Starting phenix.real_space_refine on Tue May 20 05:48:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4l_41886/05_2025/8u4l_41886_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4l_41886/05_2025/8u4l_41886.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/cci-nas-00/data/ceres_data/8u4l_41886/05_2025/8u4l_41886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4l_41886/05_2025/8u4l_41886.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4l_41886/05_2025/8u4l_41886_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4l_41886/05_2025/8u4l_41886_trim.cif" } 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 118 5.16 5 C 6179 2.51 5 N 1708 2.21 5 O 1984 1.98 5 H 9080 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19069 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 9061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 9061 Classifications: {'peptide': 598} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 570} Chain breaks: 3 Chain: "B" Number of atoms: 8787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 8787 Classifications: {'peptide': 582} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 38, 'TRANS': 543} Chain breaks: 2 Chain: "C" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 767 Classifications: {'peptide': 50} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 1 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" 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 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.41, per 1000 atoms: 0.55 Number of scatterers: 19069 At special positions: 0 Unit cell: (80.995, 146.96, 136.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 118 16.00 O 1984 8.00 N 1708 7.00 C 6179 6.00 H 9080 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 56 " distance=2.08 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 197 " distance=2.08 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 205 " distance=2.08 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 229 " distance=2.02 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 238 " distance=1.84 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=1.99 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 258 " distance=2.04 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 289 " distance=2.02 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 304 " distance=2.02 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.02 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.06 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 496 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 512 " distance=2.08 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 520 " distance=2.04 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 532 " distance=2.02 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 552 " distance=2.02 Simple disulfide: pdb=" SG CYS A 555 " - pdb=" SG CYS A 569 " distance=2.03 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 589 " distance=2.07 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 614 " distance=2.12 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 625 " distance=2.01 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 633 " distance=2.13 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.07 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.06 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.01 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.08 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.02 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.02 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.02 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.04 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.15 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.15 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=1.98 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 331 " distance=2.11 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 338 " distance=2.14 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.35 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.11 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.03 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 623 " distance=2.03 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 210 " distance=2.02 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 221 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA G 3 " - " MAN G 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 701 " - " ASN A 410 " " NAG A 702 " - " ASN