Starting phenix.real_space_refine on Sun Aug 24 11:40:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4l_41886/08_2025/8u4l_41886_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4l_41886/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8u4l_41886/08_2025/8u4l_41886_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4l_41886/08_2025/8u4l_41886_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u4l_41886/08_2025/8u4l_41886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4l_41886/08_2025/8u4l_41886.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.81, per 1000 atoms: 0.20 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: 1.84 Conformation dependent library (CDL) restraints added in 692.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.65 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: 4.99 Time building geometry restraints manager: 2.53 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: 5.280 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: 0.130 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.350 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.860 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (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 ARG 0.006 0.001 ARG A 106 TYR 0.083 0.007 TYR B 303 PHE 0.050 0.003 PHE A 252 TRP 0.101 0.007 TRP B 205 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.01266 (10198) covalent geometry : angle 1.52414 (13829) SS BOND : bond 0.06763 ( 51) SS BOND : angle 3.79917 ( 102) hydrogen bonds : bond 0.22379 ( 194) hydrogen bonds : angle 8.92988 ( 363) link_ALPHA1-3 : bond 0.03186 ( 2) link_ALPHA1-3 : angle 7.67526 ( 6) 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_NAG-ASN : bond 0.05813 ( 13) link_NAG-ASN : angle 5.45410 ( 39) *********************** 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 : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.7880 (t70) cc_final: 0.7579 (t0) REVERT: C 188 THR cc_start: 0.8279 (p) cc_final: 0.8061 (t) outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.2667 time to fit residues: 55.0447 Evaluate side-chains 73 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.137772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.092544 restraints weight = 50169.214| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.89 r_work: 0.3278 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10284 Z= 0.172 Angle : 0.810 16.979 14036 Z= 0.396 Chirality : 0.051 0.455 1620 Planarity : 0.005 0.047 1772 Dihedral : 13.690 77.060 2035 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.84 % Allowed : 5.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.23), residues: 1212 helix: -2.58 (0.47), residues: 92 sheet: -0.83 (0.36), residues: 161 loop : -0.11 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 525 TYR 0.010 0.001 TYR B 303 PHE 0.011 0.001 PHE A 120 TRP 0.017 0.002 TRP B 205 HIS 0.008 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00390 (10198) covalent geometry : angle 0.71969 (13829) SS BOND : bond 0.00441 ( 51) SS BOND : angle 1.64436 ( 102) hydrogen bonds : bond 0.06045 ( 194) hydrogen bonds : angle 7.72665 ( 363) link_ALPHA1-3 : bond 0.01844 ( 2) link_ALPHA1-3 : angle 2.17022 ( 6) link_ALPHA1-6 : bond 0.00744 ( 2) link_ALPHA1-6 : angle 1.70774 ( 6) link_BETA1-4 : bond 0.01579 ( 18) link_BETA1-4 : angle 5.25012 ( 54) link_NAG-ASN : bond 0.00825 ( 13) link_NAG-ASN : angle 2.40763 ( 39) *********************** 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: 9 poor density : 81 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8337 (m-40) cc_final: 0.8131 (m-40) REVERT: A 462 ASP cc_start: 0.8636 (t0) cc_final: 0.8118 (t0) REVERT: A 583 PHE cc_start: 0.7714 (p90) cc_final: 0.7375 (p90) REVERT: B 193 HIS cc_start: 0.8174 (t70) cc_final: 0.7799 (t70) REVERT: