Starting phenix.real_space_refine on Sun Jul 5 06:52:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rx5_54358/07_2026/9rx5_54358.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rx5_54358/07_2026/9rx5_54358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rx5_54358/07_2026/9rx5_54358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rx5_54358/07_2026/9rx5_54358.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rx5_54358/07_2026/9rx5_54358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rx5_54358/07_2026/9rx5_54358.map" } resolution = 3.15 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= 0.002 sd= 0.031 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 8 5.49 5 Mg 3 5.21 5 S 123 5.16 5 C 16152 2.51 5 N 4380 2.21 5 O 4755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25422 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6545 Classifications: {'peptide': 810} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 38, 'TRANS': 769} Chain breaks: 2 Chain: "B" Number of atoms: 9518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1197, 9518 Classifications: {'peptide': 1197} Link IDs: {'CIS': 6, 'PCIS': 4, 'PTRANS': 52, 'TRANS': 1134} Chain breaks: 5 Chain: "C" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3119 Classifications: {'peptide': 379} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 370} Chain breaks: 2 Chain: "D" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3456 Classifications: {'peptide': 423} Link IDs: {'CIS': 3, 'PTRANS': 12, 'TRANS': 407} Chain breaks: 1 Chain: "E" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1333 Classifications: {'peptide': 170} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 165} Chain: "F" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 165} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MG': 1, 'GDP': 1, 'MYR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16093 SG CYS C 18 42.944 136.631 40.233 1.00125.51 S ATOM 16119 SG CYS C 21 41.526 135.672 43.539 1.00142.00 S ATOM 16590 SG CYS C 137 39.342 138.494 41.540 1.00158.10 S ATOM 16614 SG CYS C 140 41.732 138.573 42.938 1.00155.92 S Residues with excluded nonbonded symmetry interactions: 170 residue: pdb=" N THR F 14 " occ=0.08 ... (5 atoms not shown) pdb=" CG2 THR F 14 " occ=0.08 residue: pdb=" N GLY F 15 " occ=0.14 ... (2 atoms not shown) pdb=" O GLY F 15 " occ=0.14 residue: pdb=" N ASN F 16 " occ=0.21 ... (6 atoms not shown) pdb=" ND2 ASN F 16 " occ=0.21 residue: pdb=" N LYS F 17 " occ=0.07 ... (7 atoms not shown) pdb=" NZ LYS F 17 " occ=0.07 residue: pdb=" N ILE F 18 " occ=0.20 ... (6 atoms not shown) pdb=" CD1 ILE F 18 " occ=0.20 residue: pdb=" N GLN F 20 " occ=0.29 ... (7 atoms not shown) pdb=" NE2 GLN F 20 " occ=0.29 residue: pdb=" N PHE F 21 " occ=0.16 ... (9 atoms not shown) pdb=" CZ PHE F 21 " occ=0.16 residue: pdb=" N LYS F 22 " occ=0.70 ... (7 atoms not shown) pdb=" NZ LYS F 22 " occ=0.70 residue: pdb=" N LEU F 23 " occ=0.34 ... (6 atoms not shown) pdb=" CD2 LEU F 23 " occ=0.34 residue: pdb=" N VAL F 24 " occ=0.29 ... (5 atoms not shown) pdb=" CG2 VAL F 24 " occ=0.29 residue: pdb=" N LEU F 25 " occ=0.35 ... (6 atoms not shown) pdb=" CD2 LEU F 25 " occ=0.35 residue: pdb=" N LEU F 26 " occ=0.15 ... (6 atoms not shown) pdb=" CD2 LEU F 26 " occ=0.15 ... (remaining 158 not shown) Time building chain proxies: 4.59, per 1000 atoms: 0.18 Number of scatterers: 25422 At special positions: 0 Unit cell: (109.22, 181.46, 243.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 123 16.00 P 8 15.00 Mg 3 11.99 O 4755 8.00 N 4380 7.00 C 16152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 140 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 18 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 21 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 137 " Number of angles added : 6 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5994 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 29 sheets defined 49.1% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 4.184A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.645A pdb=" N LYS A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 172 through 184 removed outlier: 3.889A pdb=" N ALA A 176 " --> pdb=" O MET A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 211 removed outlier: 4.143A pdb=" N ARG A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU A 196 " --> pdb=" O TRP A 192 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.797A pdb=" N ARG A 275 " --> pdb=" O HIS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.639A pdb=" N HIS A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 removed outlier: 3.641A pdb=" N SER A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 321 through 328 removed outlier: 3.701A pdb=" N THR A 324 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLU A 327 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS A 328 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 341 through 353 removed outlier: 3.833A pdb=" N GLN A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.780A pdb=" N LEU A 364 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.549A pdb=" N ARG A 377 " --> pdb=" O ASN A 373 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.984A pdb=" N GLN A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 removed outlier: 4.017A pdb=" N ILE A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 486 through 501 removed outlier: 3.719A pdb=" N ALA A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 500 " --> pdb=" O TYR A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 510 through 530 removed outlier: 3.694A pdb=" N HIS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 562 removed outlier: 3.556A pdb=" N ARG A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 578 removed outlier: 3.777A pdb=" N GLY A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 660 Processing helix chain 'A' and resid 690 through 698 Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.770A pdb=" N PHE A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 740 removed outlier: 3.511A pdb=" N GLY A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 787 removed outlier: 3.864A pdb=" N MET A 787 " --> pdb=" O MET A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 810 removed outlier: 4.066A pdb=" N GLN A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 806 " --> pdb=" O CYS A 802 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU A 807 " --> pdb=" O TYR A 803 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 821 removed outlier: 3.550A pdb=" N SER A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 824 No H-bonds generated for 'chain 'A' and resid 822 through 824' Processing helix chain 'A' and resid 828 through 834 removed outlier: 3.547A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 removed outlier: 4.129A pdb=" N LYS A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 845 " --> pdb=" O LYS A 841 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG A 847 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 869 Processing helix chain 'B' and resid 3 through 7 Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.868A pdb=" N SER B 21 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 22 " --> pdb=" O TYR B 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 18 through 22' Processing helix chain 'B' and resid 64 through 79 removed outlier: 3.812A pdb=" N LYS B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 Processing helix chain 'B' and resid 121 through 141 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 237 through 253 removed outlier: 4.228A pdb=" N SER B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 270 removed outlier: 3.818A pdb=" N ASN B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 303 through 311 removed outlier: 3.576A pdb=" N GLN B 311 " --> pdb=" O TYR B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.814A pdb=" N ALA B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 358 removed outlier: 3.571A pdb=" N ARG B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLY B 351 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 removed outlier: 4.049A pdb=" N LEU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 381 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.842A pdb=" N LYS B 395 " --> pdb=" O TYR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.984A pdb=" N ASP B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 425 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 430 through 445 removed outlier: 3.771A pdb=" N LEU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 469 through 473 removed outlier: 3.766A pdb=" N GLN B 472 " --> pdb=" O HIS B 469 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP B 473 " --> pdb=" O LEU B 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 469 through 473' Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.690A pdb=" N ARG B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 506 removed outlier: 3.664A pdb=" N LEU B 489 " --> pdb=" O ASN B 485 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.596A pdb=" N THR B 528 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 546 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 removed outlier: 4.280A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU B 558 " --> pdb=" O GLN B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 removed outlier: 3.944A pdb=" N LEU B 564 " --> pdb=" O GLY B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 576 Processing helix chain 'B' and resid 582 through 587 removed outlier: 3.645A pdb=" N ASP B 587 " --> pdb=" O PHE B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 609 removed outlier: 4.067A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY B 603 " --> pdb=" O ASP B 599 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 615 Processing helix chain 'B' and resid 616 through 624 removed outlier: 3.513A pdb=" N GLN B 621 " --> pdb=" O LYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 645 removed outlier: 3.970A pdb=" N ILE B 632 " --> pdb=" O GLU B 628 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 645 " --> pdb=" O CYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 661 Processing helix chain 'B' and resid 662 through 666 removed outlier: 4.248A pdb=" N CYS B 665 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.672A pdb=" N GLY B 674 " --> pdb=" O TRP B 670 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 676 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 677 " --> pdb=" O TYR B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 694 Processing helix chain 'B' and resid 695 through 700 removed outlier: 3.683A pdb=" N ASP B 700 " --> pdb=" O PRO B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 720 removed