Starting phenix.real_space_refine on Thu Feb 5 02:39:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w77_65719/02_2026/9w77_65719.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w77_65719/02_2026/9w77_65719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w77_65719/02_2026/9w77_65719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w77_65719/02_2026/9w77_65719.map" model { file = "/net/cci-nas-00/data/ceres_data/9w77_65719/02_2026/9w77_65719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w77_65719/02_2026/9w77_65719.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 9076 2.51 5 N 2366 2.21 5 O 2758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14270 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1232 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 5734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5734 Classifications: {'peptide': 698} Link IDs: {'PTRANS': 32, 'TRANS': 665} Chain breaks: 1 Chain: "A" Number of atoms: 5734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5734 Classifications: {'peptide': 698} Link IDs: {'PTRANS': 32, 'TRANS': 665} Chain breaks: 1 Chain: "D" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1224 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.28, per 1000 atoms: 0.23 Number of scatterers: 14270 At special positions: 0 Unit cell: (130.38, 133.56, 122.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2758 8.00 N 2366 7.00 C 9076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 406 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 353 " - pdb=" SG CYS D 406 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-2 " MAN H 4 " - " MAN H 5 " ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 801 " - " ASN A 322 " " NAG A 802 " - " ASN A 329 " " NAG C 801 " - " ASN C 322 " " NAG C 802 " - " ASN C 329 " " NAG E 1 " - " ASN C 53 " " NAG F 1 " - " ASN C 690 " " NAG G 1 " - " ASN C 546 " " NAG H 1 " - " ASN C 38 " " NAG I 1 " - " ASN A 53 " " NAG J 1 " - " ASN A 690 " " NAG K 1 " - " ASN A 546 " " NAG L 1 " - " ASN A 38 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 541.6 milliseconds 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3206 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 16 sheets defined 56.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'B' and resid 312 through 317 removed outlier: 3.559A pdb=" N PHE B 316 " --> pdb=" O PHE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 345 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.520A pdb=" N VAL B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 382 " --> pdb=" O ASP B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 382' Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'C' and resid 20 through 53 removed outlier: 3.721A pdb=" N GLU C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 removed outlier: 3.896A pdb=" N GLN C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 83 No H-bonds generated for 'chain 'C' and resid 82 through 83' Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.896A pdb=" N GLU C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 88 " --> pdb=" O LEU C 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 84 through 88' Processing helix chain 'C' and resid 90 through 103 removed outlier: 3.915A pdb=" N SER C 103 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 157 through 168 Processing helix chain 'C' and resid 172 through 193 Proline residue: C 178 - end of helix removed outlier: 3.652A pdb=" N VAL C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 218 through 248 removed outlier: 3.658A pdb=" N LEU C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 303 through 318 removed outlier: 3.612A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 331 removed outlier: 3.505A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 386 Processing helix chain 'C' and resid 387 through 388 No H-bonds generated for 'chain 'C' and resid 387 through 388' Processing helix chain 'C' and resid 389 through 393 Processing helix chain 'C' and resid 399 through 413 Processing helix chain 'C' and resid 414 through 422 Processing helix chain 'C' and resid 431 through 447 removed outlier: 3.502A pdb=" N GLU C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 466 Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 512 through 533 removed outlier: 3.981A pdb=" N TYR C 516 " --> pdb=" O PHE C 512 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 