B 534 PHE cc_start: 0.8534 (m-80) cc_final: 0.7906 (m-80) REVERT: C 188 THR cc_start: 0.8956 (p) cc_final: 0.8710 (t) outliers start: 9 outliers final: 7 residues processed: 90 average time/residue: 0.2461 time to fit residues: 30.1074 Evaluate side-chains 73 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.139964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.091247 restraints weight = 51972.521| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.98 r_work: 0.3237 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 10284 Z= 0.156 Angle : 0.743 14.447 14036 Z= 0.362 Chirality : 0.051 0.388 1620 Planarity : 0.004 0.038 1772 Dihedral : 10.514 63.613 2033 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.65 % Allowed : 6.60 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.23), residues: 1212 helix: -2.30 (0.50), residues: 89 sheet: -0.89 (0.36), residues: 174 loop : -0.26 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 487 TYR 0.011 0.001 TYR B 303 PHE 0.013 0.001 PHE A 447 TRP 0.013 0.001 TRP B 205 HIS 0.006 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00354 (10198) covalent geometry : angle 0.65745 (13829) SS BOND : bond 0.00550 ( 51) SS BOND : angle 2.15119 ( 102) hydrogen bonds : bond 0.05153 ( 194) hydrogen bonds : angle 7.35065 ( 363) link_ALPHA1-3 : bond 0.01308 ( 2) link_ALPHA1-3 : angle 2.54990 ( 6) link_ALPHA1-6 : bond 0.00768 ( 2) link_ALPHA1-6 : angle 1.50446 ( 6) link_BETA1-4 : bond 0.01401 ( 18) link_BETA1-4 : angle 4.49908 ( 54) link_NAG-ASN : bond 0.00624 ( 13) link_NAG-ASN : angle 1.95697 ( 39) *********************** 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 75 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.538 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: 0.8326 (m-40) cc_final: 0.8086 (m-40) REVERT: A 462 ASP cc_start: 0.8730 (t0) cc_final: 0.8085 (t0) REVERT: A 583 PHE cc_start: 0.7944 (p90) cc_final: 0.7497 (p90) REVERT: B 184 ILE cc_start: 0.8399 (mm) cc_final: 0.7832 (pt) REVERT: B 193 HIS cc_start: 0.8136 (t70) cc_final: 0.7761 (t70) REVERT: B 534 PHE cc_start: 0.8481 (m-80) cc_final: 0.7985 (m-80) REVERT: C 188 THR cc_start: 0.8994 (p) cc_final: 0.8777 (t) outliers start: 7 outliers final: 6 residues processed: 75 average time/residue: 0.2129 time to fit residues: 22.0204 Evaluate side-chains 70 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 34 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 439 GLN B 249 HIS B 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.137148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.087767 restraints weight = 51984.034| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.99 r_work: 0.3168 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10284 Z= 0.141 Angle : 0.655 12.742 14036 Z= 0.319 Chirality : 0.048 0.339 1620 Planarity : 0.004 0.036 1772 Dihedral : 7.463 48.234 2033 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.93 % Allowed : 6.60 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.23), residues: 1212 helix: -2.13 (0.51), residues: 89 sheet: -0.85 (0.37), residues: 174 loop : -0.37 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 487 TYR 0.016 0.001 TYR B 303 PHE 0.012 0.001 PHE A 447 TRP 0.012 0.001 TRP B 614 HIS 0.006 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00327 (10198) covalent geometry : angle 0.59486 (13829) SS BOND : bond 0.00347 ( 51) SS BOND : angle 1.08224 ( 102) hydrogen bonds : bond 0.04276 ( 194) hydrogen bonds : angle 6.90028 ( 363) link_ALPHA1-3 : bond 0.01464 ( 2) link_ALPHA1-3 : angle 2.67539 ( 6) link_ALPHA1-6 : bond 0.00768 ( 2) link_ALPHA1-6 : angle 1.49989 ( 6) link_BETA1-4 : bond 0.01240 ( 18) link_BETA1-4 : angle 3.90980 ( 54) link_NAG-ASN : bond 0.00467 ( 13) link_NAG-ASN : angle 1.73782 ( 39) *********************** 