outlier: 3.518A pdb=" N VAL B 719 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU B 720 " --> pdb=" O LEU B 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 716 through 720' Processing helix chain 'B' and resid 725 through 735 removed outlier: 3.822A pdb=" N SER B 735 " --> pdb=" O TYR B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 753 removed outlier: 3.892A pdb=" N ARG B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 778 removed outlier: 3.665A pdb=" N ALA B 768 " --> pdb=" O ASP B 764 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 778 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 789 removed outlier: 4.050A pdb=" N ASP B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 786 " --> pdb=" O GLU B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 809 removed outlier: 4.005A pdb=" N GLN B 807 " --> pdb=" O ASN B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 813 removed outlier: 3.610A pdb=" N SER B 813 " --> pdb=" O LEU B 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 810 through 813' Processing helix chain 'B' and resid 821 through 825 Processing helix chain 'B' and resid 940 through 966 removed outlier: 3.639A pdb=" N GLU B 966 " --> pdb=" O LYS B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 1272 through 1276 removed outlier: 3.559A pdb=" N SER B1276 " --> pdb=" O PRO B1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.541A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 Processing helix chain 'C' and resid 111 through 128 Processing helix chain 'C' and resid 138 through 169 removed outlier: 3.947A pdb=" N THR C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU C 144 " --> pdb=" O CYS C 140 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP C 146 " --> pdb=" O ASP C 142 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR C 150 " --> pdb=" O ASP C 146 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 176 through 267 removed outlier: 4.341A pdb=" N MET C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 198 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP C 200 " --> pdb=" O GLN C 196 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 243 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 257 " --> pdb=" O GLN C 253 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 274 Processing helix chain 'C' and resid 299 through 322 removed outlier: 3.909A pdb=" N LYS C 320 " --> pdb=" O ALA C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.768A pdb=" N ARG C 358 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 384 removed outlier: 4.021A pdb=" N ASP C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C 382 " --> pdb=" O GLN C 378 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 444 removed outlier: 3.554A pdb=" N TRP C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'D' and resid 41 through 45 removed outlier: 3.667A pdb=" N HIS D 44 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 45 " --> pdb=" O LEU D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 45' Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 192 through 226 removed outlier: 3.566A pdb=" N LEU D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 290 removed outlier: 3.921A pdb=" N LEU D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS D 243 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA D 257 " --> pdb=" O ARG D 253 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER D 280 " --> pdb=" O GLY D 276 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D 287 " --> pdb=" O HIS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 325 removed outlier: 3.911A pdb=" N ALA D 312 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN D 313 " --> pdb=" O LYS D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 328 No H-bonds generated for 'chain 'D' and resid 326 through 328' Processing helix chain 'D' and resid 348 through 353 removed outlier: 3.920A pdb=" N GLN D 353 " --> pdb=" O SER D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 378 removed outlier: 4.246A pdb=" N GLY D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER D 372 " --> pdb=" O ALA D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 392 Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 419 through 439 removed outlier: 3.506A pdb=" N ASP D 423 " --> pdb=" O LYS D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 459 removed outlier: 4.022A pdb=" N LYS D 455 " --> pdb=" O PRO D 452 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE D 457 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET D 458 " --> pdb=" O LYS D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 42 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.628A pdb=" N HIS E 83 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 91 removed outlier: 3.741A pdb=" N ARG E 91 " --> pdb=" O PRO E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 122 removed outlier: 3.953A pdb=" N PHE E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 141 removed outlier: 3.639A pdb=" N ALA E 138 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASN E 139 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 155 removed outlier: 3.684A pdb=" N ALA E 148 " --> pdb=" O ASP E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 181 removed outlier: 3.932A pdb=" N ILE E 173 " --> pdb=" O ASN E 169 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 41 Processing helix chain 'F' and resid 85 through 90 removed outlier: 3.687A pdb=" N TYR F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 121 removed outlier: 3.855A pdb=" N PHE F 108 " --> pdb=" O ASN F 104 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 141 removed outlier: 4.815A pdb=" N ASN F 139 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 156 removed outlier: 3.754A pdb=" N ALA F 148 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 181 removed outlier: 4.057A pdb=" N ILE F 173 " --> pdb=" O ASN F 169 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE F 174 " --> pdb=" O VAL F 170 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 233 removed outlier: 8.992A pdb=" N GLY A 232 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N HIS A 8 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 9 " --> pdb=" O ARG B 829 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 removed outlier: 7.720A pdb=" N ALA A 104 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER A 128 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 106 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR A 126 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 108 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY A 124 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 110 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 114 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N THR A 126 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS A 144 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N SER A 128 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 12.109A pdb=" N ASP A 142 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N MET A 215 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR A 216 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU A 26 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N MET A 218 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A 19 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 89 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER A 25 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TRP A 87 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 225 Processing sheet with id=AA5, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA6, first strand: chain 'A' and resid 591 through 592 removed outlier: 3.635A pdb=" N GLY A 680 " --> pdb=" O LYS A 636 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 673 " --> pdb=" O PHE A 681 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 688 through 689 Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 34 removed outlier: 6.481A pdb=" N TYR B 28 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LYS B 44 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 30 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 89 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AB1, first strand: chain 'B' and resid 175 through 176 removed outlier: 5.868A pdb=" N LEU B 175 " --> pdb=" O VAL B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 998 through 1001 Processing sheet with id=AB3, first strand: chain 'B' and resid 1045 through 1050 removed outlier: 3.808A pdb=" N THR B1047 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B1060 " --> pdb=" O THR B1047 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA B1065 " --> pdb=" O SER B1061 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1100 through 1103 removed outlier: 3.685A pdb=" N ASP B1100 " --> pdb=" O ALA B1115 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B1122 " --> pdb=" O TYR B1114 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B1121 " --> pdb=" O THR B1134 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR B1134 " --> pdb=" O LEU B1121 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY B1123 " --> pdb=" O ALA B1132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1144 through 1149 removed outlier: 6.662A pdb=" N GLY B1159 " --> pdb=" O THR B1145 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE B1147 " --> pdb=" O CYS B1157 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS B1157 " --> pdb=" O PHE B1147 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL B1149 " --> pdb=" O TRP B1155 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TRP B1155 " --> pdb=" O VAL B1149 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B1174 " --> pdb=" O ASP B1169 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1187 through 1192 removed outlier: 3.993A pdb=" N ARG B1189 " --> pdb=" O ALA B1203 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1242 through 1247 removed outlier: 4.092A pdb=" N GLY B1244 " --> pdb=" O ALA B1259 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B1259 " --> pdb=" O GLY B1244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1332 through 1339 removed outlier: 4.279A pdb=" N ASP B1334 " --> pdb=" O ALA B1348 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 16 through 17 removed outlier: 4.533A pdb=" N PHE C 16 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 276 through 279 Processing sheet with id=AC2, first strand: chain 'C' and resid 328 through 331 Processing sheet with id=AC3, first strand: chain 'C' and resid 394 through 397 removed outlier: 4.059A pdb=" N TYR C 413 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 47 through 50 removed outlier: 4.228A pdb=" N GLY D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR D 161 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 81 through 82 removed outlier: 3.925A pdb=" N TYR D 81 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY D 119 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU D 127 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LYS D 121 " --> pdb=" O TYR D 125 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TYR D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 331 through 333 Processing sheet with id=AC7, first strand: chain 'D' and resid 386 through 387 removed outlier: 3.830A pdb=" N THR D 394 " --> pdb=" O ILE D 387 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 56 through 58 removed outlier: 3.521A pdb=" N VAL E 62 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.153A pdb=" N SER E 19 " --> pdb=" O LYS E 70 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLU E 72 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE E 21 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N TRP E 74 " --> pdb=" O PHE E 21 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU E 23 " --> pdb=" O TRP E 74 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ALA E 95 " --> pdb=" O GLN E 20 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS E 22 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE E 97 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL E 24 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL E 99 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU E 26 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N ASP E 101 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA E 96 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER E 131 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL E 98 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASN E 133 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR E 100 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 158 " --> pdb=" O ILE E 128 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 56 through 58 Processing sheet with id=AD2, first strand: chain 'F' and resid 56 through 58 removed outlier: 3.798A pdb=" N SER F 19 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ALA F 95 " --> pdb=" O GLN F 20 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LYS F 22 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE F 97 " --> pdb=" O LYS F 22 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL F 24 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL F 99 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU F 26 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N ASP F 101 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU F 158 " --> pdb=" O ILE F 128 " (cutoff:3.500A) 1142 hydrogen bonds defined for protein. 3210 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: 4.98 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8198 1.34 - 1.46: 4232 1.46 - 1.58: 13297 1.58 - 1.69: 13 1.69 - 1.81: 194 Bond restraints: 25934 Sorted by residual: bond pdb=" C ASP B 700 " pdb=" N PRO B 701 " ideal model delta sigma weight residual 1.326 1.370 -0.044 1.44e-02 4.82e+03 9.42e+00 bond pdb=" N ASN B 457 " pdb=" CA ASN B 457 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.90e-02 2.77e+03 4.81e+00 bond pdb=" CB ASP A 239 " pdb=" CG ASP A 239 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.53e+00 bond pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.29e+00 bond pdb=" C GLU A 155 " pdb=" N PRO A 156 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.12e-02 7.97e+03 4.10e+00 ... (remaining 25929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 34770 3.03 - 6.07: 247 6.07 - 9.10: 39 9.10 - 12.14: 5 12.14 - 15.17: 2 Bond angle restraints: 35063 Sorted by residual: angle pdb=" C HIS A 141 " pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 121.70 136.87 -15.17 1.80e+00 3.09e-01 7.11e+01 angle pdb=" C ILE B 456 " pdb=" N ASN B 457 " pdb=" CA ASN B 457 " ideal model delta sigma weight residual 121.70 134.79 -13.09 1.80e+00 3.09e-01 5.29e+01 angle pdb=" C SER B 142 " pdb=" N GLY B 143 " pdb=" CA GLY B 143 " ideal model delta sigma weight residual 121.70 132.41 -10.71 1.80e+00 3.09e-01 3.54e+01 angle pdb=" CA SER B 142 " pdb=" C SER B 142 " pdb=" N GLY B 143 " ideal model delta sigma weight residual 117.17 123.91 -6.74 1.18e+00 7.18e-01 3.26e+01 angle pdb=" N THR E 59 " pdb=" CA THR E 59 " pdb=" C THR E 59 " ideal model delta sigma weight residual 108.19 115.19 -7.00 1.29e+00 6.01e-01 2.94e+01 ... (remaining 35058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 15450 35.97 - 71.95: 275 71.95 - 107.92: 26 107.92 - 143.89: 2 143.89 - 179.87: 3 Dihedral angle restraints: 15756 sinusoidal: 6519 harmonic: 9237 Sorted by residual: dihedral pdb=" CA GLU A 263 " pdb=" C GLU A 263 " pdb=" N ASN A 264 " pdb=" CA ASN A 264 " ideal model delta harmonic sigma weight residual 180.00 138.94 41.06 0 5.00e+00 4.00e-02 6.74e+01 dihedral pdb=" O3B GTP F 301 " pdb=" O3A GTP F 301 " pdb=" PB GTP F 301 " pdb=" PA GTP F 301 " ideal model delta sinusoidal sigma weight residual 291.08 111.21 179.87 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP E 301 " pdb=" O3A GTP E 301 " pdb=" PB GTP E 301 " pdb=" PA GTP E 301 " ideal model delta sinusoidal sigma weight residual -68.92 86.03 -154.95 1 2.00e+01 2.50e-03 4.57e+01 ... (remaining 15753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3002 0.048 - 0.097: 673 0.097 - 0.145: 200 0.145 - 0.194: 21 0.194 - 0.242: 4 Chirality restraints: 3900 Sorted by residual: chirality pdb=" CB THR E 59 " pdb=" CA THR E 59 " pdb=" OG1 THR E 59 " pdb=" CG2 THR E 59 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA VAL B1098 " pdb=" N VAL B1098 " pdb=" C VAL B1098 " pdb=" CB VAL B1098 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE B 294 " pdb=" CA ILE B 294 " pdb=" CG1 ILE B 294 " pdb=" CG2 ILE B 294 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 3897 not shown) Planarity restraints: 4484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 650 " 0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO B 651 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 651 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 651 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 239 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.86e+00 pdb=" C ASP A 239 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP A 239 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY A 240 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 666 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO B 667 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 667 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 667 " -0.036 5.00e-02 4.00e+02 ... (remaining 4481 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 130 2.59 - 3.17: 18678 3.17 - 3.75: 36464 3.75 - 4.32: 48891 4.32 - 4.90: 82654 Nonbonded interactions: 186817 Sorted by model distance: nonbonded pdb="MG MG E 300 " pdb=" O2A GTP E 301 " model vdw 2.018 2.170 nonbonded pdb="MG MG E 300 " pdb=" O1G GTP E 301 " model vdw 2.027 2.170 nonbonded pdb=" OD1 ASN B 153 " pdb="MG MG B1403 " model vdw 2.074 2.170 nonbonded pdb="MG MG F 300 " pdb=" O2A GTP F 301 " model vdw 2.110 2.170 nonbonded pdb=" OG SER F 34 " pdb="MG MG F 300 " model vdw 2.113 2.170 ... (remaining 186812 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 'E' selection = (chain 'F' and resid 15 through 301) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.06 max=1.00 mean=0.97 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 23.560 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.003 0.090 25939 Z= 0.201 Angle : 0.817 35.897 35069 Z= 0.456 Chirality : 0.045 0.242 3900 Planarity : 0.006 0.089 4484 Dihedral : 14.553 179.866 9762 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.40 % Favored : 96.47 % Rotamer: Outliers : 0.04 % Allowed : 6.31 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.43 (0.13), residues: 3118 helix: -0.95 (0.12), residues: 1297 sheet: 0.20 (0.24), residues: 421 loop : -1.20 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 210 TYR 0.030 0.001 TYR A 803 PHE 0.020 0.002 PHE B1267 TRP 0.019 0.002 TRP C 442 HIS 0.008 0.001 HIS B 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.19 (25934) covalent geometry : angle 0.76618 / 0.45 (35063) hydrogen bonds : bond 0.17915 / 11.52 ( 1128) hydrogen bonds : angle 6.15086 / 4.20 ( 3210) metal coordination : bond 0.05265 / 2.49 ( 4) metal coordination : angle 21.64972 / 13.37 ( 6) Misc. bond : bond 0.09041 / 4.76 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 805 time to evaluate : 0.939 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: symmetry clash REVERT: A 75 ARG cc_start: 0.4783 (ttm-80) cc_final: 0.4251 (ttp-170) REVERT: A 203 MET cc_start: 0.7728 (mmm) cc_final: 0.7097 (ttm) REVERT: A 236 TYR cc_start: 0.8397 (t80) cc_final: 0.7467 (t80) REVERT: A 289 ASN cc_start: 0.7384 (t0) cc_final: 0.6974 (m-40) REVERT: A 293 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6979 (mtm110) REVERT: A 370 HIS cc_start: 0.7430 (t70) cc_final: 0.7201 (t-170) REVERT: A 485 LYS cc_start: 0.8981 (mttt) cc_final: 0.8780 (mtmm) REVERT: A 498 ILE cc_start: 0.8727 (tt) cc_final: 0.8486 (tt) REVERT: A 521 MET cc_start: 0.8200 (tpp) cc_final: 0.7577 (tpt) REVERT: A 546 GLN cc_start: 0.7769 (tp40) cc_final: 0.6990 (mm-40) REVERT: A 599 VAL cc_start: 0.8152 (t) cc_final: 0.7921 (p) REVERT: A 604 ILE cc_start: 0.8513 (mt) cc_final: 0.8196 (tt) REVERT: A 613 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7443 (mttp) REVERT: A 623 PHE cc_start: 0.8156 (m-10) cc_final: 0.7812 (m-80) REVERT: A 688 VAL cc_start: 0.8435 (t) cc_final: 0.8041 (p) REVERT: A 735 ILE cc_start: 0.8247 (mm) cc_final: 0.7991 (mm) REVERT: A 750 LEU cc_start: 0.8473 (mp) cc_final: 0.8253 (mt) REVERT: A 756 LYS cc_start: 0.8050 (mttt) cc_final: 0.7792 (mtmm) REVERT: A 757 LEU cc_start: 0.7645 (mt) cc_final: 0.7444 (tt) REVERT: A 762 PHE cc_start: 0.8417 (m-80) cc_final: 0.8195 (m-80) REVERT: B 182 ASP cc_start: 0.8000 (m-30) cc_final: 0.7759 (t0) REVERT: B 291 THR cc_start: 0.8493 (m) cc_final: 0.8291 (p) REVERT: B 688 THR cc_start: 0.8218 (m) cc_final: 0.7825 (m) REVERT: B 712 ARG cc_start: 0.8560 (ptm160) cc_final: 0.8357 (ptt180) REVERT: B 977 PRO cc_start: 0.7262 (Cg_exo) cc_final: 0.7007 (Cg_endo) REVERT: B 1001 VAL cc_start: 0.8482 (t) cc_final: 0.8254 (p) REVERT: B 1041 ILE cc_start: 0.8042 (tp) cc_final: 0.7818 (tt) REVERT: B 1192 MET cc_start: 0.8385 (mmm) cc_final: 0.7705 (mmt) REVERT: B 1213 TRP cc_start: 0.5870 (p90) cc_final: 0.5324 (p90) REVERT: B 1238 SER cc_start: 0.7714 (t) cc_final: 0.7511 (p) REVERT: B 1249 PRO cc_start: 0.6651 (Cg_exo) cc_final: 0.5895 (Cg_endo) REVERT: B 1290 TYR cc_start: 0.8120 (m-80) cc_final: 0.7878 (m-80) REVERT: C 121 ASP