removed outlier: 3.590A pdb=" N CYS C 542 " --> pdb=" O LEU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 560 removed outlier: 4.067A pdb=" N VAL C 560 " --> pdb=" O GLN C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 588 through 599 Processing helix chain 'C' and resid 636 through 658 Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 696 through 707 Processing helix chain 'C' and resid 707 through 714 removed outlier: 3.515A pdb=" N ILE C 711 " --> pdb=" O SER C 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.757A pdb=" N GLU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 81 Processing helix chain 'A' and resid 90 through 103 removed outlier: 3.935A pdb=" N SER A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix removed outlier: 3.651A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 218 through 249 removed outlier: 3.683A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.593A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.519A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 Processing helix chain 'A' and resid 387 through 388 No H-bonds generated for 'chain 'A' and resid 387 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.837A pdb=" N ASN A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.711A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 3.958A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.590A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.998A pdb=" N VAL A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 636 through 658 Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'A' and resid 707 through 714 removed outlier: 3.534A pdb=" N ILE A 711 " --> pdb=" O SER A 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 317 removed outlier: 3.680A pdb=" N PHE D 316 " --> pdb=" O PHE D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 412 through 417 removed outlier: 3.605A pdb=" N ALA D 417 " --> pdb=" O ARG D 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 350 through 352 removed outlier: 3.866A pdb=" N CYS B 406 " --> pdb=" O LEU B 478 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 426 through 428 Processing sheet with id=AA3, first strand: chain 'B' and resid 446 through 449 Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AA5, first strand: chain 'C' and resid 262 through 263 removed outlier: 5.815A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 347 through 352 removed outlier: 6.178A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 618 through 621 Processing sheet with id=AA8, first strand: chain 'C' and resid 618 through 621 removed outlier: 5.989A pdb=" N ASP C 693 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AB1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.827A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.280A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 618 through 621 Processing sheet with id=AB4, first strand: chain 'A' and resid 618 through 621 removed outlier: 5.968A pdb=" N ASP A 693 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 353 through 354 removed outlier: 3.536A pdb=" N CYS D 406 " --> pdb=" O LEU D 478 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 426 through 428 Processing sheet with id=AB7, first strand: chain 'D' and resid 446 through 449 removed outlier: 3.731A pdb=" N VAL D 449 " --> pdb=" O GLN D 452 " (cutoff:3.500A) 667 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.88 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: 4485 1.34 - 1.46: 3619 1.46 - 1.58: 6432 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 14656 Sorted by residual: bond pdb=" CA SER C 687 " pdb=" CB SER C 687 " ideal model delta sigma weight residual 1.526 1.467 0.059 1.59e-02 3.96e+03 1.37e+01 bond pdb=" N PRO C 688 " pdb=" CD PRO C 688 " ideal model delta sigma weight residual 1.473 1.437 0.036 1.40e-02 5.10e+03 6.65e+00 bond pdb=" N ILE B 442 " pdb=" CA ILE B 442 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.06e+00 bond pdb=" N PRO A 688 " pdb=" CA PRO A 688 " ideal model delta sigma weight residual 1.469 1.441 0.028 1.22e-02 6.72e+03 5.22e+00 bond pdb=" N ASP B 441 " pdb=" CA ASP B 441 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.26e-02 6.30e+03 4.59e+00 ... (remaining 14651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 19646 3.11 - 6.23: 179 6.23 - 9.34: 36 9.34 - 12.45: 1 12.45 - 15.57: 3 Bond angle restraints: 19865 Sorted