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.0980 chunk 63 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 HIS B 446 GLN B 470 HIS B 570 GLN A 57 ASN A 552 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 9420 Z= 0.298 Angle : 0.660 10.028 12769 Z= 0.334 Chirality : 0.051 0.496 1425 Planarity : 0.004 0.043 1679 Dihedral : 7.161 63.820 1433 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.54 % Allowed : 11.41 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.22), residues: 1170 helix: -2.82 (0.58), residues: 60 sheet: -2.15 (0.53), residues: 82 loop : -1.88 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 200 HIS 0.006 0.001 HIS A 507 PHE 0.035 0.002 PHE A 549 TYR 0.017 0.002 TYR B 409 ARG 0.009 0.001 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 251 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 THR cc_start: 0.7806 (m) cc_final: 0.7588 (m) REVERT: B 30 ASP cc_start: 0.7578 (t70) cc_final: 0.6931 (t70) REVERT: B 112 TYR cc_start: 0.7114 (m-80) cc_final: 0.6791 (m-80) REVERT: B 147 GLU cc_start: 0.6763 (tp30) cc_final: 0.6375 (tp30) REVERT: B 164 GLN cc_start: 0.7211 (pm20) cc_final: 0.6142 (pm20) REVERT: B 228 LYS cc_start: 0.7601 (mtpt) cc_final: 0.7294 (mtmm) REVERT: B 274 TYR cc_start: 0.7845 (t80) cc_final: 0.7531 (t80) REVERT: B 284 ASN cc_start: 0.7658 (t0) cc_final: 0.7344 (t0) REVERT: B 405 GLU cc_start: 0.6916 (tt0) cc_final: 0.6698 (tt0) REVERT: B 421 ASP cc_start: 0.6585 (p0) cc_final: 0.6238 (p0) REVERT: B 452 TRP cc_start: 0.7989 (p90) cc_final: 0.7786 (p90) REVERT: B 538 GLN cc_start: 0.6532 (OUTLIER) cc_final: 0.6258 (pm20) REVERT: B 568 GLN cc_start: 0.6850 (tm-30) cc_final: 0.6420 (tm-30) REVERT: A 45 GLU cc_start: 0.7279 (mp0) cc_final: 0.7032 (mp0) REVERT: A 46 ASP cc_start: 0.7743 (t70) cc_final: 0.7269 (t0) REVERT: A 133 LYS cc_start: 0.7059 (mttt) cc_final: 0.6688 (mmmm) REVERT: A 148 VAL cc_start: 0.8337 (t) cc_final: 0.7999 (m) REVERT: A 198 SER cc_start: 0.8240 (m) cc_final: 0.7485 (p) REVERT: A 268 MET cc_start: 0.6075 (mtm) cc_final: 0.5547 (mtm) REVERT: A 277 MET cc_start: 0.5457 (mtt) cc_final: 0.5128 (mtt) REVERT: A 292 VAL cc_start: 0.8060 (m) cc_final: 0.7790 (p) REVERT: A 316 TYR cc_start: 0.6550 (t80) cc_final: 0.6232 (t80) REVERT: A 325 LYS cc_start: 0.7424 (mttt) cc_final: 0.6971 (mtmt) REVERT: A 347 ASP cc_start: 0.6667 (t0) cc_final: 0.6173 (t0) REVERT: A 360 LYS cc_start: 0.8060 (tttt) cc_final: 0.7727 (ttmm) REVERT: A 391 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 430 THR cc_start: 0.8111 (m) cc_final: 0.7480 (p) REVERT: A 431 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7746 (mtmt) REVERT: A 487 LYS cc_start: 0.7003 (mtmm) cc_final: 0.6742 (mtmm) REVERT: A 593 LYS cc_start: 0.6732 (tptp) cc_final: 0.6522 (tptp) REVERT: C 38 ILE cc_start: 0.8251 (tt) cc_final: 0.7946 (pt) outliers start: 26 outliers final: 21 residues processed: 260 average time/residue: 0.2488 time to fit residues: 85.4456 Evaluate side-chains 268 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 246 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 