cc_start: 0.8455 (m-30) cc_final: 0.8034 (m-30) REVERT: C 162 TYR cc_start: 0.7957 (m-80) cc_final: 0.7249 (m-10) REVERT: C 172 MET cc_start: 0.6159 (pmm) cc_final: 0.5881 (pmm) REVERT: C 313 LEU cc_start: 0.8780 (mt) cc_final: 0.8521 (tp) REVERT: C 321 MET cc_start: 0.7942 (tpp) cc_final: 0.7616 (tpp) REVERT: C 330 LEU cc_start: 0.8551 (mp) cc_final: 0.8275 (tt) REVERT: C 338 TYR cc_start: 0.8014 (p90) cc_final: 0.7739 (p90) REVERT: C 352 TYR cc_start: 0.7264 (p90) cc_final: 0.6962 (p90) REVERT: C 372 PHE cc_start: 0.8756 (t80) cc_final: 0.8530 (t80) REVERT: D 80 PHE cc_start: 0.7224 (t80) cc_final: 0.6519 (t80) REVERT: D 116 LYS cc_start: 0.8314 (mttt) cc_final: 0.8023 (mtmm) REVERT: D 134 CYS cc_start: 0.7783 (m) cc_final: 0.6284 (m) REVERT: D 323 SER cc_start: 0.8266 (t) cc_final: 0.8018 (p) REVERT: D 398 ASN cc_start: 0.8460 (m-40) cc_final: 0.7921 (m-40) REVERT: D 424 TYR cc_start: 0.7683 (t80) cc_final: 0.7465 (t80) REVERT: D 431 LYS cc_start: 0.8460 (tttt) cc_final: 0.8232 (tttp) REVERT: E 28 GLU cc_start: 0.7755 (mm-30) cc_final: 0.6990 (mm-30) REVERT: E 51 SER cc_start: 0.8732 (m) cc_final: 0.8329 (p) REVERT: E 81 ARG cc_start: 0.8496 (mtp85) cc_final: 0.8224 (mtp-110) REVERT: E 90 TYR cc_start: 0.8385 (p90) cc_final: 0.8066 (p90) REVERT: E 110 ARG cc_start: 0.7470 (mmm160) cc_final: 0.7037 (mmm160) REVERT: E 145 PHE cc_start: 0.7392 (t80) cc_final: 0.7160 (t80) REVERT: E 159 PHE cc_start: 0.8315 (t80) cc_final: 0.7860 (t80) REVERT: E 163 SER cc_start: 0.8144 (t) cc_final: 0.7848 (t) REVERT: F 137 LEU cc_start: 0.7332 (mt) cc_final: 0.7124 (tp) outliers start: 1 outliers final: 0 residues processed: 806 average time/residue: 0.1822 time to fit residues: 221.3676 Evaluate side-chains 594 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 594 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 637 HIS A 857 HIS ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN B 352 ASN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 363 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN D 126 GLN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS E 83 HIS E 155 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.101093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.081049 restraints weight = 65519.215| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.84 r_work: 0.3280 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25939 Z= 0.173 Angle : 0.683 15.517 35069 Z= 0.350 Chirality : 0.044 0.279 3900 Planarity : 0.005 0.065 4484 Dihedral : 8.732 176.655 3455 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Rotamer: Outliers : 3.01 % Allowed : 12.72 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.30 (0.15), residues: 3118 helix: 0.61 (0.14), residues: 1328 sheet: -0.01 (0.24), residues: 431 loop : -1.03 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1033 TYR 0.024 0.002 TYR C 394 PHE 0.026 0.002 PHE B 272 TRP 0.024 0.002 TRP B1020 HIS 0.008 0.001 HIS B1243 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (25934) covalent geometry : angle 0.67469 / 0.35 (35063) hydrogen bonds : bond 0.06158 / 3.92 ( 1128) hydrogen bonds : angle 4.51148 / 3.05 ( 3210) metal coordination : bond 0.01087 / 0.53 ( 4) metal coordination : angle 8.34396 / 5.16 ( 6) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 594 time to evaluate : 0.899 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8030 (mm-40) REVERT: A 75 ARG cc_start: 0.4487 (ttm-80) cc_final: 0.3941 (ttp-170) REVERT: A 158 LYS cc_start: 0.6794 (mtmt) cc_final: 0.6582 (mtpt) REVERT: A 203 MET cc_start: 0.7703 (mmm) cc_final: 0.7035 (ttm) REVERT: A 361 GLU cc_start: 0.6804 (pm20) cc_final: 0.6470 (pm20) REVERT: A 498 ILE cc_start: 0.8795 (tt) cc_final: 0.8501 (tt) REVERT: A 509 ARG cc_start: 0.7848 (mmm-85) cc_final: 0.7597 (mmm160) REVERT: A 521 MET cc_start: 0.8239 (tpp) cc_final: 0.7639 (tpt) REVERT: A 572 ARG cc_start: 0.7926 (tpm170) cc_final: 0.7695 (tpm170) REVERT: A 576 LEU cc_start: 0.8457 (mt) cc_final: 0.7747 (mt) REVERT: A 596 GLU cc_start: 0.7272 (tp30) cc_final: 0.6829 (tm-30) REVERT: A 598 GLN cc_start: 0.8115 (mt0) cc_final: 0.7810 (mt0) REVERT: A 623 PHE cc_start: 0.8013 (m-10) cc_final: 0.7807 (m-10) REVERT: A 704 PHE cc_start: 0.7953 (m-80) cc_final: 0.7684 (m-80) REVERT: A 735 ILE cc_start: 0.8219 (mm) cc_final: 0.7969 (mm) REVERT: A 750 LEU cc_start: 0.8528 (mp) cc_final: 0.8294 (mt) REVERT: A 756 LYS cc_start: 0.8207 (mttt) cc_final: 0.7926 (mttm) REVERT: A 761 ASP cc_start: 0.8247 (t0) cc_final: 0.8047 (t0) REVERT: A 762 PHE cc_start: 0.8515 (m-80) cc_final: 0.8234 (m-80) REVERT: A 800 LYS cc_start: 0.8852 (tppp) cc_final: 0.8648 (tppt) REVERT: A 860 GLN cc_start: 0.7990 (mt0) cc_final: 0.7766 (mt0) REVERT: B 17 GLU cc_start: 0.7719 (tt0) cc_final: 0.7472 (tt0) REVERT: B 108 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7277 (t70) REVERT: B 163 LEU cc_start: 0.8052 (mp) cc_final: 0.7617 (mt) REVERT: B 207 MET cc_start: 0.5597 (tmm) cc_final: 0.5354 (tmm) REVERT: B 275 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7261 (mm-30) REVERT: B 538 GLN cc_start: 0.8587 (tt0) cc_final: 0.8308 (mt0) REVERT: B 726 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7115 (tpt170) REVERT: B 1181 HIS cc_start: 0.7713 (t-90) cc_final: 0.7434 (t-90) REVERT: B 1213 TRP cc_start: 0.5998 (OUTLIER) cc_final: 0.5214 (p90) REVERT: B 1290 TYR cc_start: 0.8134 (m-80) cc_final: 0.7903 (m-80) REVERT: C 121 ASP cc_start: 0.8549 (m-30) cc_final: 0.8233 (m-30) REVERT: C 134 HIS cc_start: 0.7375 (m-70) cc_final: 0.7137 (m90) REVERT: C 275 HIS cc_start: 0.8268 (t70) cc_final: 0.8006 (t70) REVERT: C 310 THR cc_start: 0.8582 (m) cc_final: 0.8359 (p) REVERT: C 338 TYR cc_start: 0.8081 (p90) cc_final: 0.7688 (p90) REVERT: C 372 PHE cc_start: 0.8872 (t80) cc_final: 0.8597 (t80) REVERT: D 62 LEU cc_start: 0.7670 (mm) cc_final: 0.7453 (mt) REVERT: D 107 ASP cc_start: 0.8105 (t0) cc_final: 0.7725 (t0) REVERT: D 132 LYS cc_start: 0.7220 (pttt) cc_final: 0.6991 (pttp) REVERT: D 323 SER cc_start: 0.8537 (t) cc_final: 0.8121 (p) REVERT: D 364 LEU cc_start: 0.7299 (mt) cc_final: 0.6668 (pp) REVERT: D 396 LYS cc_start: 0.7814 (mtpp) cc_final: 0.7602 (mtpp) REVERT: D 442 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7745 (tp) REVERT: E 47 GLU cc_start: 0.7939 (tp30) cc_final: 0.7719 (tp30) REVERT: E 90 TYR cc_start: 0.8382 (p90) cc_final: 0.7769 (p90) REVERT: F 137 LEU cc_start: 0.7779 (mt) cc_final: 0.7348 (tp) REVERT: F 168 MET cc_start: 0.5766 (ptt) cc_final: 0.4515 (ppp) outliers start: 84 outliers final: 43 residues processed: 641 average time/residue: 0.1763 time to fit residues: 170.5822 Evaluate side-chains 600 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 552 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 726 ARG Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1082 ILE Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain B residue 1211 SER Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1326 VAL Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 173 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 269 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 194 optimal weight: 0.0570 chunk 255 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS A 370 HIS A 620 GLN A 780 ASN B 753 ASN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 313 GLN D 398 ASN D 400 ASN D 432 ASN E 20 GLN E 83 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.100122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080068 restraints weight = 65218.290| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.77 r_work: 0.3261 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25939 Z= 0.163 Angle : 0.670 13.440 35069 Z= 0.341 Chirality : 0.043 0.209 3900 Planarity : 0.005 0.080 4484 Dihedral : 8.631 176.009 3455 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 3.55 % Allowed : 14.59 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.02 (0.15), residues: 3118 helix: 1.09 (0.15), residues: 1344 sheet: -0.00 (0.25), residues: 408 loop : -1.04 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 174 TYR 0.022 0.002 TYR A 725 PHE 0.022 0.002 PHE B 170 TRP 0.030 0.002 TRP C 300 HIS 0.016 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (25934) covalent geometry : angle 0.66388 / 0.34 (35063) hydrogen bonds : bond 0.05846 / 3.71 ( 1128) hydrogen bonds : angle 4.32722 / 2.92 ( 3210) metal coordination : bond 0.00821 / 0.41 ( 4) metal coordination : angle 6.73056 / 4.08 ( 6) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 567 time to evaluate : 1.178 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 75 ARG cc_start: 0.4618 (ttm-80) cc_final: 0.4232 (ttm170) REVERT: A 203 MET cc_start: 0.7746 (mmm) cc_final: 0.7069 (ttm) REVERT: A 361 GLU cc_start: 0.6679 (pm20) cc_final: 0.6319 (pm20) REVERT: A 498 ILE cc_start: 0.8819 (tt) cc_final: 0.8503 (tt) REVERT: A 546 GLN cc_start: 0.7737 (mm-40) cc_final: 0.6895 (tm-30) REVERT: A 550 ASP cc_start: 0.7827 (m-30) cc_final: 0.7285 (m-30) REVERT: A 572 ARG cc_start: 0.7884 (tpm170) cc_final: 0.7613 (tpm170) REVERT: A 576 LEU cc_start: 0.8386 (mt) cc_final: 0.7932 (mt) REVERT: A 626 GLU cc_start: 0.7142 (pm20) cc_final: 0.6911 (pm20) REVERT: A 654 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7823 (ptm) REVERT: A 686 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7859 (tm-30) REVERT: A 735 ILE cc_start: 0.8222 (mm) cc_final: 0.8012 (mm) REVERT: A 750 LEU cc_start: 0.8538 (mp) cc_final: 0.8273 (mt) REVERT: A 756 LYS cc_start: 0.8256 (mttt) cc_final: 0.7975 (mttm) REVERT: A 762 PHE cc_start: 0.8443 (m-80) cc_final: 0.8202 (m-80) REVERT: A 800 LYS cc_start: 0.8833 (tppp) cc_final: 0.8602 (tppt) REVERT: B 108 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7316 (t70) REVERT: B 163 LEU cc_start: 0.8077 (mp) cc_final: 0.7667 (mt) REVERT: B 239 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7648 (mtt) REVERT: B 275 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7105 (mm-30) REVERT: B 731 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7546 (t80) REVERT: B 784 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6531 (mm-30) REVERT: B 1011 CYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6939 (p) REVERT: B 1213 TRP cc_start: 0.6088 (OUTLIER) cc_final: 0.5062 (p90) REVERT: B 1347 THR cc_start: 0.8590 (m) cc_final: 0.8353 (p) REVERT: C 25 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6986 (mm) REVERT: C 121 ASP cc_start: 0.8534 (m-30) cc_final: 0.8228 (m-30) REVERT: C 172 MET cc_start: 0.7854 (pmm) cc_final: 0.7586 (pmm) REVERT: C 260 GLN cc_start: 0.7511 (tp40) cc_final: 0.7245 (tm-30) REVERT: C 340 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7966 (tm-30) REVERT: C 352 TYR cc_start: 0.7022 (p90) cc_final: 0.6458 (p90) REVERT: C 372 PHE cc_start: 0.8871 (t80) cc_final: 0.8589 (t80) REVERT: C 429 LEU cc_start: 0.8052 (pp) cc_final: 0.7532 (pp) REVERT: C 436 LEU cc_start: 0.8978 (mm) cc_final: 0.8772 (mm) REVERT: D 62 LEU cc_start: 0.7629 (mm) cc_final: 0.7410 (mt) REVERT: D 107 ASP cc_start: 0.8126 (t0) cc_final: 0.7773 (t0) REVERT: D 323 SER cc_start: 0.8725 (t) cc_final: 0.8401 (p) REVERT: D 364 LEU cc_start: 0.7452 (mt) cc_final: 0.6827 (pp) REVERT: E 90 TYR cc_start: 0.8361 (p90) cc_final: 0.7908 (p90) REVERT: F 137 LEU cc_start: 0.7713 (mt) cc_final: 0.7236 (tp) REVERT: F 160 MET cc_start: 0.6775 (mmm) cc_final: 0.5334 (mpp) REVERT: F 168 MET cc_start: 0.5965 (ptt) cc_final: 0.4702 (ppp) outliers start: 99 outliers final: 59 residues processed: 622 average time/residue: 0.1839 time to fit residues: 172.9002 Evaluate side-chains 600 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 534 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 731 TYR Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1082 ILE Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain B residue 1211 SER Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1326 VAL Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 180 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 68 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 GLN A 370 HIS A 620 GLN ** B 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 GLN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 HIS ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN C 363 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN E 83 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.097172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.077141 restraints weight = 64861.366| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.80 r_work: 0.3197 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 56 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 25939 Z= 0.235 Angle : 0.741 14.073 35069 Z= 0.380 Chirality : 0.047 0.202 3900 Planarity : 0.005 0.061 4484 Dihedral : 8.808 176.100 3455 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.87 % Favored : 95.03 % Rotamer: Outliers : 3.87 % Allowed : 15.45 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: 0.03 (0.15), residues: 3118 helix: 1.19 (0.14), residues: 1336 sheet: -0.00 (0.25), residues: 412 loop : -1.15 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 296 TYR 0.023 0.002 TYR C 394 PHE 0.026 0.002 PHE B 259 TRP 0.027 0.002 TRP C 300 HIS 0.018 0.002 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.23 (25934) covalent geometry : angle 0.73717 / 0.38 (35063) hydrogen bonds : bond 0.06736 / 4.26 ( 1128) hydrogen bonds : angle 4.42770 / 2.99 ( 3210) metal coordination : bond 0.00714 / 0.36 ( 4) metal coordination : angle 5.63393 / 3.31 ( 6) Misc. bond : bond 0.00000 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 543 time to evaluate : 1.222 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: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.4723 (ttm-80) cc_final: 0.4204 (ttm170) REVERT: A 158 LYS cc_start: 0.6703 (mtpt) cc_final: 0.6395 (mtpt) REVERT: A 203 MET cc_start: 0.7754 (mmm) cc_final: 0.7067 (ttm) REVERT: A 361 GLU cc_start: 0.6776 (pm20) cc_final: 0.6525 (pm20) REVERT: A 498 ILE cc_start: 0.8814 (tt) cc_final: 0.8550 (tt) REVERT: A 508 GLN cc_start: 0.8302 (tp40) cc_final: 0.8058 (tm-30) REVERT: A 521 MET cc_start: 0.8191 (tpp) cc_final: 0.7766 (tpt) REVERT: A 556 MET cc_start: 0.8409 (mmm) cc_final: 0.8166 (tpt) REVERT: A 572 ARG cc_start: 0.7915 (tpm170) cc_final: 0.7622 (tpm170) REVERT: A 576 LEU cc_start: 0.8439 (mt) cc_final: 0.7978 (mt) REVERT: A 583 MET cc_start: 0.7218 (ppp) cc_final: 0.6749 (ppp) REVERT: A 616 LEU cc_start: 0.8975 (pp) cc_final: 0.8712 (pp) REVERT: A 668 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8104 (p) REVERT: A 686 GLN cc_start: 0.8248 (tm-30) cc_final: 0.8039 (tm-30) REVERT: A 750 LEU cc_start: 0.8557 (mp) cc_final: 0.8335 (mt) REVERT: A 756 LYS cc_start: 0.8347 (mttt) cc_final: 0.8004 (mttm) REVERT: A 762 PHE cc_start: 0.8404 (m-80) cc_final: 0.7761 (m-80) REVERT: A 800 LYS cc_start: 0.8877 (tppp) cc_final: 0.8616 (tppt) REVERT: B 275 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7265 (mm-30) REVERT: B 538 GLN cc_start: 0.8743 (tt0) cc_final: 0.8490 (mt0) REVERT: B 726 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7295 (tpt170) REVERT: B 771 LEU cc_start: 0.7863 (tp) cc_final: 0.7435 (mp) REVERT: B 784 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6556 (mm-30) REVERT: B 989 LEU cc_start: 0.5231 (OUTLIER) cc_final: 0.4965 (tt) REVERT: B 1095 ASP cc_start: 0.7353 (m-30) cc_final: 0.7122 (m-30) REVERT: B 1104 PHE cc_start: 0.6207 (OUTLIER) cc_final: 0.5796 (t80) REVERT: B 1347 THR cc_start: 0.8626 (m) cc_final: 0.8323 (p) REVERT: C 25 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6980 (mm) REVERT: C 121 ASP cc_start: 0.8540 (m-30) cc_final: 0.8211 (m-30) REVERT: C 126 MET cc_start: 0.8081 (ttm) cc_final: 0.7858 (ttp) REVERT: C 260 GLN cc_start: 0.7592 (tp40) cc_final: 0.7285 (tm-30) REVERT: C 352 TYR cc_start: 0.7221 (p90) cc_final: 0.6782 (p90) REVERT: C 372 PHE cc_start: 0.8897 (t80) cc_final: 0.8597 (t80) REVERT: D 62 LEU cc_start: 0.7827 (mm) cc_final: 0.7584 (mt) REVERT: D 107 ASP cc_start: 0.8118 (t0) cc_final: 0.7808 (t0) REVERT: D 221 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6853 (mm-30) REVERT: D 323 SER cc_start: 0.8969 (t) cc_final: 0.8461 (p) REVERT: D 364 LEU cc_start: 0.7680 (mt) cc_final: 0.7052 (pp) REVERT: D 427 TYR cc_start: 0.8173 (t80) cc_final: 0.7734 (t80) REVERT: D 440 HIS cc_start: 0.8489 (m-70) cc_final: 0.8156 (m-70) REVERT: D 463 MET cc_start: 0.1235 (OUTLIER) cc_final: -0.0827 (mtm) REVERT: E 59 THR cc_start: 0.7888 (t) cc_final: 0.7688 (t) REVERT: E 90 TYR cc_start: 0.8399 (p90) cc_final: 0.8004 (p90) REVERT: F 88 MET cc_start: 0.7149 (tpt) cc_final: 0.6873 (tpt) REVERT: F 137 LEU cc_start: 0.7874 (mt) cc_final: 0.7373 (tp) REVERT: F 140 LYS cc_start: 0.7896 (mmtm) cc_final: 0.7657 (mmtt) REVERT: F 160 MET cc_start: 0.6954 (mmm) cc_final: 0.5008 (mmt) REVERT: F 168 MET cc_start: 0.5925 (ptt) cc_final: 0.4771 (ppp) outliers start: 108 outliers final: 75 residues processed: 608 average time/residue: 0.2017 time to fit residues: 184.1465 Evaluate side-chains 604 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 523 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 726 ARG Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1082 ILE Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1223 THR Chi-restraints excluded: chain B residue 1326 VAL Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 180 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 252 optimal weight: 1.9990 chunk 174 optimal weight: 0.0980 chunk 219 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 95 optimal weight: 0.0030 chunk 124 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 229 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 GLN A 370 HIS A 620 GLN A 759 HIS A 860 GLN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 398 ASN E 83 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.098996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079092 restraints weight = 64843.903| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.81 r_work: 0.3242 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 56 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25939 Z= 0.138 Angle : 0.653 12.938 35069 Z= 0.333 Chirality : 0.042 0.187 3900 Planarity : 0.004 0.063 4484 Dihedral : 8.633 175.265 3455 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.01 % Favored : 95.89 % Rotamer: Outliers : 3.48 % Allowed : 16.56 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.26 (0.15), residues: 3118 helix: 1.47 (0.15), residues: 1345 sheet: -0.04 (0.25), residues: 404 loop : -1.09 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 114 TYR 0.022 0.001 TYR C 338 PHE 0.022 0.002 PHE B 272 TRP 0.020 0.001 TRP B1020 HIS 0.015 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (25934) covalent geometry : angle 0.65117 / 0.33 (35063) hydrogen bonds : bond 0.05417 / 3.44 ( 1128) hydrogen bonds : angle 4.18053 / 2.83 ( 3210) metal coordination : bond 0.00503 / 0.25 ( 4) metal coordination : angle 4.09065 / 2.38 ( 6) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 541 time to evaluate : 1.033 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 11 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7952 (m-10) REVERT: A 75 ARG cc_start: 0.4456 (ttm-80) cc_final: 0.4118 (ttp-170) REVERT: A 203 MET cc_start: 0.7698 (mmm) cc_final: 0.7011 (ttm) REVERT: A 361 GLU cc_start: 0.6631 (pm20) cc_final: 0.6278 (pm20) REVERT: A 498 ILE cc_start: 0.8819 (tt) cc_final: 0.8541 (tt) REVERT: A 521 MET cc_start: 0.8174 (tpp) cc_final: 0.7585 (tpt) REVERT: A 556 MET cc_start: 0.8390 (mmm) cc_final: 0.8115 (tpt) REVERT: A 572 ARG cc_start: 0.7893 (tpm170) cc_final: 0.7599 (tpm170) REVERT: A 576 LEU cc_start: 0.8425 (mt) cc_final: 0.7976 (mt) REVERT: A 583 MET cc_start: 0.7143 (ppp) cc_final: 0.6756 (ppp) REVERT: A 616 LEU cc_start: 0.8958 (pp) cc_final: 0.8728 (pp) REVERT: A 668 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8137 (p) REVERT: A 682 MET cc_start: 0.8050 (tpp) cc_final: 0.7752 (ttt) REVERT: A 686 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7811 (tm-30) REVERT: A 750 LEU cc_start: 0.8551 (mp) cc_final: 0.8318 (mt) REVERT: A 756 LYS cc_start: 0.8311 (mttt) cc_final: 0.7984 (mttm) REVERT: A 762 PHE cc_start: 0.8348 (m-80) cc_final: 0.7812 (m-80) REVERT: A 777 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.6344 (ptt) REVERT: A 800 LYS cc_start: 0.8832 (tppp) cc_final: 0.8574 (tppt) REVERT: B 36 ARG cc_start: 0.7616 (ttp-110) cc_final: 0.7336 (ttp-110) REVERT: B 100 MET cc_start: 0.8085 (mtt) cc_final: 0.7835 (mtp) REVERT: B 275 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7090 (mm-30) REVERT: B 726 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7166 (tpt170) REVERT: B 771 LEU cc_start: 0.7894 (tp) cc_final: 0.7468 (mp) REVERT: B 1095 ASP cc_start: 0.7352 (m-30) cc_final: 0.7148 (m-30) REVERT: B 1098 VAL cc_start: 0.7285 (p) cc_final: 0.6956 (t) REVERT: B 1104 PHE cc_start: 0.6177 (OUTLIER) cc_final: 0.5731 (t80) REVERT: C 25 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6938 (mm) REVERT: C 121 ASP cc_start: 0.8526 (m-30) cc_final: 0.8205 (m-30) REVERT: C 126 MET cc_start: 0.8127 (ttm) cc_final: 0.7921 (ttm) REVERT: C 260 GLN cc_start: 0.7588 (tp40) cc_final: 0.7328 (tm-30) REVERT: C 338 TYR cc_start: 0.8116 (p90) cc_final: 0.7823 (p90) REVERT: C 352 TYR cc_start: 0.7182 (p90) cc_final: 0.6817 (p90) REVERT: C 372 PHE cc_start: 0.8892 (t80) cc_final: 0.8600 (t80) REVERT: D 62 LEU cc_start: 0.7884 (mm) cc_final: 0.7654 (mt) REVERT: D 107 ASP cc_start: 0.8106 (t0) cc_final: 0.7793 (t0) REVERT: D 139 LYS