by residual: angle pdb=" C ASN C 38 " pdb=" N LEU C 39 " pdb=" CA LEU C 39 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C LYS D 398 " pdb=" N LEU D 399 " pdb=" CA LEU D 399 " ideal model delta sigma weight residual 121.27 136.84 -15.57 3.40e+00 8.65e-02 2.10e+01 angle pdb=" CA LYS D 398 " pdb=" CB LYS D 398 " pdb=" CG LYS D 398 " ideal model delta sigma weight residual 114.10 122.88 -8.78 2.00e+00 2.50e-01 1.93e+01 angle pdb=" CA LYS D 330 " pdb=" CB LYS D 330 " pdb=" CG LYS D 330 " ideal model delta sigma weight residual 114.10 122.80 -8.70 2.00e+00 2.50e-01 1.89e+01 angle pdb=" CA ASP B 441 " pdb=" CB ASP B 441 " pdb=" CG ASP B 441 " ideal model delta sigma weight residual 112.60 116.91 -4.31 1.00e+00 1.00e+00 1.85e+01 ... (remaining 19860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 8262 24.93 - 49.86: 626 49.86 - 74.79: 98 74.79 - 99.72: 9 99.72 - 124.65: 2 Dihedral angle restraints: 8997 sinusoidal: 4010 harmonic: 4987 Sorted by residual: dihedral pdb=" CB CYS C 344 " pdb=" SG CYS C 344 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -125.81 39.81 1 1.00e+01 1.00e-02 2.23e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -122.55 36.55 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CA VAL C 298 " pdb=" C VAL C 298 " pdb=" N LYS C 299 " pdb=" CA LYS C 299 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 8994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2038 0.105 - 0.211: 86 0.211 - 0.316: 3 0.316 - 0.421: 1 0.421 - 0.527: 1 Chirality restraints: 2129 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 546 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" C2 MAN H 4 " pdb=" C1 MAN H 4 " pdb=" C3 MAN H 4 " pdb=" O2 MAN H 4 " both_signs ideal model delta sigma weight residual False 2.52 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN C 546 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2126 not shown) Planarity restraints: 2536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 430 " 0.018 2.00e-02 2.50e+03 2.13e-02 1.14e+01 pdb=" CG TRP B 430 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP B 430 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 430 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 430 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 430 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 430 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 430 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 430 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 430 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 39 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C LEU C 39 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU C 39 " 0.021 2.00e-02 2.50e+03 pdb=" N THR C 40 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 430 " -0.018 2.00e-02 2.50e+03 1.97e-02 9.70e+00 pdb=" CG TRP D 430 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP D 430 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 430 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 430 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 430 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 430 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 430 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 430 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 430 " 0.000 2.00e-02 2.50e+03 ... (remaining 2533 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3160 2.78 - 3.31: 12989 3.31 - 3.84: 25268 3.84 - 4.37: 29292 4.37 - 4.90: 50397 Nonbonded interactions: 121106 Sorted by model distance: nonbonded pdb=" O ALA A 36 " pdb=" OG1 THR A 40 " model vdw 2.249 3.040 nonbonded pdb=" O ALA C 36 " pdb=" OG1 THR C 40 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR C 41 " pdb=" O SER D 465 " model vdw 2.267 3.040 nonbonded pdb=" O ASP A 499 " pdb=" OG SER A 502 " model vdw 2.270 3.040 nonbonded pdb=" OE1 GLU B 380 " pdb=" OH TYR B 460 " model vdw 2.277 3.040 ... (remaining 121101 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 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 311 through 354 or resid 369 through 480)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.370 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14691 Z= 0.191 Angle : 0.817 15.567 19959 Z= 0.402 Chirality : 0.048 0.527 2129 Planarity : 0.006 0.076 2524 Dihedral : 16.801 124.652 5767 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 2.38 % Allowed : 