108 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 552 ASN ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 9420 Z= 0.323 Angle : 0.676 9.709 12769 Z= 0.342 Chirality : 0.051 0.447 1425 Planarity : 0.005 0.044 1679 Dihedral : 7.245 64.431 1433 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.22 % Allowed : 11.41 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.23), residues: 1170 helix: -2.90 (0.56), residues: 59 sheet: -2.09 (0.57), residues: 72 loop : -1.81 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 49 HIS 0.007 0.001 HIS A 507 PHE 0.040 0.002 PHE A 549 TYR 0.017 0.002 TYR B 50 ARG 0.010 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 266 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7592 (t70) cc_final: 0.6971 (t70) REVERT: B 49 LEU cc_start: 0.8019 (tt) cc_final: 0.7804 (tp) REVERT: B 75 GLN cc_start: 0.7656 (pt0) cc_final: 0.7421 (pt0) REVERT: B 112 TYR cc_start: 0.7290 (m-80) cc_final: 0.6997 (m-80) REVERT: B 138 ARG cc_start: 0.6731 (mmm160) cc_final: 0.6169 (mmm160) REVERT: B 139 GLU cc_start: 0.6399 (mp0) cc_final: 0.6184 (mp0) REVERT: B 147 GLU cc_start: 0.6795 (tp30) cc_final: 0.6356 (tp30) REVERT: B 164 GLN cc_start: 0.7675 (pm20) cc_final: 0.7415 (pm20) REVERT: B 183 LEU cc_start: 0.8135 (mp) cc_final: 0.7933 (mt) REVERT: B 228 LYS cc_start: 0.7678 (mtpt) cc_final: 0.7354 (mtmm) REVERT: B 265 GLU cc_start: 0.7504 (pm20) cc_final: 0.6886 (pm20) REVERT: B 274 TYR cc_start: 0.7834 (t80) cc_final: 0.7576 (t80) REVERT: B 284 ASN cc_start: 0.7823 (t0) cc_final: 0.7517 (t0) REVERT: B 421 ASP cc_start: 0.6633 (p0) cc_final: 0.6358 (p0) REVERT: B 441 TYR cc_start: 0.8374 (m-80) cc_final: 0.8011 (m-80) REVERT: B 450 ILE cc_start: 0.8065 (tt) cc_final: 0.7803 (pt) REVERT: B 538 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.6334 (pm20) REVERT: A 46 ASP cc_start: 0.7680 (t70) cc_final: 0.7220 (t0) REVERT: A 125 TYR cc_start: 0.7816 (p90) cc_final: 0.7366 (p90) REVERT: A 133 LYS cc_start: 0.7126 (mttt) cc_final: 0.6679 (mmmm) REVERT: A 142 GLU cc_start: 0.6992 (tt0) cc_final: 0.6713 (tp30) REVERT: A 148 VAL cc_start: 0.8359 (t) cc_final: 0.7993 (m) REVERT: A 198 SER cc_start: 0.8302 (m) cc_final: 0.7550 (p) REVERT: A 263 THR cc_start: 0.7920 (m) cc_final: 0.7630 (p) REVERT: A 268 MET cc_start: 0.6146 (mtm) cc_final: 0.5640 (mtm) REVERT: A 277 MET cc_start: 0.5605 (mtt) cc_final: 0.5244 (mtt) REVERT: A 292 VAL cc_start: 0.8054 (m) cc_final: 0.7772 (p) REVERT: A 325 LYS cc_start: 0.6923 (mttt) cc_final: 0.6536 (mtmt) REVERT: A 360 LYS cc_start: 0.8052 (tttt) cc_final: 0.7699 (ttmm) REVERT: A 391 GLU cc_start: 0.7837 (mm-30) cc_final: 0.6979 (tp30) REVERT: A 430 THR cc_start: 0.8142 (m) cc_final: 0.7527 (p) REVERT: A 431 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7806 (mttp) REVERT: A 487 LYS cc_start: 0.7250 (mtmm) cc_final: 0.6941 (mtmm) REVERT: A 489 LYS cc_start: 0.8044 (tttt) cc_final: 0.7708 (tttp) REVERT: A 584 HIS cc_start: 0.6091 (m90) cc_final: 0.5641 (m170) REVERT: A 593 LYS cc_start: 0.6777 (tptp) cc_final: 0.6329 (tptp) outliers start: 33 outliers final: 