A 495 " " NAG B 701 " - " ASN B 68 " " NAG D 1 " - " ASN A 138 " " NAG E 1 " - " ASN A 358 " " NAG F 1 " - " ASN A 473 " " NAG G 1 " - " ASN A 576 " " NAG H 1 " - " ASN A 548 " " NAG I 1 " - " ASN A 253 " " NAG J 1 " - " ASN B 187 " " NAG K 1 " - " ASN B 259 " " NAG L 1 " - " ASN B 530 " " NAG M 1 " - " ASN B 571 " Time building additional restraints: 5.69 Conformation dependent library (CDL) restraints added in 1.5 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 30 sheets defined 16.7% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.931A pdb=" N SER A 79 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.070A pdb=" N ILE A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.811A pdb=" N CYS A 205 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.928A pdb=" N CYS A 229 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 385 through 395 removed outlier: 3.781A pdb=" N THR A 394 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.853A pdb=" N CYS A 577 " --> pdb=" O PRO A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 633 removed outlier: 4.317A pdb=" N CYS A 633 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 71 through 77 removed outlier: 4.345A pdb=" N ASP B 76 " --> pdb=" O PHE B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 110 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 208 through 212 removed outlier: 4.138A pdb=" N CYS B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.590A pdb=" N ASN B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.811A pdb=" N GLN B 398 " --> pdb=" O PRO B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.712A pdb=" N HIS B 478 " --> pdb=" O CYS B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 removed outlier: 3.873A pdb=" N LEU B 485 " --> pdb=" O PRO B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 removed outlier: 3.666A pdb=" N GLU B 507 " --> pdb=" O GLU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.785A pdb=" N GLY B 518 " --> pdb=" O CYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 Processing helix chain 'C' and resid 186 through 190 removed outlier: 3.925A pdb=" N CYS C 190 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.553A pdb=" N CYS A 29 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 7.077A pdb=" N SER A 38 " --> pdb=" O CYS C 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 5.666A pdb=" N GLY A 146 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 238 removed outlier: 5.623A pdb=" N ALA A 235 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N CYS A 249 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY A 237 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 254 Processing sheet with id=AA6, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA7, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 299 Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 317 Processing sheet with id=AB1, first strand: chain 'A' and resid 334 through 335 removed outlier: 6.425A pdb=" N CYS A 334 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 366 through 368 removed outlier: 7.632A pdb=" N TYR A 459 " --> pdb=" O SER A 433 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 435 " --> pdb=" O TYR A 459 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N THR A 461 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU A 437 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 458 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG A 488 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A 460 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 526 through 528 Processing sheet with id=AB4, first strand: chain 'A' and resid 545 through 546 Processing sheet with id=AB5, first strand: chain 'A' and resid 583 through 585 removed outlier: 3.690A pdb=" N PHE A 583 " --> pdb=" O VAL A 590 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AB7, first strand: chain 'B' and resid 25 through 27 removed outlier: 6.669A pdb=" N CYS B 26 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 60 through 63 removed outlier: 5.348A pdb=" N GLY B 152 " --> pdb=" O TYR B 112 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 240 through 244 removed outlier: 7.514A pdb=" N GLY B 243 " --> pdb=" O CYS B 252 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N CYS B 252 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AC2, first strand: chain 'B' and resid 272 through 275 removed outlier: 3.752A pdb=" N GLU B 280 " --> pdb=" O ASN B 275 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AC4, first