cc_start: 0.7894 (ptmt) cc_final: 0.7678 (mtmt) REVERT: D 194 PHE cc_start: 0.7788 (m-10) cc_final: 0.7493 (p90) REVERT: D 323 SER cc_start: 0.8950 (t) cc_final: 0.8492 (p) REVERT: D 364 LEU cc_start: 0.7587 (mt) cc_final: 0.6997 (pp) REVERT: D 369 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7675 (t-90) REVERT: D 427 TYR cc_start: 0.8168 (t80) cc_final: 0.7751 (t80) REVERT: E 39 ARG cc_start: 0.7980 (ttm170) cc_final: 0.7651 (tpp80) REVERT: E 90 TYR cc_start: 0.8348 (p90) cc_final: 0.8047 (p90) REVERT: F 88 MET cc_start: 0.6974 (tpt) cc_final: 0.6597 (tpt) REVERT: F 137 LEU cc_start: 0.7914 (mt) cc_final: 0.7437 (tt) REVERT: F 160 MET cc_start: 0.6897 (mmm) cc_final: 0.4958 (mmt) REVERT: F 168 MET cc_start: 0.5923 (ptt) cc_final: 0.4850 (ppp) outliers start: 97 outliers final: 64 residues processed: 596 average time/residue: 0.2005 time to fit residues: 179.9091 Evaluate side-chains 589 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 518 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 726 ARG Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 1081 LYS Chi-restraints excluded: chain B residue 1082 ILE Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1211 SER Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1326 VAL Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 369 HIS Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 157 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 54 optimal weight: 0.8980 chunk 260 optimal weight: 0.8980 chunk 301 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 62 optimal weight: 0.0470 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 HIS A 620 GLN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 GLN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.098530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.078695 restraints weight = 65186.443| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.79 r_work: 0.3235 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25939 Z= 0.149 Angle : 0.663 13.210 35069 Z= 0.338 Chirality : 0.043 0.185 3900 Planarity : 0.005 0.062 4484 Dihedral : 8.498 174.879 3455 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.51 % Rotamer: Outliers : 3.44 % Allowed : 16.99 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.33 (0.15), residues: 3118 helix: 1.56 (0.15), residues: 1346 sheet: 0.02 (0.25), residues: 405 loop : -1.10 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 81 TYR 0.021 0.001 TYR A 725 PHE 0.028 0.002 PHE B 272 TRP 0.029 0.002 TRP C 300 HIS 0.009 0.001 HIS B1181 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (25934) covalent geometry : angle 0.66108 / 0.34 (35063) hydrogen bonds : bond 0.05473 / 3.47 ( 1128) hydrogen bonds : angle 4.13947 / 2.81 ( 3210) metal coordination : bond 0.00403 / 0.20 ( 4) metal coordination : angle 3.46236 / 1.97 ( 6) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 545 time to evaluate : 1.071 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: symmetry clash REVERT: A 11 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7900 (m-10) REVERT: A 43 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8487 (tpp) REVERT: A 75 ARG cc_start: 0.4447 (ttm-80) cc_final: 0.4133 (ttm170) REVERT: A 203 MET cc_start: 0.7678 (mmm) cc_final: 0.6944 (ttm) REVERT: A 361 GLU cc_start: 0.6551 (pm20) cc_final: 0.6312 (pm20) REVERT: A 498 ILE cc_start: 0.8829 (tt) cc_final: 0.8544 (tt) REVERT: A 521 MET cc_start: 0.8192 (tpp) cc_final: 0.7643 (tpt) REVERT: A 556 MET cc_start: 0.8373 (mmm) cc_final: 0.8137 (tpt) REVERT: A 576 LEU cc_start: 0.8424 (mt) cc_final: 0.7960 (mt) REVERT: A 583 MET cc_start: 0.7195 (ppp) cc_final: 0.6967 (ppp) REVERT: A 616 LEU cc_start: 0.8965 (pp) cc_final: 0.8727 (pp) REVERT: A 661 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8030 (mt-10) REVERT: A 668 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 682 MET cc_start: 0.8052 (tpp) cc_final: 0.7744 (ttt) REVERT: A 686 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7768 (tm-30) REVERT: A 750 LEU cc_start: 0.8561 (mp) cc_final: 0.8328 (mt) REVERT: A 756 LYS cc_start: 0.8314 (mttt) cc_final: 0.7978 (mttm) REVERT: A 762 PHE cc_start: 0.8295 (m-80) cc_final: 0.7811 (m-80) REVERT: A 777 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6362 (ptt) REVERT: A 800 LYS cc_start: 0.8843 (tppp) cc_final: 0.8576 (tppt) REVERT: B 100 MET cc_start: 0.8088 (mtt) cc_final: 0.7830 (mtp) REVERT: B 275 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7136 (mm-30) REVERT: B 726 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7192 (tpt170) REVERT: B 771 LEU cc_start: 0.7889 (tp) cc_final: 0.7473 (mp) REVERT: B 784 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6474 (mm-30) REVERT: B 1095 ASP cc_start: 0.7324 (m-30) cc_final: 0.7103 (m-30) REVERT: B 1098 VAL cc_start: 0.7305 (p) cc_final: 0.6982 (t) REVERT: B 1104 PHE cc_start: 0.6157 (OUTLIER) cc_final: 0.5717 (t80) REVERT: C 25 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6987 (mm) REVERT: C 121 ASP cc_start: 0.8527 (m-30) cc_final: 0.8214 (m-30) REVERT: C 126 MET cc_start: 0.8141 (ttm) cc_final: 0.7892 (ttp) REVERT: C 260 GLN cc_start: 0.7595 (tp40) cc_final: 0.7387 (tm-30) REVERT: C 338 TYR cc_start: 0.8164 (p90) cc_final: 0.7811 (p90) REVERT: C 352 TYR cc_start: 0.7187 (p90) cc_final: 0.6886 (p90) REVERT: C 372 PHE cc_start: 0.8856 (t80) cc_final: 0.8606 (t80) REVERT: D 62 LEU cc_start: 0.7942 (mm) cc_final: 0.7697 (mt) REVERT: D 107 ASP cc_start: 0.8138 (t0) cc_final: 0.7859 (t0) REVERT: D 132 LYS cc_start: 0.7416 (pptt) cc_final: 0.7212 (pptt) REVERT: D 364 LEU cc_start: 0.7670 (mt) cc_final: 0.7061 (pp) REVERT: D 369 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7675 (t-90) REVERT: D 427 TYR cc_start: 0.8140 (t80) cc_final: 0.7755 (t80) REVERT: E 28 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7254 (mm-30) REVERT: E 39 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7537 (tpp80) REVERT: E 90 TYR cc_start: 0.8331 (p90) cc_final: 0.8081 (p90) REVERT: E 159 PHE cc_start: 0.8125 (t80) cc_final: 0.7845 (t80) REVERT: F 88 MET cc_start: 0.6903 (tpt) cc_final: 0.6561 (tpt) REVERT: F 137 LEU cc_start: 0.7898 (mt) cc_final: 0.7434 (tt) REVERT: F 158 LEU cc_start: 0.6290 (mm) cc_final: 0.5765 (tt) REVERT: F 168 MET cc_start: 0.5809 (ptt) cc_final: 0.4823 (ppp) outliers start: 96 outliers final: 68 residues processed: 606 average time/residue: 0.2057 time to fit residues: 187.1754 Evaluate side-chains 607 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 531 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 726 ARG Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 971 GLU Chi-restraints excluded: chain B residue 1081 LYS Chi-restraints excluded: chain B residue 1082 ILE Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1211 SER Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1326 VAL Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 369 HIS Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 173 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 86 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 113 optimal weight: 0.0470 chunk 245 optimal weight: 3.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 HIS A 620 GLN A 860 GLN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.095788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.076088 restraints weight = 64546.786| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.69 r_work: 0.3181 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 25939 Z= 0.262 Angle : 0.783 13.389 35069 Z= 0.400 Chirality : 0.047 0.198 3900 Planarity : 0.005 0.066 4484 Dihedral : 8.727 174.766 3455 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.39 % Favored : 94.52 % Rotamer: Outliers : 3.80 % Allowed : 17.53 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: 0.01 (0.15), residues: 3118 helix: 1.30 (0.14), residues: 1347 sheet: -0.15 (0.24), residues: 428 loop : -1.29 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 110 TYR 0.062 0.002 TYR A 58 PHE 0.037 0.003 PHE C 379 TRP 0.030 0.003 TRP C 300 HIS 0.012 0.002 HIS B1243 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.26 (25934) covalent geometry : angle 0.78026 / 0.40 (35063) hydrogen bonds : bond 0.06841 / 4.31 ( 1128) hydrogen bonds : angle 4.40025 / 2.99 ( 3210) metal coordination : bond 0.00631 / 0.31 ( 4) metal coordination : angle 4.62494 / 2.57 ( 6) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 537 time to evaluate : 1.032 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: symmetry clash revert: symmetry clash REVERT: A 11 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7887 (m-10) REVERT: A 75 ARG cc_start: 0.4546 (ttm-80) cc_final: 0.4218 (ttp-170) REVERT: A 203 MET cc_start: 0.7706 (mmm) cc_final: 0.6919 (ttm) REVERT: A 218 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6687 (tmm) REVERT: A 361 GLU cc_start: 0.6709 (pm20) cc_final: 0.6450 (pm20) REVERT: A 498 ILE cc_start: 0.8802 (tt) cc_final: 0.8527 (tt) REVERT: A 521 MET cc_start: 0.8180 (tpp) cc_final: 0.7606 (tpt) REVERT: A 556 MET cc_start: 0.8379 (mmm) cc_final: 0.7801 (tpt) REVERT: A 572 ARG cc_start: 0.7902 (tpm170) cc_final: 0.7471 (tpt170) REVERT: A 576 LEU cc_start: 0.8474 (mt) cc_final: 0.8154 (mt) REVERT: A 583 MET cc_start: 0.7279 (ppp) cc_final: 0.6971 (ppp) REVERT: A 600 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7718 (mmmt) REVERT: A 616 LEU cc_start: 0.9014 (pp) cc_final: 0.8652 (pp) REVERT: A 661 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8156 (mt-10) REVERT: A 668 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8139 (p) REVERT: A 682 MET cc_start: 0.8020 (tpp) cc_final: 0.7730 (ttt) REVERT: A 750 LEU cc_start: 0.8544 (mp) cc_final: 0.8329 (mt) REVERT: A 756 LYS cc_start: 0.8397 (mttt) cc_final: 0.8054 (mttm) REVERT: A 777 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6495 (ptt) REVERT: A 781 LYS cc_start: 0.6889 (tptt) cc_final: 0.6280 (tptt) REVERT: A 800 LYS cc_start: 0.8892 (tppp) cc_final: 0.8628 (tppt) REVERT: B 36 ARG cc_start: 0.7548 (ttp-110) cc_final: 0.7250 (ttp-110) REVERT: B 275 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7246 (mm-30) REVERT: B 726 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7314 (tpt170) REVERT: B 771 LEU cc_start: 0.7841 (tp) cc_final: 0.7497 (mp) REVERT: B 784 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6446 (mm-30) REVERT: B 1028 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8543 (mppt) REVERT: B 1095 ASP cc_start: 0.7416 (m-30) cc_final: 0.7189 (m-30) REVERT: B 1098 VAL cc_start: 0.7438 (p) cc_final: 0.7140 (t) REVERT: B 1104 PHE cc_start: 0.6199 (OUTLIER) cc_final: 0.5553 (t80) REVERT: C 25 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6899 (mm) REVERT: C 121 ASP cc_start: 0.8551 (m-30) cc_final: 0.8233 (m-30) REVERT: C 126 