23 residues processed: 277 average time/residue: 0.2387 time to fit residues: 87.9086 Evaluate side-chains 275 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 251 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 0.0370 chunk 94 optimal weight: 0.0070 chunk 62 optimal weight: 0.2980 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 HIS ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN A 358 HIS ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9420 Z= 0.204 Angle : 0.644 9.780 12769 Z= 0.324 Chirality : 0.049 0.435 1425 Planarity : 0.004 0.041 1679 Dihedral : 6.878 59.546 1433 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.83 % Allowed : 13.46 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.23), residues: 1170 helix: -2.92 (0.55), residues: 65 sheet: -2.33 (0.52), residues: 82 loop : -1.71 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 49 HIS 0.006 0.001 HIS A 507 PHE 0.024 0.002 PHE A 549 TYR 0.034 0.002 TYR B 163 ARG 0.009 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 248 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6551 (pp30) cc_final: 0.6316 (pp30) REVERT: B 30 ASP cc_start: 0.7530 (t70) cc_final: 0.6921 (t70) REVERT: B 49 LEU cc_start: 0.8023 (tt) cc_final: 0.7818 (tp) REVERT: B 75 GLN cc_start: 0.7600 (pt0) cc_final: 0.7387 (pt0) REVERT: B 112 TYR cc_start: 0.7123 (m-80) cc_final: 0.6840 (m-80) REVERT: B 138 ARG cc_start: 0.6716 (mmm160) cc_final: 0.6209 (mmm160) REVERT: B 147 GLU cc_start: 0.6777 (tp30) cc_final: 0.6391 (tp30) REVERT: B 164 GLN cc_start: 0.7206 (pm20) cc_final: 0.6837 (pm20) REVERT: B 228 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7400 (mtmm) REVERT: B 274 TYR cc_start: 0.7924 (t80) cc_final: 0.7603 (t80) REVERT: B 284 ASN cc_start: 0.7781 (t0) cc_final: 0.7474 (t0) REVERT: B 290 THR cc_start: 0.7609 (m) cc_final: 0.7265 (m) REVERT: B 405 GLU cc_start: 0.6867 (tt0) cc_final: 0.6631 (tt0) REVERT: B 421 ASP cc_start: 0.6604 (p0) cc_final: 0.6274 (p0) REVERT: B 441 TYR cc_start: 0.8324 (m-80) cc_final: 0.7917 (m-80) REVERT: B 538 GLN cc_start: 0.6520 (OUTLIER) cc_final: 0.6292 (pm20) REVERT: B 568 GLN cc_start: 0.6968 (tm-30) cc_final: 0.6565 (tm-30) REVERT: A 46 ASP cc_start: 0.7659 (t70) cc_final: 0.7178 (t0) REVERT: A 125 TYR cc_start: 0.7599 (p90) cc_final: 0.7272 (p90) REVERT: A 142 GLU cc_start: 0.7029 (tt0) cc_final: 0.6732 (tp30) REVERT: A 148 VAL cc_start: 0.8329 (t) cc_final: 0.8011 (m) REVERT: A 152 ASN cc_start: 0.7085 (t0) cc_final: 0.6757 (t0) REVERT: A 160 GLU cc_start: 0.7709 (pm20) cc_final: 0.7379 (pm20) REVERT: A 198 SER cc_start: 0.8313 (m) cc_final: 0.7609 (p) REVERT: A 222 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7065 (ttm-80) REVERT: A 250 VAL cc_start: 0.7578 (t) cc_final: 0.7324 (m) REVERT: A 263 THR cc_start: 0.7913 (m) cc_final: 0.7634 (p) REVERT: A 268 MET cc_start: 0.6122 (mtm) cc_final: 0.5555 (mtm) REVERT: A 277 MET cc_start: 0.5573 (mtt) cc_final: 0.5215 (mtt) REVERT: A 292 VAL cc_start: 0.8010 (m) cc_final: 0.7722 (p) REVERT: A 325 LYS cc_start: 0.7044 (mttt) cc_final: 0.6601 (mtmm) REVERT: A 