21.41 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.19), residues: 1675 helix: 0.18 (0.16), residues: 847 sheet: 0.32 (0.44), residues: 122 loop : -1.16 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 429 TYR 0.023 0.002 TYR A 385 PHE 0.018 0.001 PHE A 369 TRP 0.058 0.002 TRP B 430 HIS 0.007 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00392 (14656) covalent geometry : angle 0.77112 (19865) SS BOND : bond 0.00318 ( 8) SS BOND : angle 0.78093 ( 16) hydrogen bonds : bond 0.13799 ( 659) hydrogen bonds : angle 5.96699 ( 1935) Misc. bond : bond 0.00017 ( 1) link_ALPHA1-2 : bond 0.01440 ( 1) link_ALPHA1-2 : angle 5.26169 ( 3) link_ALPHA1-3 : bond 0.00818 ( 2) link_ALPHA1-3 : angle 1.87112 ( 6) link_ALPHA1-6 : bond 0.01150 ( 1) link_ALPHA1-6 : angle 2.39407 ( 3) link_BETA1-4 : bond 0.01262 ( 10) link_BETA1-4 : angle 3.90064 ( 30) link_NAG-ASN : bond 0.01553 ( 12) link_NAG-ASN : angle 5.03004 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7824 (tm-30) REVERT: B 380 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8421 (mt-10) REVERT: B 413 ARG cc_start: 0.8330 (ptm160) cc_final: 0.8077 (ptm160) REVERT: B 439 GLU cc_start: 0.6856 (tt0) cc_final: 0.6205 (mt-10) REVERT: B 452 GLN cc_start: 0.8350 (pt0) cc_final: 0.7794 (pm20) REVERT: B 459 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.7854 (p0) REVERT: C 35 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: C 98 GLN cc_start: 0.8678 (tt0) cc_final: 0.8209 (mt0) REVERT: C 270 MET cc_start: 0.8858 (tpp) cc_final: 0.8261 (tpp) REVERT: C 347 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8642 (p) REVERT: C 429 ARG cc_start: 0.8234 (tpp-160) cc_final: 0.7706 (mmp80) REVERT: C 678 ARG cc_start: 0.9020 (mtm-85) cc_final: 0.8761 (ttm-80) REVERT: A 63 ASP cc_start: 0.9203 (m-30) cc_final: 0.8956 (m-30) REVERT: A 270 MET cc_start: 0.7592 (ttp) cc_final: 0.7374 (ttm) REVERT: A 325 GLU cc_start: 0.8743 (tt0) cc_final: 0.8330 (tp30) REVERT: A 332 MET cc_start: 0.8929 (ttp) cc_final: 0.8727 (ttt) REVERT: A 406 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8608 (mm-30) REVERT: A 637 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8630 (m-30) REVERT: A 678 ARG cc_start: 0.8987 (mtm-85) cc_final: 0.8740 (tpp-160) REVERT: D 352 GLN cc_start: 0.8594 (tp-100) cc_final: 0.8068 (tm-30) REVERT: D 382 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8537 (pmm-80) REVERT: D 452 GLN cc_start: 0.8549 (pm20) cc_final: 0.8286 (pm20) REVERT: D 458 LYS cc_start: 0.8752 (mttm) cc_final: 0.8493 (mtpt) REVERT: D 459 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8011 (p0) outliers start: 36 outliers final: 17 residues processed: 162 average time/residue: 0.6814 time to fit residues: 120.5539 Evaluate side-chains 155 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 382 ARG Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 459 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN C 493 HIS C 526 HIS A 239 HIS ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 HIS ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.089606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056741 restraints weight = 29357.642| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.77 r_work: 0.2661 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14691 Z= 0.191 Angle : 0.658 13.306 19959 Z= 0.314 Chirality : 0.045 0.553 2129 Planarity : 0.004 0.048 2524 Dihedral : 8.035 100.682 2444 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.38 % Allowed : 19.10 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.20), residues: 1675 helix: 1.07 (0.18), residues: 869 sheet: 0.14 (0.43), residues: 121 loop : -0.75 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 429 TYR 0.017 0.001 TYR C 385 PHE 0.017 0.001 PHE A 523 TRP 0.018 0.001 TRP B 430 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00430 (14656) covalent geometry : angle 0.61086 (19865) SS BOND : bond 0.00313 ( 8) SS BOND : angle 0.73753 ( 16) hydrogen bonds : bond 0.04812 ( 659) hydrogen bonds : angle 4.55451 ( 1935) Misc. bond : bond 0.00038 ( 1) link_ALPHA1-2 : bond 0.00644 ( 1) link_ALPHA1-2 : angle 4.49725 ( 3) link_ALPHA1-3 : bond 0.00950 ( 2) link_ALPHA1-3 : angle 2.64622 ( 6) link_ALPHA1-6 : bond 0.00972 ( 1) link_ALPHA1-6 : angle 2.09677 ( 3) link_BETA1-4 : bond 0.01140 ( 10) link_BETA1-4 : angle 3.48483 ( 30) link_NAG-ASN : bond 0.00559 ( 12) link_NAG-ASN : angle 4.51828 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 