MET cc_start: 0.8126 (ttm) cc_final: 0.7883 (ttp) REVERT: C 260 GLN cc_start: 0.7627 (tp40) cc_final: 0.7338 (tm-30) REVERT: C 338 TYR cc_start: 0.8183 (p90) cc_final: 0.7747 (p90) REVERT: C 352 TYR cc_start: 0.7346 (p90) cc_final: 0.7106 (p90) REVERT: C 363 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7698 (t0) REVERT: C 372 PHE cc_start: 0.8892 (t80) cc_final: 0.8617 (t80) REVERT: D 62 LEU cc_start: 0.8059 (mm) cc_final: 0.7790 (mt) REVERT: D 107 ASP cc_start: 0.8126 (t0) cc_final: 0.7890 (t0) REVERT: D 132 LYS cc_start: 0.7483 (pptt) cc_final: 0.7224 (pptt) REVERT: D 362 VAL cc_start: 0.6642 (OUTLIER) cc_final: 0.6432 (t) REVERT: D 364 LEU cc_start: 0.7731 (mt) cc_final: 0.7105 (pp) REVERT: D 369 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7705 (t-90) REVERT: D 427 TYR cc_start: 0.8223 (t80) cc_final: 0.7875 (t80) REVERT: D 439 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: D 440 HIS cc_start: 0.8520 (m-70) cc_final: 0.8162 (m-70) REVERT: E 90 TYR cc_start: 0.8377 (p90) cc_final: 0.8123 (p90) REVERT: E 110 ARG cc_start: 0.7381 (mmm160) cc_final: 0.7061 (mmm160) REVERT: E 159 PHE cc_start: 0.8191 (t80) cc_final: 0.7954 (t80) REVERT: F 88 MET cc_start: 0.6849 (tpt) cc_final: 0.6537 (tpt) REVERT: F 137 LEU cc_start: 0.7895 (mt) cc_final: 0.7419 (tp) REVERT: F 158 LEU cc_start: 0.6314 (mm) cc_final: 0.5811 (tt) REVERT: F 168 MET cc_start: 0.6023 (ptt) cc_final: 0.5036 (ppp) outliers start: 106 outliers final: 84 residues processed: 601 average time/residue: 0.1943 time to fit residues: 176.1514 Evaluate side-chains 623 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 528 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 726 ARG Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 971 GLU Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1081 LYS Chi-restraints excluded: chain B residue 1082 ILE Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1170 MET Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1211 SER Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1326 VAL Chi-restraints excluded: chain B residue 1333 THR Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 369 HIS Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 36 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 36 optimal weight: 0.6980 chunk 257 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 129 optimal weight: 0.2980 chunk 54 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 184 GLN A 370 HIS A 620 GLN B 798 ASN ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.097671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.078022 restraints weight = 64912.267| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.77 r_work: 0.3219 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25939 Z= 0.154 Angle : 0.700 13.498 35069 Z= 0.355 Chirality : 0.043 0.195 3900 Planarity : 0.005 0.063 4484 Dihedral : 8.536 173.450 3455 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.09 % Rotamer: Outliers : 3.44 % Allowed : 18.57 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.26 (0.15), residues: 3118 helix: 1.56 (0.15), residues: 1348 sheet: -0.04 (0.25), residues: 403 loop : -1.19 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 114 TYR 0.051 0.002 TYR A 58 PHE 0.049 0.002 PHE C 379 TRP 0.031 0.002 TRP C 300 HIS 0.008 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (25934) covalent geometry : angle 0.69826 / 0.36 (35063) hydrogen bonds : bond 0.05543 / 3.51 ( 1128) hydrogen bonds : angle 4.16703 / 2.83 ( 3210) metal coordination : bond 0.00424 / 0.21 ( 4) metal coordination : angle 3.28937 / 1.84 ( 6) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 536 time to evaluate : 0.984 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: symmetry clash revert: symmetry clash REVERT: A 11 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7876 (m-10) REVERT: A 158 LYS cc_start: 0.6742 (mtpt) cc_final: 0.6528 (mtpt) REVERT: A 203 MET cc_start: 0.7685 (mmm) cc_final: 0.6925 (ttm) REVERT: A 361 GLU cc_start: 0.6598 (pm20) cc_final: 0.6339 (pm20) REVERT: A 498 ILE cc_start: 0.8812 (tt) cc_final: 0.8528 (tt) REVERT: A 521 MET cc_start: 0.8213 (tpp) cc_final: 0.7674 (tpt) REVERT: A 556 MET cc_start: 0.8399 (mmm) cc_final: 0.7795 (tpt) REVERT: A 572 ARG cc_start: 0.7875 (tpm170) cc_final: 0.7460 (tpt170) REVERT: A 576 LEU cc_start: 0.8494 (mt) cc_final: 0.8130 (mt) REVERT: A 583 MET cc_start: 0.7227 (ppp) cc_final: 0.6898 (ppp) REVERT: A 616 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8639 (pp) REVERT: A 661 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8082 (mt-10) REVERT: A 668 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 682 MET cc_start: 0.8055 (tpp) cc_final: 0.7773 (ttt) REVERT: A 686 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 750 LEU cc_start: 0.8568 (mp) cc_final: 0.8342 (mt) REVERT: A 756 LYS cc_start: 0.8356 (mttt) cc_final: 0.8005 (mttm) REVERT: A 777 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.6258 (ptt) REVERT: A 781 LYS cc_start: 0.6774 (tptt) cc_final: 0.6148 (tptt) REVERT: A 800 LYS cc_start: 0.8852 (tppp) cc_final: 0.8592 (tppt) REVERT: B 36 ARG cc_start: 0.7596 (ttp-110) cc_final: 0.7322 (ttp-110) REVERT: B 275 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7226 (mm-30) REVERT: B 726 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7175 (tpt170) REVERT: B 771 LEU cc_start: 0.7894 (tp) cc_final: 0.7495 (mp) REVERT: B 784 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6422 (mm-30) REVERT: B 816 LYS cc_start: 0.8380 (mmtm) cc_final: 0.8166 (mmtm) REVERT: B 1095 ASP cc_start: 0.7362 (m-30) cc_final: 0.7157 (m-30) REVERT: B 1098 VAL cc_start: 0.7247 (p) cc_final: 0.6922 (t) REVERT: B 1104 PHE cc_start: 0.6175 (OUTLIER) cc_final: 0.5580 (t80) REVERT: C 25 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6964 (mm) REVERT: C 26 LYS cc_start: 0.8246 (tppt) cc_final: 0.7928 (tppt) REVERT: C 37 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8860 (p) REVERT: C 80 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6593 (ptp-170) REVERT: C 121 ASP cc_start: 0.8527 (m-30) cc_final: 0.8232 (m-30) REVERT: C 126 MET cc_start: 0.8151 (ttm) cc_final: 0.7918 (ttp) REVERT: C 338 TYR cc_start: 0.8130 (p90) cc_final: 0.7697 (p90) REVERT: C 352 TYR cc_start: 0.7244 (p90) cc_final: 0.7027 (p90) REVERT: C 372 PHE cc_start: 0.8889 (t80) cc_final: 0.8609 (t80) REVERT: C 436 LEU cc_start: 0.9002 (mm) cc_final: 0.8676 (mt) REVERT: D 62 LEU cc_start: 0.8067 (mm) cc_final: 0.7786 (mt) REVERT: D 107 ASP cc_start: 0.8147 (t0) cc_final: 0.7871 (t0) REVERT: D 116 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7687 (mtmm) REVERT: D 132 LYS cc_start: 0.7491 (pptt) cc_final: 0.7260 (pptt) REVERT: D 362 VAL cc_start: 0.6689 (OUTLIER) cc_final: 0.6468 (t) REVERT: D 364 LEU cc_start: 0.7698 (mt) cc_final: 0.7103 (pp) REVERT: D 369 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.7746 (t-90) REVERT: D 427 TYR cc_start: 0.8201 (t80) cc_final: 0.7746 (t80) REVERT: D 431 LYS cc_start: 0.8528 (tttp) cc_final: 0.8043 (ttpp) REVERT: D 439 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: D 440 HIS cc_start: 0.8543 (m-70) cc_final: 0.8173 (m-70) REVERT: E 39 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7513 (tpp80) REVERT: E 59 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7565 (t) REVERT: E 90 TYR cc_start: 0.8328 (p90) cc_final: 0.8121 (p90) REVERT: E 159 PHE cc_start: 0.8212 (t80) cc_final: 0.7935 (t80) REVERT: F 137 LEU cc_start: 0.7919 (mt) cc_final: 0.7456 (tp) REVERT: F 158 LEU cc_start: 0.6342 (mm) cc_final: 0.5859 (tt) REVERT: F 168 MET cc_start: 0.5893 (ptt) cc_final: 0.5038 (ppp) outliers start: 96 outliers final: 69 residues processed: 592 average time/residue: 0.2004 time to fit residues: 178.3417 Evaluate side-chains 607 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 525 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 726 ARG Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 971 GLU Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1082 ILE Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1211 SER Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1245 ILE Chi-restraints excluded: chain B residue 1326 VAL Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 369 HIS Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 167 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 266 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 101 optimal weight: 0.0170 chunk 88 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 200 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 184 GLN A 370 HIS ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN A 860 GLN ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN E 83 HIS ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.098137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.078655 restraints weight = 65246.019| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.73 r_work: 0.3238 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 76 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 69 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25939 Z= 0.140 Angle : 0.695 13.527 35069 Z= 0.352 Chirality : 0.043 0.197 3900 Planarity : 0.005 0.062 4484 Dihedral : 8.408 172.635 3455 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.06 % Rotamer: Outliers : 3.19 % Allowed : 18.89 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.34 (0.16), residues: 3118 helix: 1.63 (0.15), residues: 1360 sheet: -0.06 (0.25), residues: 411 loop : -1.16 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 293 TYR 0.045 0.002 TYR A 58 PHE 0.067 0.002 PHE C 379 TRP 0.049 0.002 TRP D 118 HIS 0.015 0.001 HIS B1181 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (25934) covalent geometry : angle 0.69390 / 0.35 (35063) hydrogen bonds : bond 0.05209 / 3.31 ( 1128) hydrogen bonds : angle 4.10019 / 2.78 ( 3210) metal coordination : bond 0.00426 / 0.21 ( 4) metal coordination : angle 3.32652 / 1.86 ( 6) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 535 time to evaluate : 1.079 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 11 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7820 (m-10) REVERT: A 158 LYS cc_start: 0.6739 (mtpt) cc_final: 0.6447 (mtpt) REVERT: A 203 MET cc_start: 0.7650 (mmm) cc_final: 0.6885 (ttm) REVERT: A 361 GLU cc_start: 0.6523 (pm20) cc_final: 0.6265 (pm20) REVERT: A 498 ILE cc_start: 0.8795 (tt) cc_final: 0.8513 (tt) REVERT: A 521 MET cc_start: 0.8197 (tpp) cc_final: 0.7667 (tpt) REVERT: A 556 MET cc_start: 0.8397 (mmm) cc_final: 0.7803 (tpt) REVERT: A 583 MET cc_start: 0.7056 (ppp) cc_final: 0.6723 (ppp) REVERT: A 588 VAL cc_start: 0.7824 (OUTLIER) cc_final: 0.7597 (m) REVERT: A 616 LEU cc_start: 0.8969 (pp) cc_final: 0.8640 (pp) REVERT: A 661 