357 LYS cc_start: 0.8196 (pptt) cc_final: 0.7972 (pptt) REVERT: A 360 LYS cc_start: 0.8011 (tttt) cc_final: 0.7664 (ttmm) REVERT: A 391 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 424 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6892 (mt-10) REVERT: A 430 THR cc_start: 0.7986 (m) cc_final: 0.7379 (p) REVERT: A 487 LYS cc_start: 0.7230 (mtmm) cc_final: 0.6900 (mtmm) REVERT: A 524 VAL cc_start: 0.8275 (t) cc_final: 0.8048 (p) REVERT: A 584 HIS cc_start: 0.6080 (m90) cc_final: 0.5632 (m170) REVERT: A 593 LYS cc_start: 0.6769 (tptp) cc_final: 0.6297 (tptp) outliers start: 29 outliers final: 19 residues processed: 259 average time/residue: 0.2579 time to fit residues: 89.3524 Evaluate side-chains 260 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 240 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 462 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 71 optimal weight: 0.0980 chunk 76 optimal weight: 0.0980 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 0.1980 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN A 304 HIS ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9420 Z= 0.245 Angle : 0.652 9.830 12769 Z= 0.329 Chirality : 0.049 0.431 1425 Planarity : 0.004 0.038 1679 Dihedral : 6.854 59.067 1433 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.63 % Allowed : 14.34 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.23), residues: 1170 helix: -2.85 (0.53), residues: 72 sheet: -2.52 (0.48), residues: 92 loop : -1.67 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 49 HIS 0.007 0.001 HIS A 507 PHE 0.020 0.002 PHE A 549 TYR 0.039 0.002 TYR B 163 ARG 0.012 0.001 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 255 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6522 (pp30) cc_final: 0.6198 (pp30) REVERT: B 30 ASP cc_start: 0.7568 (t70) cc_final: 0.6982 (t70) REVERT: B 75 GLN cc_start: 0.7651 (pt0) cc_final: 0.7433 (pt0) REVERT: B 112 TYR cc_start: 0.7164 (m-80) cc_final: 0.6918 (m-80) REVERT: B 138 ARG cc_start: 0.6773 (mmm160) cc_final: 0.6565 (mmm160) REVERT: B 147 GLU cc_start: 0.6796 (tp30) cc_final: 0.6407 (tp30) REVERT: B 274 TYR cc_start: 0.7939 (t80) cc_final: 0.7608 (t80) REVERT: B 284 ASN cc_start: 0.7831 (t0) cc_final: 0.7528 (t0) REVERT: B 290 THR cc_start: 0.7735 (m) cc_final: 0.7440 (m) REVERT: B 405 GLU cc_start: 0.6844 (tt0) cc_final: 0.6586 (tt0) REVERT: B 421 ASP cc_start: 0.6619 (p0) cc_final: 0.6264 (p0) REVERT: B 441 TYR cc_start: 0.8354 (m-80) cc_final: 0.7977 (m-80) REVERT: B 538 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.6319 (pm20) REVERT: B 568 GLN cc_start: 0.6908 (tm-30) cc_final: 0.6503 (tm-30) REVERT: A 46 ASP cc_start: 0.7664 (t70) cc_final: 0.7176 (t0) REVERT: A 125 TYR cc_start: 0.7576 (p90) cc_final: 0.7321 (p90) REVERT: A 133 LYS cc_start: 0.7368 (tppt) cc_final: 0.6629 (mppt) REVERT: A 142 GLU cc_start: 0.6977 (tt0) cc_final: 0.6671 (tp30) REVERT: A 148 VAL cc_start: 0.8344 (t) cc_final: 0.8016 (m) REVERT: A 160 GLU cc_start: 0.7750 (pm20) cc_final: 0.7402 (pm20) REVERT: A 198 SER cc_start: 0.8291 (m) cc_final: 0.7552 (p) REVERT: A 250 VAL cc_start: 0.7643 (t) cc_final: 0.7412 (m) REVERT: A 263 THR cc_start: 0.7938 (m) cc_final: 0.7688 (p) REVERT: A 268 MET cc_start: 0.6193 (mtm) cc_final: 0.5373 (mtm) REVERT: A 277 MET cc_start: 0.5610 (mtt) cc_final: 0.5250 (mtt) REVERT: A 292 VAL cc_start: 0.8007 (m) cc_final: 0.7713 (p) REVERT: A 325 LYS cc_start: 0.7000 (mttt) cc_final: 0.6587 (mtmm) REVERT: A 347 ASP cc_start: 0.6753 (t0) cc_final: 0.6281 (t0) REVERT: A 357 LYS cc_start: 0.8261 (pptt) cc_final: 0.8022 (pptt) REVERT: A 360 LYS cc_start: 0.7996 (tttt) cc_final: 0.7654 (ttmm) REVERT: A 391 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7520 (mm-30) REVERT: A 424 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6885 (mt-10) REVERT: A 430 THR cc_start: 0.8003 (m) cc_final: 0.7387 (p) REVERT: A 551 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6967 (tm-30) REVERT: A 584 HIS cc_start: 0.6114 (m90) cc_final: 0.5640 (m170) REVERT: A 593 LYS cc_start: 0.6743 (tptp) cc_final: 0.6276 (tptp) outliers start: 27 outliers final: 20 residues processed: 266 average time/residue: 0.2551 time to fit residues: 90.2257 Evaluate side-chains 268 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 247 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 484 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 chunk 31 optimal weight: 0.0570 chunk 94 optimal weight: 0.0770 chunk 98 optimal weight: 0.3980 chunk 103 optimal weight: 0.0270 chunk 68 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 0.0670 overall best weight: 0.0652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN B 478 HIS ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN B 530 ASN A 271 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9420 Z= 0.165 Angle : 0.621 9.781 12769 Z= 0.314 Chirality : 0.047 0.427 1425 Planarity : 0.004 0.039 1679 Dihedral : 6.441 56.740 1433 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 1.66 % Allowed : 15.71 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.23), residues: 1170 helix: -2.37 (0.64), residues: 60 sheet: -2.44 (0.54), residues: 82 loop : -1.57 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 49 HIS 0.005 0.001 HIS A 507 PHE 0.020 0.001 PHE A 549 TYR 0.026 0.001 TYR B 163 ARG 0.010 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 244 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7463 (t70) cc_final: 0.6866 (t70) REVERT: B 67 THR cc_start: 0.8271 (m) cc_final: 0.8069 (t) REVERT: B 112 TYR cc_start: 0.6913 (m-80) cc_final: 0.6699 (m-80) REVERT: B 138 ARG cc_start: 0.6798 (mmm160) cc_final: 0.6559 (mmm160) REVERT: B 147 GLU cc_start: 0.6785 (tp30) cc_final: 0.6443 (tp30) REVERT: B 256 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7465 (mp) REVERT: B 274 TYR cc_start: 0.7943 (t80) cc_final: 0.7534 (t80) REVERT: B 280 GLU cc_start: 0.6785 (pt0) cc_final: 0.6247 (pm20) REVERT: B 284 ASN cc_start: 0.7794 (t0) cc_final: 0.7305 (t0) REVERT: B 290 THR cc_start: 0.7552 (m) cc_final: 0.7200 (m) REVERT: B 376 PHE cc_start: 0.8327 (m-10) cc_final: 0.8094 (m-80) REVERT: B 405 GLU cc_start: 0.6829 (tt0) cc_final: 0.6564 (tt0) REVERT: B 421 ASP cc_start: 0.6590 (p0) cc_final: 0.6208 (p0) REVERT: B 441 TYR cc_start: 0.8299 (m-80) cc_final: 0.7902 (m-80) REVERT: B 538 GLN cc_start: 0.6480 (OUTLIER) cc_final: 0.6224 (pm20) REVERT: B 568 GLN cc_start: 0.6900 (tm-30) cc_final: 0.6495 (tm-30) REVERT: A 46 ASP cc_start: 0.7658 (t70) cc_final: 0.7177 (t0) REVERT: A 133 LYS cc_start: 0.7289 (tppt) cc_final: 0.6553 (mppt) REVERT: A 142 GLU cc_start: 0.6985 (tt0) cc_final: 0.6726 (tp30) REVERT: A 148 VAL cc_start: 0.8294 (t) cc_final: 0.8005 (m) REVERT: A 160 GLU cc_start: 0.7649 (pm20) cc_final: 0.7275 (pm20) REVERT: A 198 SER cc_start: 0.8296 (m) cc_final: 0.7560 (p) REVERT: A 263 THR cc_start: 0.7906 (m) cc_final: 0.7608 (p) REVERT: A 268 MET cc_start: 0.6176 (mtm) cc_final: 0.5317 (mtm) REVERT: A 277 MET cc_start: 0.5518 (mtt) cc_final: 0.5146 (mtt) REVERT: A 292 VAL cc_start: 0.7970 (m) cc_final: 0.7619 (p) REVERT: A 325 LYS cc_start: 0.6984 (mttt) cc_final: 0.6608 (mtmm) REVERT: A 347 ASP cc_start: 0.6704 (t0) cc_final: 0.6237 (t0) REVERT: A 357 LYS cc_start: 0.8270 (pptt) cc_final: 0.8023 (pptt) REVERT: A 360 LYS cc_start: 0.7992 (tttt) cc_final: 0.7646 (ttmm) REVERT: A 391 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7416 (mm-30) REVERT: A 424 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6915 (mt-10) REVERT: A 430 THR cc_start: 0.7960 (m) cc_final: 0.7363 (p) REVERT: A 489 LYS cc_start: 0.7909 (tttm) cc_final: 0.7514 (ttmt) REVERT: A 584 HIS cc_start: 0.5997 (m90) cc_final: 0.5538 (m170) REVERT: A 593 LYS cc_start: 0.6726 (tptp) cc_final: 0.6234 (tptp) outliers start: 17 outliers final: 11 residues processed: 248 average time/residue: 0.2515 time to fit residues: 82.7629 Evaluate side-chains 252 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 239 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 0.2980 chunk 115 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 92 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 71 optimal weight: 0.0270 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9420 Z= 0.254 Angle : 0.657 9.854 12769 Z= 0.333 Chirality : 0.050 0.425 1425 Planarity : 0.004 0.036 1679 Dihedral : 6.660 56.702 1433 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.56 % Allowed : 16.49 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.23), residues: 1170 helix: -2.72 (0.54), residues: 70 sheet: -2.41 (0.51), residues: 92 loop : -1.56 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 49 HIS 0.005 0.001 HIS A 507 PHE 0.018 0.002 PHE A 549 TYR 0.024 0.002 TYR B 409 ARG 0.012 0.001 ARG B 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 242 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7616 (t70) cc_final: 0.7030 (t70) REVERT: B 75 GLN cc_start: 0.7617 (pt0) cc_final: 0.7414 (pt0) REVERT: B 138 ARG cc_start: 0.6796 (mmm160) cc_final: 0.5598 (mmm160) REVERT: B 147 GLU cc_start: 0.6787 (tp30) cc_final: 0.6410 (tp30) REVERT: B 190 ARG cc_start: 0.6678 (ttt-90) cc_final: 0.6401 (ttt-90) REVERT: B 274 TYR cc_start: 0.7930 (t80) cc_final: 0.7610 (t80) REVERT: B 284 ASN