strand: chain 'B' and resid 304 through 306 removed outlier: 3.623A pdb=" N SER B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AC6, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AC7, first strand: chain 'B' and resid 374 through 376 removed outlier: 4.597A pdb=" N TYR B 441 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU B 467 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU B 443 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N HIS B 469 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 445 " --> pdb=" O HIS B 469 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 534 through 536 Processing sheet with id=AC9, first strand: chain 'B' and resid 553 through 555 Processing sheet with id=AD1, first strand: chain 'B' and resid 591 through 592 Processing sheet with id=AD2, first strand: chain 'B' and resid 615 through 617 Processing sheet with id=AD3, first strand: chain 'C' and resid 216 through 217 194 hydrogen bonds defined for protein. 363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.25 Time building geometry restraints manager: 6.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 9079 1.13 - 1.30: 1704 1.30 - 1.48: 3989 1.48 - 1.65: 4373 1.65 - 1.82: 133 Bond restraints: 19278 Sorted by residual: bond pdb=" N MET B 282 " pdb=" H MET B 282 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NE2 GLN A 206 " pdb="HE21 GLN A 206 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN A 352 " pdb="HD22 ASN A 352 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ASN A 358 " pdb=" H ASN A 358 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N CYS A 625 " pdb=" H CYS A 625 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 19273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 29102 1.94 - 3.89: 3163 3.89 - 5.83: 1462 5.83 - 7.78: 811 7.78 - 9.72: 16 Bond angle restraints: 34554 Sorted by residual: angle pdb=" N GLU A 141 " pdb=" CA GLU A 141 " pdb=" C GLU A 141 " ideal model delta sigma weight residual 108.99 118.71 -9.72 1.57e+00 4.06e-01 3.83e+01 angle pdb=" C GLU B 348 " pdb=" CA GLU B 348 " pdb=" CB GLU B 348 " ideal model delta sigma weight residual 116.54 109.47 7.07 1.15e+00 7.56e-01 3.78e+01 angle pdb=" C ASP A 328 " pdb=" CA ASP A 328 " pdb=" CB ASP A 328 " ideal model delta sigma weight residual 116.54 109.93 6.61 1.15e+00 7.56e-01 3.31e+01 angle pdb=" C LYS A 35 " pdb=" CA LYS A 35 " pdb=" CB LYS A 35 " ideal model delta sigma weight residual 116.63 110.14 6.49 1.16e+00 7.43e-01 3.13e+01 angle pdb=" C LYS B 32 " pdb=" CA LYS B 32 " pdb=" CB LYS B 32 " ideal model delta sigma weight residual 116.54 110.22 6.32 1.15e+00 7.56e-01 3.02e+01 ... (remaining 34549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 9033 21.25 - 42.49: 420 42.49 - 63.74: 234 63.74 - 84.98: 68 84.98 - 106.23: 36 Dihedral angle restraints: 9791 sinusoidal: 5677 harmonic: 4114 Sorted by residual: dihedral pdb=" CB CYS A 217 " pdb=" SG CYS A 217 " pdb=" SG CYS A 229 " pdb=" CB CYS A 229 " ideal model delta sinusoidal sigma weight residual -86.00 -176.48 90.48 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS A 293 " pdb=" SG CYS A 293 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 177.18 -84.18 1 1.00e+01 1.00e-02 8.63e+01 dihedral pdb=" CB CYS B 315 " pdb=" SG CYS B 315 " pdb=" SG CYS B 331 " pdb=" CB CYS B 331 " ideal model delta sinusoidal sigma weight residual 93.00 176.91 -83.91 1 1.00e+01 1.00e-02 8.58e+01 ... (remaining 9788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1310 0.095 - 0.189: 252 0.189 - 0.284: 40 0.284 - 0.379: 15 0.379 - 0.474: 3 Chirality restraints: 1620 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.75e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.39e+02 chirality pdb=" C1 MAN D 4 " pdb=" O3 BMA D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 2.10 0.30 2.00e-02 2.50e+03 2.22e+02 ... (remaining 1617 not shown) Planarity restraints: 2940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.319 2.00e-02 2.50e+03 2.70e-01 9.13e+02 pdb=" C7 NAG E 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.469 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 410 " 0.250 2.00e-02 2.50e+03 1.99e-01 5.97e+02 pdb=" CG ASN A 410 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 410 " -0.198 2.00e-02 2.50e+03 pdb=" ND2 ASN A 410 " -0.034 2.00e-02 2.50e+03 pdb="HD21 ASN A 410 " -0.258 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " 0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.189 2.00e-02 2.50e+03 1.58e-01 3.13e+02 pdb=" C7 NAG E 2 " 0.042 