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8171 (mt-10) REVERT: A 668 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8171 (p) REVERT: A 682 MET cc_start: 0.8034 (tpp) cc_final: 0.7739 (ttt) REVERT: A 686 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7787 (tm-30) REVERT: A 750 LEU cc_start: 0.8560 (mp) cc_final: 0.8330 (mt) REVERT: A 756 LYS cc_start: 0.8317 (mttt) cc_final: 0.7966 (mttm) REVERT: A 777 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6187 (ptt) REVERT: A 781 LYS cc_start: 0.6770 (tptt) cc_final: 0.6165 (tptt) REVERT: A 800 LYS cc_start: 0.8844 (tppp) cc_final: 0.8573 (tppt) REVERT: B 36 ARG cc_start: 0.7585 (ttp-110) cc_final: 0.7324 (ttp-110) REVERT: B 100 MET cc_start: 0.8045 (mtt) cc_final: 0.7832 (mtp) REVERT: B 275 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7220 (mm-30) REVERT: B 726 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7116 (tpt170) REVERT: B 771 LEU cc_start: 0.7868 (tp) cc_final: 0.7466 (mp) REVERT: B 784 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6408 (mm-30) REVERT: B 816 LYS cc_start: 0.8385 (mmtm) cc_final: 0.8177 (mmtm) REVERT: B 1028 LYS cc_start: 0.8630 (mppt) cc_final: 0.8370 (mppt) REVERT: B 1095 ASP cc_start: 0.7323 (m-30) cc_final: 0.7120 (m-30) REVERT: B 1098 VAL cc_start: 0.7185 (p) cc_final: 0.6871 (t) REVERT: B 1104 PHE cc_start: 0.6124 (OUTLIER) cc_final: 0.5539 (t80) REVERT: C 25 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6923 (mm) REVERT: C 26 LYS cc_start: 0.8262 (tppt) cc_final: 0.7930 (tppt) REVERT: C 80 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6639 (ptp-170) REVERT: C 121 ASP cc_start: 0.8511 (m-30) cc_final: 0.8223 (m-30) REVERT: C 126 MET cc_start: 0.8154 (ttm) cc_final: 0.7911 (ttp) REVERT: C 338 TYR cc_start: 0.8133 (p90) cc_final: 0.7713 (p90) REVERT: C 372 PHE cc_start: 0.8907 (t80) cc_final: 0.8623 (t80) REVERT: C 436 LEU cc_start: 0.9011 (mm) cc_final: 0.8653 (mt) REVERT: D 75 LYS cc_start: 0.7849 (tppt) cc_final: 0.7601 (tppt) REVERT: D 345 LYS cc_start: 0.7084 (tppt) cc_final: 0.6470 (tppt) REVERT: D 427 TYR cc_start: 0.8206 (t80) cc_final: 0.7747 (t80) REVERT: D 431 LYS cc_start: 0.8512 (tttp) cc_final: 0.8032 (ttpp) REVERT: D 440 HIS cc_start: 0.8546 (m-70) cc_final: 0.8175 (m-70) REVERT: E 39 ARG cc_start: 0.7899 (ttm170) cc_final: 0.7505 (tpp80) REVERT: E 59 THR cc_start: 0.7857 (OUTLIER) cc_final: 0.7514 (t) REVERT: E 91 ARG cc_start: 0.8636 (ttm110) cc_final: 0.8395 (ttp-110) REVERT: E 141 ARG cc_start: 0.7202 (ttm-80) cc_final: 0.6997 (ttm-80) REVERT: E 159 PHE cc_start: 0.8176 (t80) cc_final: 0.7888 (t80) REVERT: F 137 LEU cc_start: 0.7892 (mt) cc_final: 0.7441 (tp) REVERT: F 158 LEU cc_start: 0.6293 (mm) cc_final: 0.5824 (tt) outliers start: 89 outliers final: 66 residues processed: 588 average time/residue: 0.2064 time to fit residues: 182.4220 Evaluate side-chains 605 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 530 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 726 ARG Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 1081 LYS Chi-restraints excluded: chain B residue 1082 ILE Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1211 SER Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1245 ILE Chi-restraints excluded: chain B residue 1326 VAL Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 327 TYR Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 253 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 302 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 184 GLN A 370 HIS ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN A 860 GLN ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.097190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.077572 restraints weight = 65000.520| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.77 r_work: 0.3211 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 69 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25939 Z= 0.174 Angle : 0.750 14.852 35069 Z= 0.379 Chirality : 0.044 0.192 3900 Planarity : 0.005 0.062 4484 Dihedral : 8.513 171.762 3455 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.16 % Favored : 94.74 % Rotamer: Outliers : 2.94 % Allowed : 19.53 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.28 (0.15), residues: 3118 helix: 1.58 (0.15), residues: 1360 sheet: -0.02 (0.25), residues: 401 loop : -1.22 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 36 TYR 0.049 0.002 TYR A 58 PHE 0.055 0.002 PHE C 379 TRP 0.077 0.002 TRP D 118 HIS 0.013 0.001 HIS B1181 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (25934) covalent geometry : angle 0.74888 / 0.38 (35063) hydrogen bonds : bond 0.05637 / 3.55 ( 1128) hydrogen bonds : angle 4.16461 / 2.83 ( 3210) metal coordination : bond 0.00439 / 0.22 ( 4) metal coordination : angle 3.65653 / 2.03 ( 6) Misc. bond : bond 0.00012 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 532 time to evaluate : 1.109 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 11 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7836 (m-10) REVERT: A 158 LYS cc_start: 0.6784 (mtpt) cc_final: 0.6541 (mtpt) REVERT: A 203 MET cc_start: 0.7687 (mmm) cc_final: 0.6900 (ttm) REVERT: A 361 GLU cc_start: 0.6582 (pm20) cc_final: 0.6323 (pm20) REVERT: A 498 ILE cc_start: 0.8817 (tt) cc_final: 0.8528 (tt) REVERT: A 521 MET cc_start: 0.8204 (tpp) cc_final: 0.7660 (tpt) REVERT: A 556 MET cc_start: 0.8415 (mmm) cc_final: 0.7817 (tpt) REVERT: A 572 ARG cc_start: 0.8014 (tpt170) cc_final: 0.7552 (tpm170) REVERT: A 576 LEU cc_start: 0.8588 (mt) cc_final: 0.8188 (mt) REVERT: A 583 MET cc_start: 0.7090 (ppp) cc_final: 0.6662 (ppp) REVERT: A 588 VAL cc_start: 0.7936 (OUTLIER) cc_final: 0.7705 (m) REVERT: A 616 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8701 (pp) REVERT: A 661 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8207 (mt-10) REVERT: A 668 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8168 (p) REVERT: A 682 MET cc_start: 0.8066 (tpp) cc_final: 0.7778 (ttt) REVERT: A 686 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7817 (tm-30) REVERT: A 750 LEU cc_start: 0.8572 (mp) cc_final: 0.8342 (mt) REVERT: A 756 LYS cc_start: 0.8356 (mttt) cc_final: 0.7999 (mttm) REVERT: A 777 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.6271 (ptt) REVERT: A 781 LYS cc_start: 0.6825 (tptt) cc_final: 0.5753 (tptp) REVERT: A 800 LYS cc_start: 0.8856 (tppp) cc_final: 0.8594 (tppt) REVERT: B 36 ARG cc_start: 0.7594 (ttp-110) cc_final: 0.7314 (ttp-110) REVERT: B 100 MET cc_start: 0.8062 (mtt) cc_final: 0.7851 (mtp) REVERT: B 275 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7256 (mm-30) REVERT: B 630 PHE cc_start: 0.6235 (m-10) cc_final: 0.5972 (m-10) REVERT: B 726 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7202 (tpt170) REVERT: B 771 LEU cc_start: 0.7880 (tp) cc_final: 0.7479 (mp) REVERT: B 784 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6438 (mm-30) REVERT: B 816 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8206 (mmtm) REVERT: B 1028 LYS cc_start: 0.8693 (mppt) cc_final: 0.8431 (mppt) REVERT: B 1095 ASP cc_start: 0.7409 (m-30) cc_final: 0.7178 (m-30) REVERT: B 1098 VAL cc_start: 0.7261 (p) cc_final: 0.6941 (t) REVERT: B 1104 PHE cc_start: 0.6132 (OUTLIER) cc_final: 0.5508 (t80) REVERT: C 25 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6933 (mm) REVERT: C 26 LYS cc_start: 0.8295 (tppt) cc_final: 0.7982 (tppt) REVERT: C 80 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6650 (ptp-170) REVERT: C 121 ASP cc_start: 0.8535 (m-30) cc_final: 0.8240 (m-30) REVERT: C 126 MET cc_start: 0.8182 (ttm) cc_final: 0.7936 (ttp) REVERT: C 338 TYR cc_start: 0.8162 (p90) cc_final: 0.7956 (p90) REVERT: C 372 PHE cc_start: 0.8935 (t80) cc_final: 0.8662 (t80) REVERT: C 436 LEU cc_start: 0.8991 (mm) cc_final: 0.8678 (mt) REVERT: D 75 LYS cc_start: 0.7849 (tppt) cc_final: 0.7618 (tppt) REVERT: D 345 LYS cc_start: 0.7117 (tppt) cc_final: 0.6704 (tppt) REVERT: D 362 VAL cc_start: 0.6826 (OUTLIER) cc_final: 0.6600 (t) REVERT: D 427 TYR cc_start: 0.8228 (t80) cc_final: 0.7764 (t80) REVERT: D 431 LYS cc_start: 0.8538 (tttp) cc_final: 0.8057 (ttpp) REVERT: D 440 HIS cc_start: 0.8552 (m-70) cc_final: 0.8200 (m-70) REVERT: E 59 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7530 (t) REVERT: E 91 ARG cc_start: 0.8618 (ttm110) cc_final: 0.8398 (ttp-110) REVERT: E 125 ASN cc_start: 0.6797 (m-40) cc_final: 0.6546 (m-40) REVERT: E 141 ARG cc_start: 0.7199 (ttm-80) cc_final: 0.6962 (ttm-80) REVERT: E 159 PHE cc_start: 0.8239 (t80) cc_final: 0.7963 (t80) REVERT: F 137 LEU cc_start: 0.7850 (mt) cc_final: 0.7388 (tp) REVERT: F 158 LEU cc_start: 0.6319 (mm) cc_final: 0.5845 (tt) outliers start: 82 outliers final: 67 residues processed: 581 average time/residue: 0.2074 time to fit residues: 181.1825 Evaluate side-chains 600 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 522 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 32 GLN Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 726 ARG Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 1081 LYS Chi-restraints excluded: chain B residue 1082 ILE Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1104 PHE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1211 SER Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1326 VAL Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 50 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 251 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 GLN ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.097084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.077598 restraints weight = 64968.349| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.71 r_work: 0.3213 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 69 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.175 25939 Z= 0.255 Angle : 0.985 59.111 35069 Z= 0.542 Chirality : 0.045 0.309 3900 Planarity : 0.006 0.208 4484 Dihedral : 8.530 171.740 3455 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.07 % Favored : 94.80 % Rotamer: Outliers : 3.05 % Allowed : 19.64 % Favored : 77.31 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.27 (0.15), residues: 3118 helix: 1.58 (0.15), residues: 1360 sheet: -0.03 (0.25), residues: 401 loop : -1.22 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 293 TYR 0.045 0.002 TYR A 58 PHE 0.024 0.002 PHE C 379 TRP 0.060 0.002 TRP D 118 HIS 0.340 0.004 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.26 (25934) covalent geometry : angle 0.98378 / 0.54 (35063) hydrogen bonds : bond 0.05683 / 3.58 ( 1128) hydrogen bonds : angle 4.18911 / 2.84 ( 3210) metal coordination : bond 0.00417 / 0.21 ( 4) metal coordination : angle 3.66531 / 2.04 ( 6) Misc. bond : bond 0.00017 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7948.67 seconds wall clock time: 136 minutes 43.15 seconds (8203.15 seconds total)