PHE cc_start: 0.6362 (OUTLIER) cc_final: 0.6080 (t80) REVERT: B 380 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8709 (mt-10) REVERT: B 398 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8176 (tppt) REVERT: B 416 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7703 (p0) REVERT: B 442 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8894 (mp) REVERT: C 35 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8123 (mm-30) REVERT: C 270 MET cc_start: 0.9125 (tpp) cc_final: 0.8795 (tpp) REVERT: C 383 MET cc_start: 0.9118 (mtp) cc_final: 0.8885 (mtp) REVERT: C 481 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8678 (tpt90) REVERT: C 678 ARG cc_start: 0.9036 (mtm-85) cc_final: 0.8782 (ttm-80) REVERT: A 63 ASP cc_start: 0.9258 (m-30) cc_final: 0.9017 (m-30) REVERT: A 270 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7773 (ttp) REVERT: A 325 GLU cc_start: 0.8728 (tt0) cc_final: 0.8343 (tp30) REVERT: A 332 MET cc_start: 0.8978 (ttp) cc_final: 0.8755 (ttt) REVERT: A 637 ASP cc_start: 0.8879 (m-30) cc_final: 0.8638 (m-30) REVERT: A 678 ARG cc_start: 0.9021 (mtm-85) cc_final: 0.8747 (tpp-160) REVERT: D 352 GLN cc_start: 0.8623 (tp-100) cc_final: 0.8126 (tm-30) REVERT: D 452 GLN cc_start: 0.7970 (pm20) cc_final: 0.7714 (pm20) outliers start: 36 outliers final: 18 residues processed: 157 average time/residue: 0.6883 time to fit residues: 117.8465 Evaluate side-chains 153 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain D residue 458 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 130 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 146 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 GLN B 422 ASN B 470 HIS C 98 GLN C 442 GLN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.090648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.057992 restraints weight = 29515.930| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.82 r_work: 0.2668 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14691 Z= 0.118 Angle : 0.605 12.368 19959 Z= 0.285 Chirality : 0.043 0.506 2129 Planarity : 0.004 0.043 2524 Dihedral : 7.303 85.323 2416 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.78 % Allowed : 19.23 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1675 helix: 1.44 (0.18), residues: 878 sheet: 0.23 (0.45), residues: 112 loop : -0.76 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 428 TYR 0.017 0.001 TYR A 385 PHE 0.015 0.001 PHE A 369 TRP 0.022 0.001 TRP D 430 HIS 0.005 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00253 (14656) covalent geometry : angle 0.55909 (19865) SS BOND : bond 0.00180 ( 8) SS BOND : angle 0.63004 ( 16) hydrogen bonds : bond 0.04000 ( 659) hydrogen bonds : angle 4.33712 ( 1935) Misc. bond : bond 0.00021 ( 1) link_ALPHA1-2 : bond 0.00635 ( 1) link_ALPHA1-2 : angle 4.42772 ( 3) link_ALPHA1-3 : bond 0.01022 ( 2) link_ALPHA1-3 : angle 2.54711 ( 6) link_ALPHA1-6 : bond 0.00858 ( 1) link_ALPHA1-6 : angle 2.02651 ( 3) link_BETA1-4 : bond 0.01104 ( 10) link_BETA1-4 : angle 3.29786 ( 30) link_NAG-ASN : bond 0.00537 ( 12) link_NAG-ASN : angle 4.22756 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 PHE cc_start: 0.6410 (OUTLIER) cc_final: 0.6193 (t80) REVERT: B 352 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: B 380 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8669 (mt-10) REVERT: B 398 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8142 (tppt) REVERT: B 416 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7695 (p0) REVERT: B 430 TRP cc_start: 0.9022 (t60) cc_final: 0.8816 (t60) REVERT: B 439 GLU cc_start: 0.7248 (tt0) cc_final: 0.6373 (mt-10) REVERT: B 442 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8932 (mp) REVERT: C 35 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7986 (mm-30) REVERT: C 270 MET cc_start: 0.9068 (tpp) cc_final: 0.8701 (tpp) REVERT: C 678 ARG cc_start: 0.9042 (mtm-85) cc_final: 0.8779 (ttm-80) REVERT: A 63 ASP cc_start: 0.9273 (m-30) cc_final: 0.9039 (m-30) REVERT: A 270 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7539 (ttm) REVERT: A 325 GLU cc_start: 0.8767 (tt0) cc_final: 0.8447 (tp30) REVERT: A 637 ASP cc_start: 0.8896 (m-30) cc_final: 0.8656 (m-30) REVERT: D 352 GLN cc_start: 0.8597 (tp-100) cc_final: 0.8115 (tm-30) REVERT: D 380 GLU cc_start: 0.8806 (pt0) cc_final: 0.8376 (pm20) REVERT: D 452 GLN cc_start: 0.7963 (pm20) cc_final: 0.7659 (pm20) REVERT: D 458 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8285 (mttm) outliers start: 42 outliers final: 17 residues processed: 165 average time/residue: 0.6883 time to fit residues: 124.0075 Evaluate side-chains 154 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 458 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 153 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 158 optimal weight: 0.0570 chunk 6 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 54 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 overall best weight: 1.