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.132 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.265 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.015 2.00e-02 2.50e+03 ... (remaining 2937 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 746 2.08 - 2.71: 25626 2.71 - 3.34: 52693 3.34 - 3.97: 68678 3.97 - 4.60: 99884 Nonbonded interactions: 247627 Sorted by model distance: nonbonded pdb=" OE2 GLU A 317 " pdb=" HZ1 LYS A 324 " model vdw 1.452 2.450 nonbonded pdb=" HB3 LYS B 32 " pdb=" H LEU B 33 " model vdw 1.504 2.270 nonbonded pdb=" HG SER B 358 " pdb=" O ALA B 390 " model vdw 1.531 2.450 nonbonded pdb=" OE1 GLU A 202 " pdb=" H GLU A 202 " model vdw 1.601 2.450 nonbonded pdb=" OG1 THR A 209 " pdb="HH11 ARG A 220 " model vdw 1.610 2.450 ... (remaining 247622 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.210 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: 0.310 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 44.060 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.090 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.014 0.320 10284 Z= 0.827 Angle : 1.669 26.067 14036 Z= 1.045 Chirality : 0.085 0.474 1620 Planarity : 0.013 0.270 1772 Dihedral : 15.706 106.231 4294 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.09 % Allowed : 0.93 % Favored : 98.98 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1212 helix: -2.96 (0.45), residues: 80 sheet: -0.96 (0.39), residues: 139 loop : 0.16 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.007 TRP B 205 HIS 0.007 0.001 HIS B 519 PHE 0.050 0.003 PHE A 252 TYR 0.083 0.007 TYR B 303 ARG 0.006 0.001 ARG A 106 Details of bonding type rmsd link_NAG-ASN : bond 0.05813 ( 13) link_NAG-ASN : angle 5.45410 ( 39) link_ALPHA1-6 : bond 0.02568 ( 2) link_ALPHA1-6 : angle 4.09298 ( 6) link_BETA1-4 : bond 0.02634 ( 18) link_BETA1-4 : angle 8.47405 ( 54) link_ALPHA1-3 : bond 0.03186 ( 2) link_ALPHA1-3 : angle 7.67526 ( 6) hydrogen bonds : bond 0.22379 ( 194) hydrogen bonds : angle 8.92988 ( 363) SS BOND : bond 0.06763 ( 51) SS BOND : angle 3.79917 ( 102) covalent geometry : bond 0.01266 (10198) covalent geometry : angle 1.52414 (13829) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.7880 (t70) cc_final: 0.7579 (t0) REVERT: C 188 THR cc_start: 0.8279 (p) cc_final: 0.8069 (t) outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.5894 time to fit residues: 120.2077 Evaluate side-chains 74 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN B 239 GLN B 302 ASN B 329 GLN B 470 HIS C 222 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.141336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.092721 restraints weight = 51636.885| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.98 r_work: 0.3270 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10284 Z= 0.175 Angle : 0.810 16.591 14036 Z= 0.399 Chirality : 0.051 0.474 1620 Planarity : 0.005 0.043 1772 Dihedral : 13.789 77.282 2035 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.93 % Allowed : 5.20 % Favored : 93.87 % 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: -0.66 (0.23), residues: 1212 helix: -2.57 (0.47), residues: 92 sheet: -0.83 (0.36), residues: 161 loop : -0.10 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 205 HIS 0.007 0.001 HIS A 505 PHE 0.012 0.001 PHE A 447 TYR 0.011 0.001 TYR B 303 ARG 0.003 0.001 ARG A 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00845 ( 13) link_NAG-ASN : angle 2.42361 ( 39) link_ALPHA1-6 : bond 0.00770 ( 2) link_ALPHA1-6 : angle 1.71735 ( 6) link_BETA1-4 : bond 0.01737 ( 18) link_BETA1-4 : angle 5.22502 ( 54) link_ALPHA1-3 : bond 0.01814 ( 2) link_ALPHA1-3 : angle 2.27044 ( 6) hydrogen bonds : bond 0.06329 ( 194) hydrogen bonds : angle 7.74006 ( 363) SS BOND : bond 0.00458 ( 51) SS BOND : angle 1.73183 ( 102) covalent geometry : bond 0.00390 (10198) covalent geometry : angle 0.71948 (13829) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8351 (m-40) cc_final: 0.8147 (m-40) REVERT: A 462 ASP cc_start: 0.8638 (t0) cc_final: 0.8107 (t0) REVERT: A 583 PHE cc_start: 0.7613 (p90) cc_final: 0.7232 (p90) REVERT: B 534 PHE cc_start: 0.8549 (m-80) cc_final: 0.7912 (m-80) REVERT: C 188 THR cc_start: 0.8967 (p) cc_final: 0.8723 (t) outliers start: 10 outliers final: 8 residues processed: 90 average time/residue: 0.5301 time to fit residues: 65.5241 Evaluate side-chains 74 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 373 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 86 optimal weight: 0.7980 chunk 16 optimal weight: 0.0050 