Starting phenix.real_space_refine on Tue Jun 17 05:34:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4l_41886/06_2025/8u4l_41886_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4l_41886/06_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_41886/06_2025/8u4l_41886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4l_41886/06_2025/8u4l_41886.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4l_41886/06_2025/8u4l_41886_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4l_41886/06_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-5710/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: 9.29, per 1000 atoms: 0.49 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: 4.81 Conformation dependent library (CDL) restraints added in 1.4 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: 1.74 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: 6.59 Time building geometry restraints manager: 5.89 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: 4.800 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: 0.340 Extract box with map and model: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.240 Find NCS groups from input model: 0.270 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.540 ------------------------------------------------------------------------------- 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 : 1.365 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: 0.5871 time to fit residues: 120.3713 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 : 1.371 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.137572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.092302 restraints weight = 49908.796| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.88 r_work: 0.3274 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 1.426 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: 0.8326 (m-40) cc_final: 0.8119 (m-40) REVERT: A 462 ASP cc_start: 0.8630 (t0) cc_final: 0.8092 (t0) REVERT: A 583 PHE cc_start: 0.7616 (p90) cc_final: 0.7235 (p90) REVERT: B 534 PHE cc_start: 0.8540 (m-80) cc_final: 0.7910 (m-80) REVERT: C 188 THR cc_start: 0.8956 (p) cc_final: 0.8708 (t) outliers start: 10 outliers final: 8 residues processed: 90 average time/residue: 0.5232 time to fit residues: 65.1702 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 : 1.458 ------------------------------------------------------------------------------- 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: 0.4980 chunk 16 optimal weight: 0.0050 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 71 optimal weight: 0.0050 chunk 36 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.4208 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.137694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.092545 restraints weight = 49795.298| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.88 r_work: 0.3282 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10284 Z= 0.125 Angle : 0.713 14.115 14036 Z= 0.346 Chirality : 0.050 0.382 1620 Planarity : 0.004 0.037 1772 Dihedral : 10.244 62.959 2033 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.56 % Allowed : 6.41 % 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: -0.72 (0.23), residues: 1212 helix: -2.33 (0.50), residues: 89 sheet: -0.87 (0.36), residues: 173 loop : -0.18 (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 0.011 0.001 TYR B 303 ARG 0.002 0.000 ARG B 487 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 13) link_NAG-ASN : angle 1.91083 ( 39) link_ALPHA1-6 : bond 0.00774 ( 2) link_ALPHA1-6 : angle 1.51855 ( 6) link_BETA1-4 : bond 0.01375 ( 18) link_BETA1-4 : angle 4.41721 ( 54) link_ALPHA1-3 : bond 0.01454 ( 2) link_ALPHA1-3 : angle 2.57243 ( 6) hydrogen bonds : bond 0.04841 ( 194) hydrogen bonds : angle 7.31426 ( 363) SS BOND : bond 0.00359 ( 51) SS BOND : angle 1.62216 ( 102) covalent geometry : bond 0.00260 (10198) covalent geometry : angle 0.63746 (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 77 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8309 (m-40) cc_final: 0.8071 (m-40) REVERT: A 462 ASP cc_start: 0.8706 (t0) cc_final: 0.8029 (t0) REVERT: A 583 PHE cc_start: 0.7935 (p90) cc_final: 0.7481 (p90) REVERT: B 184 ILE cc_start: 0.8327 (mm) cc_final: 0.7790 (pt) REVERT: B 193 HIS cc_start: 0.8139 (t70) cc_final: 0.7796 (t70) REVERT: B 534 PHE cc_start: 0.8468 (m-80) cc_final: 0.8004 (m-80) REVERT: C 188 THR cc_start: 0.8967 (p) cc_final: 0.8745 (t) outliers start: 6 outliers final: 5 residues processed: 77 average time/residue: 0.5191 time to fit residues: 55.8366 Evaluate side-chains 71 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 1.432 ------------------------------------------------------------------------------- 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 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: 0.0970 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 302 ASN B 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.128592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.081888 restraints weight = 50135.117| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.96 r_work: 0.3202 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10284 Z= 0.133 Angle : 0.636 12.601 14036 Z= 0.310 Chirality : 0.047 0.330 1620 Planarity : 0.004 0.035 1772 Dihedral : 7.158 47.915 2033 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.84 % Allowed : 6.41 % 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 (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: -0.84 (0.23), residues: 1212 helix: -2.06 (0.52), residues: 89 sheet: -0.83 (0.37), residues: 174 loop : -0.33 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 614 HIS 0.006 0.001 HIS A 231 PHE 0.011 0.001 PHE A 447 TYR 0.016 0.001 TYR B 303 ARG 0.003 0.000 ARG B 487 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 13) link_NAG-ASN : angle 1.71119 ( 39) link_ALPHA1-6 : bond 0.00735 ( 2) link_ALPHA1-6 : angle 1.44176 ( 6) link_BETA1-4 : bond 0.01215 ( 18) link_BETA1-4 : angle 3.81649 ( 54) link_ALPHA1-3 : bond 0.01359 ( 2) link_ALPHA1-3 : angle 2.72901 ( 6) hydrogen bonds : bond 0.04113 ( 194) hydrogen bonds : angle 6.77265 ( 363) SS BOND : bond 0.00341 ( 51) SS BOND : angle 1.07276 ( 102) covalent geometry : bond 0.00306 (10198) covalent geometry : angle 0.57727 (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 74 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 1.422 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: 0.8320 (m-40) cc_final: 0.8086 (m-40) REVERT: A 462 ASP cc_start: 0.8744 (t0) cc_final: 0.8015 (t0) REVERT: A 583 PHE cc_start: 0.8116 (p90) cc_final: 0.7660 (p90) REVERT: B 534 PHE cc_start: 0.8520 (m-80) cc_final: 0.8002 (m-80) REVERT: C 188 THR cc_start: 0.9043 (p) cc_final: 0.8826 (t) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.5279 time to fit residues: 54.6266 Evaluate side-chains 70 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 570 HIS Chi-restraints excluded: chain B residue 59 ASN 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: 9.9990 chunk 46 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 0.0980 chunk 115 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.136764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.088563 restraints weight = 50294.786| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.65 r_work: 0.3198 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10284 Z= 0.117 Angle : 0.597 12.059 14036 Z= 0.293 Chirality : 0.046 0.305 1620 Planarity : 0.004 0.035 1772 Dihedral : 6.118 48.553 2033 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.84 % Allowed : 6.51 % Favored : 92.66 % 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: -0.76 (0.24), residues: 1212 helix: -2.00 (0.52), residues: 89 sheet: -0.73 (0.38), residues: 174 loop : -0.28 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 205 HIS 0.003 0.001 HIS A 231 PHE 0.010 0.001 PHE A 546 TYR 0.006 0.001 TYR B 274 ARG 0.001 0.000 ARG B 330 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 13) link_NAG-ASN : angle 1.63923 ( 39) link_ALPHA1-6 : bond 0.00670 ( 2) link_ALPHA1-6 : angle 1.34464 ( 6) link_BETA1-4 : bond 0.01142 ( 18) link_BETA1-4 : angle 3.38894 ( 54) link_ALPHA1-3 : bond 0.01437 ( 2) link_ALPHA1-3 : angle 3.05402 ( 6) hydrogen bonds : bond 0.03771 ( 194) hydrogen bonds : angle 6.33628 ( 363) SS BOND : bond 0.00317 ( 51) SS BOND : angle 1.13956 ( 102) covalent geometry : bond 0.00274 (10198) covalent geometry : angle 0.54323 (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 73 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.485 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: 0.8305 (m-40) cc_final: 0.8057 (m-40) REVERT: A 462 ASP cc_start: 0.8797 (t0) cc_final: 0.8079 (t0) REVERT: A 583 PHE cc_start: 0.8167 (p90) cc_final: 