cc_start: 0.8022 (t0) cc_final: 0.7670 (t0) REVERT: B 290 THR cc_start: 0.7745 (m) cc_final: 0.7450 (m) REVERT: B 376 PHE cc_start: 0.8349 (m-10) cc_final: 0.8125 (m-80) REVERT: B 405 GLU cc_start: 0.6821 (tt0) cc_final: 0.6559 (tt0) REVERT: B 421 ASP cc_start: 0.6584 (p0) cc_final: 0.6235 (p0) REVERT: B 441 TYR cc_start: 0.8324 (m-80) cc_final: 0.7962 (m-80) REVERT: B 538 GLN cc_start: 0.6564 (OUTLIER) cc_final: 0.6345 (pm20) REVERT: B 568 GLN cc_start: 0.6875 (tm-30) cc_final: 0.6449 (tm-30) REVERT: A 46 ASP cc_start: 0.7654 (t70) cc_final: 0.7168 (t0) REVERT: A 142 GLU cc_start: 0.6988 (tt0) cc_final: 0.6661 (tp30) REVERT: A 148 VAL cc_start: 0.8326 (t) cc_final: 0.7989 (m) REVERT: A 158 ASN cc_start: 0.7178 (m-40) cc_final: 0.6919 (t0) REVERT: A 166 ASP cc_start: 0.7370 (t70) cc_final: 0.6978 (t70) REVERT: A 198 SER cc_start: 0.8257 (m) cc_final: 0.7574 (p) REVERT: A 263 THR cc_start: 0.7958 (m) cc_final: 0.7694 (p) REVERT: A 268 MET cc_start: 0.6217 (mtm) cc_final: 0.5196 (mtm) REVERT: A 277 MET cc_start: 0.5634 (mtt) cc_final: 0.5242 (mtt) REVERT: A 292 VAL cc_start: 0.7995 (m) cc_final: 0.7680 (p) REVERT: A 325 LYS cc_start: 0.7038 (mttt) cc_final: 0.6699 (mtmm) REVERT: A 347 ASP cc_start: 0.6763 (t0) cc_final: 0.6314 (t0) REVERT: A 357 LYS cc_start: 0.8345 (pptt) cc_final: 0.8059 (pptt) REVERT: A 360 LYS cc_start: 0.8016 (tttt) cc_final: 0.7614 (ttmm) REVERT: A 391 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7103 (tp30) REVERT: A 430 THR cc_start: 0.8020 (m) cc_final: 0.7404 (p) REVERT: A 489 LYS cc_start: 0.7976 (tttm) cc_final: 0.7664 (tttp) REVERT: A 584 HIS cc_start: 0.5989 (m90) cc_final: 0.5556 (m170) REVERT: A 593 LYS cc_start: 0.6735 (tptp) cc_final: 0.6252 (tptp) outliers start: 16 outliers final: 14 residues processed: 248 average time/residue: 0.2548 time to fit residues: 84.2057 Evaluate side-chains 255 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 240 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 487 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.0570 chunk 38 optimal weight: 0.4980 chunk 94 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN B 530 ASN A 152 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.146377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.123971 restraints weight = 13220.089| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.74 r_work: 0.3469 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9420 Z= 0.277 Angle : 0.673 9.700 12769 Z= 0.342 Chirality : 0.050 0.423 1425 Planarity : 0.004 0.037 1679 Dihedral : 6.814 56.291 1433 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 1.95 % Allowed : 16.88 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.23), residues: 1170 helix: -2.19 (0.63), residues: 60 sheet: -2.41 (0.47), residues: 102 loop : -1.57 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 49 HIS 0.007 0.001 HIS A 507 PHE 0.015 0.002 PHE A 549 TYR 0.024 0.002 TYR B 409 ARG 0.009 0.001 ARG A 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2858.02 seconds wall clock time: 51 minutes 59.38 seconds (3119.38 seconds total)