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 HIS A 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.140839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.092364 restraints weight = 51592.279| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.98 r_work: 0.3259 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 10284 Z= 0.135 Angle : 0.719 14.159 14036 Z= 0.349 Chirality : 0.050 0.384 1620 Planarity : 0.004 0.037 1772 Dihedral : 10.279 62.969 2033 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.65 % Allowed : 6.32 % Favored : 93.03 % 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: -0.75 (0.23), residues: 1212 helix: -2.31 (0.50), residues: 89 sheet: -0.88 (0.36), residues: 173 loop : -0.20 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 205 HIS 0.006 0.001 HIS A 505 PHE 0.012 0.001 PHE A 252 TYR 0.012 0.001 TYR B 303 ARG 0.002 0.000 ARG B 487 Details of bonding type rmsd link_NAG-ASN : bond 0.00653 ( 13) link_NAG-ASN : angle 1.92853 ( 39) link_ALPHA1-6 : bond 0.00761 ( 2) link_ALPHA1-6 : angle 1.51769 ( 6) link_BETA1-4 : bond 0.01383 ( 18) link_BETA1-4 : angle 4.43514 ( 54) link_ALPHA1-3 : bond 0.01402 ( 2) link_ALPHA1-3 : angle 2.54911 ( 6) hydrogen bonds : bond 0.04902 ( 194) hydrogen bonds : angle 7.32635 ( 363) SS BOND : bond 0.00480 ( 51) SS BOND : angle 1.61385 ( 102) covalent geometry : bond 0.00295 (10198) covalent geometry : angle 0.64359 (13829) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8300 (m-40) cc_final: 0.8068 (m-40) REVERT: A 462 ASP cc_start: 0.8716 (t0) cc_final: 0.8077 (t0) REVERT: A 583 PHE cc_start: 0.7946 (p90) cc_final: 0.7498 (p90) REVERT: B 184 ILE cc_start: 0.8367 (mm) cc_final: 0.7813 (pt) REVERT: B 193 HIS cc_start: 0.8137 (t70) cc_final: 0.7796 (t70) REVERT: B 534 PHE cc_start: 0.8480 (m-80) cc_final: 0.8003 (m-80) REVERT: C 188 THR cc_start: 0.8980 (p) cc_final: 0.8761 (t) outliers start: 7 outliers final: 6 residues processed: 76 average time/residue: 0.5058 time to fit residues: 53.3623 Evaluate side-chains 72 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 373 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 102 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 439 GLN B 249 HIS B 320 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.136367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.086876 restraints weight = 51934.682| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.99 r_work: 0.3157 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10284 Z= 0.166 Angle : 0.657 12.550 14036 Z= 0.323 Chirality : 0.048 0.332 1620 Planarity : 0.004 0.034 1772 Dihedral : 7.254 48.369 2033 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.12 % Allowed : 6.13 % Favored : 92.75 % 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: -0.91 (0.23), residues: 1212 helix: -2.02 (0.52), residues: 89 sheet: -0.87 (0.37), residues: 174 loop : -0.40 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 614 HIS 0.006 0.001 HIS A 231 PHE 0.014 0.001 PHE A 447 TYR 0.017 0.001 TYR B 303 ARG 0.002 0.000 ARG A 396 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 13) link_NAG-ASN : angle 1.75622 ( 39) link_ALPHA1-6 : bond 0.00748 ( 2) link_ALPHA1-6 : angle 1.45796 ( 6) link_BETA1-4 : bond 0.01201 ( 18) link_BETA1-4 : angle 3.82621 ( 54) link_ALPHA1-3 : bond 0.01427 ( 2) link_ALPHA1-3 : angle 2.71623 ( 6) hydrogen bonds : bond 0.04375 ( 194) hydrogen bonds : angle 6.83243 ( 363) SS BOND : bond 0.00413 ( 51) SS BOND : angle 0.99762 ( 102) covalent geometry : bond 0.00384 (10198) covalent geometry : angle 0.60101 (13829) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8393 (m-40) cc_final: 0.8148 (m-40) REVERT: A 462 ASP cc_start: 0.8837 (t0) cc_final: 0.8095 (t0) REVERT: A 583 PHE cc_start: 0.8124 (p90) cc_final: 0.7672 (p90) REVERT: B 534 PHE cc_start: 0.8531 (m-80) cc_final: 0.8005 (m-80) REVERT: C 188 THR cc_start: 0.9082 (p) cc_final: 0.8873 (t) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.5157 time to fit residues: 53.5829 Evaluate side-chains 69 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 377 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 53 optimal weight: 0.4980 chunk 46 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 94 optimal weight: 0.0870 chunk 115 optimal weight: 20.0000 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.137391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.089277 restraints weight = 50170.143| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.65 r_work: 0.3215 