0.7751 (p90) REVERT: B 193 HIS cc_start: 0.8144 (t70) cc_final: 0.7795 (t70) REVERT: C 188 THR cc_start: 0.9093 (p) cc_final: 0.8869 (t) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.5202 time to fit residues: 52.0602 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 : 1.361 ------------------------------------------------------------------------------- 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 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 98 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.136514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.088435 restraints weight = 49844.290| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.62 r_work: 0.3198 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10284 Z= 0.109 Angle : 0.577 11.847 14036 Z= 0.282 Chirality : 0.045 0.291 1620 Planarity : 0.004 0.033 1772 Dihedral : 5.776 50.675 2033 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.65 % Allowed : 6.88 % Favored : 92.47 % 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: -0.70 (0.24), residues: 1212 helix: -1.96 (0.52), residues: 89 sheet: -0.65 (0.40), residues: 172 loop : -0.24 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 205 HIS 0.003 0.001 HIS A 231 PHE 0.010 0.001 PHE A 447 TYR 0.011 0.001 TYR B 303 ARG 0.002 0.000 ARG A 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 13) link_NAG-ASN : angle 1.56980 ( 39) link_ALPHA1-6 : bond 0.00645 ( 2) link_ALPHA1-6 : angle 1.31190 ( 6) link_BETA1-4 : bond 0.01124 ( 18) link_BETA1-4 : angle 3.26423 ( 54) link_ALPHA1-3 : bond 0.01220 ( 2) link_ALPHA1-3 : angle 3.03191 ( 6) hydrogen bonds : bond 0.03497 ( 194) hydrogen bonds : angle 6.21064 ( 363) SS BOND : bond 0.00291 ( 51) SS BOND : angle 0.96290 ( 102) covalent geometry : bond 0.00253 (10198) covalent geometry : angle 0.52684 (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: 7 poor density : 61 time to evaluate : 1.574 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 71 ASN cc_start: 0.8282 (m-40) cc_final: 0.8035 (m-40) REVERT: A 72 ARG cc_start: 0.8709 (mmt-90) cc_final: 0.8481 (mmt-90) REVERT: A 462 ASP cc_start: 0.8803 (t0) cc_final: 0.8086 (t0) REVERT: A 583 PHE cc_start: 0.8213 (p90) cc_final: 0.7832 (p90) REVERT: B 193 HIS cc_start: 0.8141 (t70) cc_final: 0.7804 (t70) REVERT: B 534 PHE cc_start: 0.8562 (m-80) cc_final: 0.7948 (m-80) REVERT: C 186 GLU cc_start: 0.8119 (pt0) cc_final: 0.7525 (pm20) REVERT: C 188 THR cc_start: 0.9082 (p) cc_final: 0.8847 (t) outliers start: 7 outliers final: 7 residues processed: 67 average time/residue: 0.5600 time to fit residues: 51.7663 Evaluate side-chains 65 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 373 SER Chi-restraints excluded: chain B residue 377 LEU 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: 1.9990 chunk 112 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.134713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.084167 restraints weight = 52135.129| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 4.01 r_work: 0.3104 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10284 Z= 0.215 Angle : 0.641 11.782 14036 Z= 0.322 Chirality : 0.047 0.287 1620 Planarity : 0.004 0.038 1772 Dihedral : 5.874 55.583 2033 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.12 % Allowed : 7.34 % 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: -0.83 (0.24), residues: 1212 helix: -2.11 (0.51), residues: 89 sheet: -0.61 (0.40), residues: 172 loop : -0.37 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 205 HIS 0.005 0.001 HIS B 174 PHE 0.017 0.002 PHE A 447 TYR 0.013 0.001 TYR B 303 ARG 0.003 0.000 ARG B 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 13) link_NAG-ASN : angle 1.80489 ( 39) link_ALPHA1-6 : bond 0.00636 ( 2) link_ALPHA1-6 : angle 1.31259 ( 6) link_BETA1-4 : bond 0.01076 ( 18) link_BETA1-4 : angle 3.17188 ( 54) link_ALPHA1-3 : bond 0.01067 ( 2) link_ALPHA1-3 : angle 2.83116 ( 6) hydrogen bonds : bond 0.04412 ( 194) hydrogen bonds : angle 6.40437 ( 363) SS BOND : bond 0.00526 ( 51) SS BOND : angle 1.26763 ( 102) covalent geometry : bond 0.00508 (10198) covalent geometry : angle 0.59387 (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 71 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 1.524 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: 0.8378 (m-40) cc_final: 0.8153 (m-40) REVERT: A 462 ASP cc_start: 0.8870 (t0) cc_final: 