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 72 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8370 (m-40) cc_final: 0.8124 (m-40) REVERT: A 462 ASP cc_start: 0.8817 (t0) cc_final: 0.8081 (t0) REVERT: A 583 PHE cc_start: 0.8079 (p90) cc_final: 0.7639 (p90) REVERT: B 534 PHE cc_start: 0.8505 (m-80) cc_final: 0.7990 (m-80) REVERT: C 188 THR cc_start: 0.9060 (p) cc_final: 0.8826 (t) outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 0.2248 time to fit residues: 22.2790 Evaluate side-chains 68 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 166 THR 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 29 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.136439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.086714 restraints weight = 51961.251| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 4.01 r_work: 0.3295 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10284 Z= 0.130 Angle : 0.607 12.160 14036 Z= 0.298 Chirality : 0.046 0.306 1620 Planarity : 0.004 0.035 1772 Dihedral : 6.159 50.176 2033 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.93 % Allowed : 6.88 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.24), residues: 1212 helix: -2.05 (0.52), residues: 89 sheet: -0.74 (0.38), residues: 174 loop : -0.31 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 330 TYR 0.007 0.001 TYR B 303 PHE 0.012 0.001 PHE A 447 TRP 0.008 0.001 TRP B 205 HIS 0.004 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00305 (10198) covalent geometry : angle 0.55201 (13829) SS BOND : bond 0.00366 ( 51) SS BOND : angle 1.27398 ( 102) hydrogen bonds : bond 0.03855 ( 194) hydrogen bonds : angle 6.36837 ( 363) link_ALPHA1-3 : bond 0.01424 ( 2) link_ALPHA1-3 : angle 3.08664 ( 6) link_ALPHA1-6 : bond 0.00681 ( 2) link_ALPHA1-6 : angle 1.31503 ( 6) link_BETA1-4 : bond 0.01141 ( 18) link_BETA1-4 : angle 3.38194 ( 54) link_NAG-ASN : bond 0.00372 ( 13) link_NAG-ASN : angle 1.66608 ( 39) *********************** 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 74 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.481 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: 0.8249 (m-40) cc_final: 0.8010 (m-40) REVERT: A 462 ASP cc_start: 0.8779 (t0) cc_final: 0.8088 (t0) REVERT: A 583 PHE cc_start: 0.8151 (p90) cc_final: 0.7747 (p90) REVERT: B 181 LEU cc_start: 0.8079 (mt) cc_final: 0.7365 (tp) REVERT: B 193 HIS cc_start: 0.8154 (t70) cc_final: 0.7812 (t70) REVERT: C 186 GLU cc_start: 0.8200 (pt0) cc_final: 0.7623 (pm20) REVERT: C 188 THR cc_start: 0.9061 (p) cc_final: 0.8823 (t) outliers start: 10 outliers final: 8 residues processed: 73 average time/residue: 0.2503 time to fit residues: 25.1716 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 : 0.641 ------------------------------------------------------------------------------- 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 570 HIS Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 377 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 109 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 51 optimal weight: 0.0170 chunk 63 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.136218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.086550 restraints weight = 51750.499| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 4.02 r_work: 0.3149 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.003 0.028 10284 Z= 0.118 Angle : 0.583 11.818 14036 Z= 0.286 Chirality : 0.045 0.289 1620 Planarity : 0.004 0.035 1772 Dihedral : 5.827 52.825 2033 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.02 % Allowed : 6.97 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.24), residues: 1212 helix: -2.03 (0.52), residues: 89 sheet: -0.49 (0.41), residues: 162 loop : -0.27 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.010 0.001 