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10284 Z= 0.099 Angle : 0.590 12.052 14036 Z= 0.288 Chirality : 0.045 0.305 1620 Planarity : 0.004 0.034 1772 Dihedral : 6.126 49.556 2033 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.65 % Allowed : 6.78 % Favored : 92.57 % 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: -0.75 (0.24), residues: 1212 helix: -2.04 (0.52), residues: 89 sheet: -0.75 (0.38), residues: 174 loop : -0.26 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 205 HIS 0.003 0.001 HIS A 231 PHE 0.012 0.001 PHE A 546 TYR 0.006 0.001 TYR B 411 ARG 0.001 0.000 ARG B 330 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 13) link_NAG-ASN : angle 1.60971 ( 39) link_ALPHA1-6 : bond 0.00657 ( 2) link_ALPHA1-6 : angle 1.36477 ( 6) link_BETA1-4 : bond 0.01149 ( 18) link_BETA1-4 : angle 3.39158 ( 54) link_ALPHA1-3 : bond 0.01447 ( 2) link_ALPHA1-3 : angle 3.06651 ( 6) hydrogen bonds : bond 0.03537 ( 194) hydrogen bonds : angle 6.34363 ( 363) SS BOND : bond 0.00255 ( 51) SS BOND : angle 1.00951 ( 102) covalent geometry : bond 0.00225 (10198) covalent geometry : angle 0.53783 (13829) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8298 (m-40) cc_final: 0.8047 (m-40) REVERT: A 462 ASP cc_start: 0.8807 (t0) cc_final: 0.8102 (t0) REVERT: A 583 PHE cc_start: 0.8152 (p90) cc_final: 0.7736 (p90) REVERT: B 181 LEU cc_start: 0.8063 (mt) cc_final: 0.7358 (tp) REVERT: C 186 GLU cc_start: 0.8147 (pt0) cc_final: 0.7518 (pm20) REVERT: C 188 THR cc_start: 0.9104 (p) cc_final: 0.8884 (t) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 0.5322 time to fit residues: 50.5319 Evaluate side-chains 65 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 570 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 98 optimal weight: 0.9980 chunk 83 optimal weight: 0.0570 chunk 109 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.136356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.086554 restraints weight = 52049.009| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 4.03 r_work: 0.3153 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10284 Z= 0.133 Angle : 0.589 11.886 14036 Z= 0.289 Chirality : 0.045 0.292 1620 Planarity : 0.004 0.035 1772 Dihedral : 5.832 51.507 2033 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.74 % Allowed : 7.34 % Favored : 91.91 % 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: -0.72 (0.24), residues: 1212 helix: -1.93 (0.53), residues: 89 sheet: -0.65 (0.39), residues: 174 loop : -0.27 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 205 HIS 0.004 0.001 HIS B 174 PHE 0.011 0.001 PHE A 447 TYR 0.010 0.001 TYR B 303 ARG 0.002 0.000 ARG A 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 13) link_NAG-ASN : angle 1.61795 ( 39) link_ALPHA1-6 : bond 0.00653 ( 2) link_ALPHA1-6 : angle 1.30339 ( 6) link_BETA1-4 : bond 0.01109 ( 18) link_BETA1-4 : angle 3.27948 ( 54) link_ALPHA1-3 : bond 0.01203 ( 2) link_ALPHA1-3 : angle 3.03198 ( 6) hydrogen bonds : bond 0.03679 ( 194) hydrogen bonds : angle 6.27466 ( 363) SS BOND : bond 0.00356 ( 51) SS BOND : angle 1.02864 ( 102) covalent geometry : bond 0.00310 (10198) covalent geometry : angle 0.53885 (13829) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8380 (m-40) cc_final: 0.8127 (m-40) REVERT: A 72 ARG cc_start: 0.8759 (mmt-90) cc_final: 0.8515 (mmt-90) REVERT: A 462 ASP cc_start: 0.8843 (t0) cc_final: 0.8113 (t0) REVERT: A 583 PHE cc_start: 0.8235 (p90) cc_final: 0.7850 (p90) REVERT: B 193 HIS cc_start: 0.8160 (t70) cc_final: 0.7812 (t70) REVERT: B 534 PHE cc_start: 0.8617 (m-80) cc_final: 0.7992 (m-80) REVERT: C 186 GLU cc_start: 0.8196 (pt0) cc_final: 0.7506 (pm20) REVERT: C 188 THR cc_start: 0.9115 (p) cc_final: 0.8872 (t) REVERT: C 207 ARG cc_start: 0.8283 (ptp90) cc_final: 0.8055 (ptp90) outliers start: 8 outliers final: 8 residues processed: 66 average time/residue: 0.5605 time to fit residues: 50.3737 Evaluate side-chains 66 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.135044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.085173 restraints weight = 51844.612| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 4.02 r_work: 0.3125 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10284 Z= 0.159 Angle : 0.597 11.712 14036 Z= 0.296 Chirality : 0.046 0.282 1620 Planarity : 0.004 0.036 1772 Dihedral : 5.743 55.629 2033 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.02 % Allowed : 7.43 % Favored : 91.54 % 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: -0.75 (0.24), residues: 1212 helix: -2.00 (0.52), residues: 89 sheet: -0.59 (0.40), residues: 172 loop : -0.31 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 205 HIS 0.003 0.001 HIS B 174 PHE 0.013 0.001 PHE A 447 TYR 0.010 0.001 TYR A 469 ARG 0.002 0.000 ARG A 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 13) link_NAG-ASN : angle 1.64331 ( 39) link_ALPHA1-6 : bond 0.00630 ( 2) link_ALPHA1-6 : angle 1.32099 ( 6) link_BETA1-4 : bond 0.01112 ( 18) link_BETA1-4 : angle 3.15926 ( 54) link_ALPHA1-3 : bond 0.01107 ( 2) link_ALPHA1-3 : angle 2.87112 ( 6) hydrogen bonds : bond 0.03883 ( 194) hydrogen bonds : angle 6.29774 ( 363) SS BOND : bond 0.00405 ( 51) SS BOND : angle 1.08795 ( 102) covalent geometry : bond 0.00373 (10198) covalent geometry : angle 0.55004 (13829) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8388 (m-40) cc_final: 0.8154 (m-40) REVERT: A 462 ASP cc_start: 0.8866 (t0) cc_final: 0.8118 (t0) REVERT: A 583 PHE cc_start: 0.8144 (p90) cc_final: 0.7892 (p90) REVERT: B 193 HIS cc_start: 0.8176 (t70) cc_final: 0.7797 (t70) REVERT: C 186 GLU cc_start: 0.8179 (pt0) cc_final: 0.7522 (pm20) REVERT: C 188 THR cc_start: 0.9128 (p) cc_final: 0.8896 (t) outliers start: 11 outliers final: 9 residues processed: 67 average time/residue: 0.5558 time to fit residues: 51.0302 Evaluate side-chains 65 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 67 optimal weight: 0.0270 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN B 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.135259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.085447 restraints weight = 51989.090| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 4.02 r_work: 0.3132 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 10284 Z= 0.134 Angle : 0.584 11.568 14036 Z= 0.290 Chirality : 0.045 0.275 1620 Planarity : 0.004 0.039 1772 Dihedral : 5.650 57.861 2033 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.02 % Allowed : 7.71 % Favored : 91.26 % 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: -0.69 (0.24), residues: 1212 helix: -2.11 (0.51), residues: 89 sheet: -0.41 (0.42), residues: 162 loop : -0.28 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 205 HIS 0.003 0.001 HIS B 267 PHE 0.011 0.001 PHE A 447 TYR 0.009 0.001 TYR B 303 ARG 0.002 0.000 ARG A 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 13) link_NAG-ASN : angle 1.59209 ( 39) link_ALPHA1-6 : bond 0.00614 ( 2) link_ALPHA1-6 : angle 1.33105 ( 6) link_BETA1-4 : bond 0.01090 ( 18) link_BETA1-4 : angle 3.08864 ( 54) link_ALPHA1-3 : bond 0.01007 ( 2) link_ALPHA1-3 : angle 2.76451 ( 6) hydrogen bonds : bond 0.03716 ( 194) hydrogen bonds : angle 6.17435 ( 363) SS BOND : bond 0.00388 ( 51) SS BOND : angle 1.07958 ( 102) covalent geometry : bond 0.00343 (10198) covalent geometry : angle 0.53781 (13829) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8392 (m-40) cc_final: 0.8179 (m-40) REVERT: A 462 ASP cc_start: 0.8860 (t0) cc_final: 0.8115 (t0) REVERT: A 583 PHE cc_start: 0.7920 (p90) cc_final: 0.7613 (p90) REVERT: B 193 HIS cc_start: 0.8175 (t70) cc_final: 0.7807 (t70) REVERT: B 302 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.8100 (t0) REVERT: C 186 GLU cc_start: 0.8167 (pt0) cc_final: 0.7527 (pm20) REVERT: C 188 THR cc_start: 0.9141 (p) cc_final: 0.8908 (t) outliers start: 11 outliers final: 10 residues processed: 66 average time/residue: 0.5499 time to fit residues: 49.9305 Evaluate side-chains 68 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 51 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 120 optimal weight: 0.0010 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.135758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.085522 restraints weight = 51963.171| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 4.07 r_work: 0.3140 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 10284 Z= 0.108 Angle : 0.569 11.528 14036 Z= 0.281 Chirality : 0.044 0.272 1620 Planarity : 0.004 0.038 1772 Dihedral : 5.595 58.890 2033 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.02 % Allowed : 7.53 % Favored : 91.45 % 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: -0.67 (0.24), residues: 1212 helix: -2.12 (0.51), residues: 89 sheet: -0.41 (0.42), residues: 162 loop : -0.26 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 205 HIS 0.002 0.001 HIS B 267 PHE 0.011 0.001 PHE A 546 TYR 0.010 0.001 TYR B 301 ARG 0.001 0.000 ARG B 552 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 13) link_NAG-ASN : angle 1.54119 ( 39) link_ALPHA1-6 : bond 0.00606 ( 2) link_ALPHA1-6 : angle 1.33139 ( 6) link_BETA1-4 : bond 0.01087 ( 18) link_BETA1-4 : angle 3.04644 ( 54) link_ALPHA1-3 : bond 0.00972 ( 2) link_ALPHA1-3 : angle 2.69251 ( 6) hydrogen bonds : bond 0.03503 ( 194) hydrogen bonds : angle 6.10632 ( 363) SS BOND : bond 0.00322 ( 51) SS BOND : angle 1.02563 ( 102) covalent geometry : bond 0.00264 (10198) covalent geometry : angle 0.52360 (13829) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 ASP cc_start: 0.8847 (t0) cc_final: 0.8126 (t0) REVERT: A 583 PHE cc_start: 0.7848 (p90) cc_final: 0.7523 (p90) REVERT: B 193 HIS cc_start: 0.8174 (t70) cc_final: 0.7811 (t70) REVERT: B 534 PHE cc_start: 0.8618 (m-80) cc_final: 0.8111 (m-80) REVERT: C 186 GLU cc_start: 0.8148 (pt0) cc_final: 0.7539 (pm20) REVERT: C 188 THR cc_start: 0.9142 (p) cc_final: 0.8906 (t) outliers start: 11 outliers final: 11 residues processed: 66 average time/residue: 0.5513 time to fit residues: 49.9519 Evaluate side-chains 66 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 48 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.135785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.085501 restraints weight = 51724.692| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 4.06 r_work: 0.3139 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10284 Z= 0.111 Angle : 0.562 11.426 14036 Z= 0.278 Chirality : 0.044 0.268 1620 Planarity : 0.004 0.036 1772 Dihedral : 5.496 59.568 2033 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.02 % Allowed : 7.62 % Favored : 91.36 % 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: -0.71 (0.24), residues: 1212 helix: -2.13 (0.50), residues: 89 sheet: -0.63 (0.40), residues: 174 loop : -0.24 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 205 HIS 0.004 0.001 HIS A 70 PHE 0.014 0.001 PHE A 546 TYR 0.011 0.001 TYR B 303 ARG 0.006 0.000 ARG A 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 13) link_NAG-ASN : angle 1.52879 ( 39) link_ALPHA1-6 : bond 0.00597 ( 2) link_ALPHA1-6 : angle 1.33472 ( 6) link_BETA1-4 : bond 0.01074 ( 18) link_BETA1-4 : angle 2.99016 ( 54) link_ALPHA1-3 : bond 0.00884 ( 2) link_ALPHA1-3 : angle 2.52009 ( 6) hydrogen bonds : bond 0.03411 ( 194) hydrogen bonds : angle 6.03710 ( 363) SS BOND : bond 0.00317 ( 51) SS BOND : angle 0.98647 ( 102) covalent geometry : bond 0.00266 (10198) covalent geometry : angle 0.51778 (13829) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 ASP cc_start: 0.8857 (t0) cc_final: 0.8116 (t0) REVERT: A 583 PHE cc_start: 0.7853 (p90) cc_final: 0.7555 (p90) REVERT: B 193 HIS cc_start: 0.8163 (t70) cc_final: 0.7807 (t70) REVERT: C 186 GLU cc_start: 0.8140 (pt0) cc_final: 0.7526 (pm20) REVERT: C 188 THR cc_start: 0.9130 (p) cc_final: 0.8881 (t) outliers start: 11 outliers final: 11 residues processed: 67 average time/residue: 0.4955 time to fit residues: 47.7129 Evaluate side-chains 66 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 45 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 63 optimal weight: 0.0470 chunk 42 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 94 optimal weight: 0.0270 chunk 36 optimal weight: 1.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.136251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.088103 restraints weight = 49814.256| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.64 r_work: 0.3190 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10284 Z= 0.087 Angle : 0.540 11.269 14036 Z= 0.266 Chirality : 0.044 0.260 1620 Planarity : 0.004 0.035 1772 Dihedral : 5.318 59.778 2033 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.74 % Allowed : 7.90 % Favored : 91.36 % 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: -0.56 (0.24), residues: 1212 helix: -2.13 (0.50), residues: 89 sheet: -0.42 (0.42), residues: 164 loop : -0.15 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 205 HIS 0.002 0.000 HIS A 505 PHE 0.016 0.001 PHE A 543 TYR 0.007 0.001 TYR B 554 ARG 0.004 0.000 ARG A 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 13) link_NAG-ASN : angle 1.44625 ( 39) link_ALPHA1-6 : bond 0.00582 ( 2) link_ALPHA1-6 : angle 1.34512 ( 6) link_BETA1-4 : bond 0.01074 ( 18) link_BETA1-4 : angle 2.91921 ( 54) link_ALPHA1-3 : bond 0.00807 ( 2) link_ALPHA1-3 : angle 2.33077 ( 6) hydrogen bonds : bond 0.03041 ( 194) hydrogen bonds : angle 5.87707 ( 363) SS BOND : bond 0.00252 ( 51) SS BOND : angle 0.89802 ( 102) covalent geometry : bond 0.00204 (10198) covalent geometry : angle 0.49778 (13829) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9240.66 seconds wall clock time: 159 minutes 0.95 seconds (9540.95 seconds total)