0.8121 (t0) REVERT: A 583 PHE cc_start: 0.8166 (p90) cc_final: 0.7904 (p90) REVERT: B 193 HIS cc_start: 0.8192 (t70) cc_final: 0.7741 (t70) REVERT: C 186 GLU cc_start: 0.8224 (pt0) cc_final: 0.7518 (pm20) REVERT: C 188 THR cc_start: 0.9146 (p) cc_final: 0.8916 (t) outliers start: 12 outliers final: 11 residues processed: 69 average time/residue: 0.5923 time to fit residues: 54.9225 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 : 1.509 ------------------------------------------------------------------------------- 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 22 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 104 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.135194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.085318 restraints weight = 51971.495| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 4.04 r_work: 0.3130 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.146 10284 Z= 0.114 Angle : 0.583 11.608 14036 Z= 0.289 Chirality : 0.045 0.276 1620 Planarity : 0.004 0.047 1772 Dihedral : 5.694 57.986 2033 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.84 % Allowed : 7.71 % 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: -0.72 (0.24), residues: 1212 helix: -2.11 (0.51), residues: 89 sheet: -0.59 (0.40), residues: 172 loop : -0.26 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 169 HIS 0.004 0.001 HIS A 570 PHE 0.011 0.001 PHE A 447 TYR 0.010 0.001 TYR B 303 ARG 0.009 0.000 ARG B 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 13) link_NAG-ASN : angle 1.59174 ( 39) link_ALPHA1-6 : bond 0.00608 ( 2) link_ALPHA1-6 : angle 1.33654 ( 6) link_BETA1-4 : bond 0.01093 ( 18) link_BETA1-4 : angle 3.09195 ( 54) link_ALPHA1-3 : bond 0.01027 ( 2) link_ALPHA1-3 : angle 2.78712 ( 6) hydrogen bonds : bond 0.03689 ( 194) hydrogen bonds : angle 6.22047 ( 363) SS BOND : bond 0.00368 ( 51) SS BOND : angle 1.18480 ( 102) covalent geometry : bond 0.00295 (10198) covalent geometry : angle 0.53515 (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 67 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 1.405 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 72 ARG cc_start: 0.8810 (mmt-90) cc_final: 0.8554 (mmt-90) REVERT: A 462 ASP cc_start: 0.8878 (t0) cc_final: 0.8130 (t0) REVERT: A 583 PHE cc_start: 0.7869 (p90) cc_final: 0.7534 (p90) REVERT: B 193 HIS cc_start: 0.8165 (t70) cc_final: 0.7760 (t70) REVERT: C 186 GLU cc_start: 0.8208 (pt0) cc_final: 0.7514 (pm20) REVERT: C 188 THR cc_start: 0.9135 (p) cc_final: 0.8896 (t) outliers start: 9 outliers final: 9 residues processed: 65 average time/residue: 0.5395 time to fit residues: 48.0940 Evaluate side-chains 66 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 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: 0.0670 chunk 36 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.135586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085739 restraints weight = 51938.275| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 4.03 r_work: 0.3140 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4492 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= 0.112 Angle : 0.565 11.477 14036 Z= 0.279 Chirality : 0.044 0.270 1620 Planarity : 0.004 0.044 1772 Dihedral : 5.540 59.624 2033 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.93 % Allowed : 7.71 % 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: -0.67 (0.24), residues: 1212 helix: -2.08 (0.51), residues: 89 sheet: -0.60 (0.41), residues: 172 loop : -0.21 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 205 HIS 0.004 0.001 HIS B 478 PHE 0.015 0.001 PHE A 543 TYR 0.008 0.001 TYR B 303 ARG 0.009 0.000 ARG B 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 13) link_NAG-ASN : angle 1.53122 ( 39) link_ALPHA1-6 : bond 0.00602 ( 2) link_ALPHA1-6 : angle 1.33351 ( 6) link_BETA1-4 : bond 0.01081 ( 18) link_BETA1-4 : angle 3.02046 ( 54) link_ALPHA1-3 : bond 0.00913 ( 2) link_ALPHA1-3 : angle 2.59282 ( 6) hydrogen bonds : bond 0.03431 ( 194) hydrogen bonds : angle 6.07061 ( 363) SS BOND : bond 0.00320 ( 51) SS BOND : angle 1.02441 ( 102) covalent geometry : bond 0.00267 (10198) covalent geometry : angle 0.51953 (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 66 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.576 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 72 ARG cc_start: 0.8775 (mmt-90) cc_final: 0.8522 (mmt-90) REVERT: A 275 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8808 (mt) REVERT: A 462 ASP cc_start: 0.8861 (t0) cc_final: 0.8122 (t0) REVERT: A 583 PHE cc_start: 0.7791 (p90) cc_final: 0.7469 (p90) REVERT: B 193 HIS cc_start: 0.8172 (t70) cc_final: 0.7817 (t70) REVERT: B 534 PHE cc_start: 0.8628 (m-80) cc_final: 0.8071 (m-80) REVERT: C 186 GLU cc_start: 0.8227 (pt0) cc_final: 0.7532 (pm20) REVERT: C 188 THR cc_start: 0.9129 (p) cc_final: 0.8880 (t) outliers start: 10 outliers final: 9 residues processed: 65 average time/residue: 0.4857 time to fit residues: 45.4931 Evaluate side-chains 66 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 111 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 70 optimal weight: 0.0370 chunk 35 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4057 r_free = 0.4057 target = 0.134091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.085476 restraints weight = 49901.315| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.64 r_work: 0.3144 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10284 Z= 0.151 Angle : 0.582 11.463 14036 Z= 0.290 Chirality : 0.045 0.266 1620 Planarity : 0.004 0.044 1772 Dihedral : 5.559 59.333 2033 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.93 % Allowed : 7.90 % 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 (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: -0.73 (0.24), residues: 1212 helix: -2.13 (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 TRP 0.006 0.001 TRP B 205 HIS 0.004 0.001 HIS B 478 PHE 0.013 0.001 PHE A 447 TYR 0.012 0.001 TYR B 303 ARG 0.007 0.000 ARG B 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 13) link_NAG-ASN : angle 1.60683 ( 39) link_ALPHA1-6 : bond 0.00598 ( 2) link_ALPHA1-6 : angle 1.33304 ( 6) link_BETA1-4 : bond 0.01068 ( 18) link_BETA1-4 : angle 2.99099 ( 54) link_ALPHA1-3 : bond 0.00807 ( 2) link_ALPHA1-3 : angle 2.39419 ( 6) hydrogen bonds : bond 0.03743 ( 194) hydrogen bonds : angle 6.13441 ( 363) SS BOND : bond 0.00398 ( 51) SS BOND : angle 1.07096 ( 102) covalent geometry : bond 0.00365 (10198) covalent geometry : angle 0.53824 (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 68 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 1.393 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 72 ARG cc_start: 0.8769 (mmt-90) cc_final: 0.8518 (mmt-90) REVERT: A 462 ASP cc_start: 0.8838 (t0) cc_final: 0.8108 (t0) REVERT: A 583 PHE cc_start: 0.7842 (p90) cc_final: 0.7569 (p90) REVERT: B 193 HIS cc_start: 0.8166 (t70) cc_final: 0.7700 (t70) REVERT: C 186 GLU cc_start: 0.8216 (pt0) cc_final: 0.7548 (pm20) REVERT: C 188 THR cc_start: 0.9128 (p) cc_final: 0.8873 (t) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.5048 time to fit residues: 46.9232 Evaluate side-chains 66 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 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: 0.0060 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 94 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.136202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.087248 restraints weight = 49781.441| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.61 r_work: 0.3168 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10284 Z= 0.097 Angle : 0.551 11.244 14036 Z= 0.273 Chirality : 0.044 0.259 1620 Planarity : 0.004 0.043 1772 Dihedral : 5.398 57.960 2033 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.84 % Allowed : 7.81 % 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: -0.65 (0.25), residues: 1212 helix: -2.17 (0.50), residues: 89 sheet: -0.70 (0.40), residues: 174 loop : -0.17 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 169 HIS 0.004 0.001 HIS A 70 PHE 0.015 0.001 PHE A 546 TYR 0.007 0.001 TYR B 303 ARG 0.008 0.000 ARG B 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 13) link_NAG-ASN : angle 1.48614 ( 39) link_ALPHA1-6 : bond 0.00582 ( 2) link_ALPHA1-6 : angle 1.35009 ( 6) link_BETA1-4 : bond 0.01070 ( 18) link_BETA1-4 : angle 2.91865 ( 54) link_ALPHA1-3 : bond 0.00746 ( 2) link_ALPHA1-3 : angle 2.27728 ( 6) hydrogen bonds : bond 0.03278 ( 194) hydrogen bonds : angle 5.96437 ( 363) SS BOND : bond 0.00279 ( 51) SS BOND : angle 0.93632 ( 102) covalent geometry : bond 0.00229 (10198) covalent geometry : angle 0.50884 (13829) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9134.77 seconds wall clock time: 155 minutes 18.56 seconds (9318.56 seconds total)