TYR B 303 PHE 0.011 0.001 PHE A 447 TRP 0.006 0.001 TRP B 205 HIS 0.003 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00275 (10198) covalent geometry : angle 0.53336 (13829) SS BOND : bond 0.00313 ( 51) SS BOND : angle 0.98244 ( 102) hydrogen bonds : bond 0.03560 ( 194) hydrogen bonds : angle 6.25753 ( 363) link_ALPHA1-3 : bond 0.01150 ( 2) link_ALPHA1-3 : angle 3.03639 ( 6) link_ALPHA1-6 : bond 0.00648 ( 2) link_ALPHA1-6 : angle 1.31754 ( 6) link_BETA1-4 : bond 0.01119 ( 18) link_BETA1-4 : angle 3.25238 ( 54) link_NAG-ASN : bond 0.00299 ( 13) link_NAG-ASN : angle 1.57305 ( 39) *********************** 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 73 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.554 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: 0.8377 (m-40) cc_final: 0.8144 (m-40) REVERT: A 72 ARG cc_start: 0.8745 (mmt-90) cc_final: 0.8521 (mmt-90) REVERT: A 462 ASP cc_start: 0.8855 (t0) cc_final: 0.8125 (t0) REVERT: A 583 PHE cc_start: 0.8150 (p90) cc_final: 0.7878 (p90) REVERT: B 193 HIS cc_start: 0.8156 (t70) cc_final: 0.7823 (t70) REVERT: B 534 PHE cc_start: 0.8616 (m-80) cc_final: 0.7985 (m-80) REVERT: C 186 GLU cc_start: 0.8201 (pt0) cc_final: 0.7565 (pm20) REVERT: C 188 THR cc_start: 0.9091 (p) cc_final: 0.8842 (t) outliers start: 11 outliers final: 10 residues processed: 71 average time/residue: 0.2733 time to fit residues: 26.2475 Evaluate side-chains 70 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.135927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.085645 restraints weight = 52091.275| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 4.07 r_work: 0.3139 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.145 10284 Z= 0.129 Angle : 0.582 11.751 14036 Z= 0.286 Chirality : 0.045 0.284 1620 Planarity : 0.004 0.036 1772 Dihedral : 5.705 54.355 2033 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.24), residues: 1212 helix: -2.10 (0.51), residues: 89 sheet: -0.62 (0.40), residues: 172 loop : -0.26 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 552 TYR 0.008 0.001 TYR B 303 PHE 0.011 0.001 PHE A 546 TRP 0.006 0.001 TRP B 205 HIS 0.003 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00331 (10198) covalent geometry : angle 0.53185 (13829) SS BOND : bond 0.00378 ( 51) SS BOND : angle 1.14058 ( 102) hydrogen bonds : bond 0.03654 ( 194) hydrogen bonds : angle 6.18725 ( 363) link_ALPHA1-3 : bond 0.01137 ( 2) link_ALPHA1-3 : angle 2.95985 ( 6) link_ALPHA1-6 : bond 0.00625 ( 2) link_ALPHA1-6 : angle 1.31812 ( 6) link_BETA1-4 : bond 0.01101 ( 18) link_BETA1-4 : angle 3.17633 ( 54) link_NAG-ASN : bond 0.00268 ( 13) link_NAG-ASN : angle 1.60199 ( 39) *********************** 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 70 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.553 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: 0.8404 (m-40) cc_final: 0.8173 (m-40) REVERT: A 462 ASP cc_start: 0.8871 (t0) cc_final: 0.8128 (t0) REVERT: A 583 PHE cc_start: 0.7930 (p90) cc_final: 0.7589 (p90) REVERT: B 193 HIS cc_start: 0.8157 (t70) cc_final: 0.7790 (t70) REVERT: C 186 GLU cc_start: 0.8246 (pt0) cc_final: 0.7525 (pm20) REVERT: C 188 THR cc_start: 0.9083 (p) cc_final: 0.8841 (t) outliers start: 11 outliers final: 11 residues processed: 68 average time/residue: 0.2497 time to fit residues: 23.1191 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 : 0.405 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 6 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 B 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.134652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.084802 restraints weight = 51799.408| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 4.00 r_work: 0.3122 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10284 Z= 0.142 Angle : 0.584 11.536 14036 Z= 0.290 Chirality : 0.045 0.271 1620 Planarity : 0.004 0.039 1772 Dihedral : 5.609 59.472 2033 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.24), residues: 1212 helix: -2.19 (0.50), residues: 89 sheet: -0.44 (0.42), residues: 162 loop : -0.29 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 100 TYR 0.010 0.001 TYR B 303 PHE 0.013 0.001 PHE A 546 TRP 0.006 0.001 TRP B 205 HIS 0.004 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00334 (10198) covalent geometry : angle 0.53870 (13829) SS BOND : bond 0.00390 ( 51) SS BOND : angle 1.08969 ( 102) hydrogen bonds : bond 0.03669 ( 194) hydrogen bonds : angle 6.13732 ( 363) link_ALPHA1-3 : bond 0.00932 ( 2) link_ALPHA1-3 : angle 2.62148 ( 6) link_ALPHA1-6 : bond 0.00622 ( 2) link_ALPHA1-6 : angle 1.32719 ( 6) link_BETA1-4 : bond 0.01076 ( 18) link_BETA1-4 : angle 3.04532 ( 54) link_NAG-ASN : bond 0.00221 ( 13) link_NAG-ASN : angle 1.60127 ( 39) *********************** 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 69 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.322 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: 0.8389 (m-40) cc_final: 0.8180 (m-40) REVERT: A 462 ASP cc_start: 0.8870 (t0) cc_final: 0.8116 (t0) REVERT: A 583 PHE cc_start: 0.7755 (p90) cc_final: 0.7454 (p90) REVERT: B 193 HIS cc_start: 0.8174 (t70) cc_final: 0.7782 (t70) REVERT: C 186 GLU cc_start: 0.8189 (pt0) cc_final: 0.7564 (pm20) REVERT: C 188 THR cc_start: 0.9101 (p) cc_final: 0.8838 (t) outliers start: 11 outliers final: 11 residues processed: 67 average time/residue: 0.2456 time to fit residues: 22.1747 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 : 0.544 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 81 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 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 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 = 0.134845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.085019 restraints weight = 51854.175| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 4.03 r_work: 0.3126 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10284 Z= 0.122 Angle : 0.565 11.413 14036 Z= 0.280 Chirality : 0.044 0.265 1620 Planarity : 0.004 0.037 1772 Dihedral : 5.518 59.905 2033 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.24), residues: 1212 helix: -2.18 (0.50), residues: 89 sheet: -0.52 (0.41), residues: 174 loop : -0.24 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 552 TYR 0.008 0.001 TYR B 303 PHE 0.013 0.001 PHE A 546 TRP 0.005 0.001 TRP B 169 HIS 0.004 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00293 (10198) covalent geometry : angle 0.52070 (13829) SS BOND : bond 0.00340 ( 51) SS BOND : angle 0.99814 ( 102) hydrogen bonds : bond 0.03528 ( 194) hydrogen bonds : angle 6.08337 ( 363) link_ALPHA1-3 : bond 0.00830 ( 2) link_ALPHA1-3 : angle 2.45825 ( 6) link_ALPHA1-6 : bond 0.00622 ( 2) link_ALPHA1-6 : angle 1.34720 ( 6) link_BETA1-4 : bond 0.01077 ( 18) link_BETA1-4 : angle 2.98582 ( 54) link_NAG-ASN : bond 0.00234 ( 13) link_NAG-ASN : angle 1.55542 ( 39) *********************** 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 : 0.397 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 275 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8786 (mt) REVERT: A 462 ASP cc_start: 0.8870 (t0) cc_final: 0.8117 (t0) REVERT: A 583 PHE cc_start: 0.7899 (p90) cc_final: 0.7595 (p90) REVERT: B 193 HIS cc_start: 0.8181 (t70) cc_final: 0.7717 (t70) REVERT: C 186 GLU cc_start: 0.8186 (pt0) cc_final: 0.7610 (pm20) REVERT: C 188 THR cc_start: 0.9107 (p) cc_final: 0.8840 (t) outliers start: 11 outliers final: 10 residues processed: 66 average time/residue: 0.2656 time to fit residues: 23.8929 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 : 0.538 ------------------------------------------------------------------------------- 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 275 LEU 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 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 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 86 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.134533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.086144 restraints weight = 49533.995| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.61 r_work: 0.3155 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10284 Z= 0.121 Angle : 0.563 11.344 14036 Z= 0.279 Chirality : 0.044 0.262 1620 Planarity : 0.004 0.036 1772 Dihedral : 5.459 58.593 2033 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.02 % Allowed : 7.81 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.24), residues: 1212 helix: -2.18 (0.50), residues: 89 sheet: -0.53 (0.42), residues: 164 loop : -0.23 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.008 0.001 TYR B 303 PHE 0.014 0.001 PHE A 546 TRP 0.006 0.001 TRP B 205 HIS 0.004 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00289 (10198) covalent geometry : angle 0.52030 (13829) SS BOND : bond 0.00332 ( 51) SS BOND : angle 0.98269 ( 102) hydrogen bonds : bond 0.03484 ( 194) hydrogen bonds : angle 6.04756 ( 363) link_ALPHA1-3 : bond 0.00770 ( 2) link_ALPHA1-3 : angle 2.31588 ( 6) link_ALPHA1-6 : bond 0.00589 ( 2) link_ALPHA1-6 : angle 1.34181 ( 6) link_BETA1-4 : bond 0.01069 ( 18) link_BETA1-4 : angle 2.94545 ( 54) link_NAG-ASN : bond 0.00222 ( 13) link_NAG-ASN : angle 1.53819 ( 39) ********************** 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 66 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.607 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 462 ASP cc_start: 0.8839 (t0) cc_final: 0.8110 (t0) REVERT: A 583 PHE cc_start: 0.7835 (p90) cc_final: 0.7556 (p90) REVERT: B 193 HIS cc_start: 0.8186 (t70) cc_final: 0.7733 (t70) REVERT: C 186 GLU cc_start: 0.8126 (pt0) cc_final: 0.7606 (pm20) REVERT: C 188 THR cc_start: 0.9085 (p) cc_final: 0.8816 (t) outliers start: 11 outliers final: 10 residues processed: 64 average time/residue: 0.2095 time to fit residues: 19.6677 Evaluate side-chains 65 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 15 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 117 optimal weight: 0.0870 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.135609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.087482 restraints weight = 49719.325| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.62 r_work: 0.3179 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10284 Z= 0.090 Angle : 0.538 11.131 14036 Z= 0.266 Chirality : 0.044 0.255 1620 Planarity : 0.004 0.035 1772 Dihedral : 5.266 56.922 2033 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.65 % Allowed : 8.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.25), residues: 1212 helix: -2.16 (0.50), residues: 89 sheet: -0.54 (0.41), residues: 174 loop : -0.12 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.007 0.001 TYR B 411 PHE 0.017 0.001 PHE A 546 TRP 0.005 0.001 TRP A 198 HIS 0.003 0.000 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00214 (10198) covalent geometry : angle 0.49713 (13829) SS BOND : bond 0.00249 ( 51) SS BOND : angle 0.88315 ( 102) hydrogen bonds : bond 0.03012 ( 194) hydrogen bonds : angle 5.86306 ( 363) link_ALPHA1-3 : bond 0.00718 ( 2) link_ALPHA1-3 : angle 2.13408 ( 6) link_ALPHA1-6 : bond 0.00566 ( 2) link_ALPHA1-6 : angle 1.35470 ( 6) link_BETA1-4 : bond 0.01064 ( 18) link_BETA1-4 : angle 2.86822 ( 54) link_NAG-ASN : bond 0.00282 ( 13) link_NAG-ASN : angle 1.45210 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4343.41 seconds wall clock time: 74 minutes 21.09 seconds (4461.09 seconds total)