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN C 98 GLN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.088887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.055923 restraints weight = 29437.804| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.82 r_work: 0.2615 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14691 Z= 0.195 Angle : 0.637 12.316 19959 Z= 0.303 Chirality : 0.045 0.519 2129 Planarity : 0.004 0.038 2524 Dihedral : 7.030 65.580 2416 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.58 % Allowed : 19.50 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1675 helix: 1.61 (0.18), residues: 878 sheet: 0.11 (0.45), residues: 115 loop : -0.69 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 429 TYR 0.019 0.001 TYR A 385 PHE 0.018 0.001 PHE A 523 TRP 0.022 0.001 TRP D 430 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00447 (14656) covalent geometry : angle 0.59514 (19865) SS BOND : bond 0.00272 ( 8) SS BOND : angle 0.74733 ( 16) hydrogen bonds : bond 0.04549 ( 659) hydrogen bonds : angle 4.32996 ( 1935) Misc. bond : bond 0.00025 ( 1) link_ALPHA1-2 : bond 0.00649 ( 1) link_ALPHA1-2 : angle 4.33234 ( 3) link_ALPHA1-3 : bond 0.01101 ( 2) link_ALPHA1-3 : angle 2.56400 ( 6) link_ALPHA1-6 : bond 0.01001 ( 1) link_ALPHA1-6 : angle 2.13068 ( 3) link_BETA1-4 : bond 0.00989 ( 10) link_BETA1-4 : angle 3.22286 ( 30) link_NAG-ASN : bond 0.00516 ( 12) link_NAG-ASN : angle 4.18575 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 PHE cc_start: 0.6757 (OUTLIER) cc_final: 0.6330 (t80) REVERT: B 352 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 380 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8729 (mt-10) REVERT: B 398 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8108 (tppt) REVERT: B 430 TRP cc_start: 0.9056 (t60) cc_final: 0.8855 (t60) REVERT: B 442 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8960 (mp) REVERT: C 35 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8109 (mm-30) REVERT: C 270 MET cc_start: 0.9212 (tpp) cc_final: 0.8995 (tpp) REVERT: C 678 ARG cc_start: 0.9037 (mtm-85) cc_final: 0.8773 (ttm-80) REVERT: A 35 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8312 (mp0) REVERT: A 63 ASP cc_start: 0.9271 (m-30) cc_final: 0.9023 (m-30) REVERT: A 325 GLU cc_start: 0.8782 (tt0) cc_final: 0.8429 (tp30) REVERT: A 637 ASP cc_start: 0.8916 (m-30) cc_final: 0.8679 (m-30) REVERT: A 723 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: D 352 GLN cc_start: 0.8594 (tp-100) cc_final: 0.8052 (tm-30) REVERT: D 452 GLN cc_start: 0.8029 (pm20) cc_final: 0.7722 (pm20) outliers start: 39 outliers final: 20 residues processed: 164 average time/residue: 0.7092 time to fit residues: 126.8766 Evaluate side-chains 154 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN B 448 GLN C 98 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 444 HIS ** 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 = 0.3497 r_free = 0.3497 target = 0.088743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.055660 restraints weight = 29754.763| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.84 r_work: 0.2614 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14691 Z= 0.167 Angle : 0.616 12.106 19959 Z= 0.293 Chirality : 0.044 0.506 2129 Planarity : 0.004 0.047 2524 Dihedral : 6.654 56.792 2416 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.51 % Allowed : 19.96 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.21), residues: 1675 helix: 1.68 (0.18), residues: 880 sheet: 0.13 (0.45), residues: 115 loop : -0.62 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 600 TYR 0.018 0.001 TYR C 385 PHE 0.016 0.001 PHE A 523 TRP 0.029 0.001 TRP D 430 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00379 (14656) covalent geometry : angle 0.57465 (19865) SS BOND : bond 0.00239 ( 8) SS BOND : angle 0.69164 ( 16) hydrogen bonds : bond 0.04278 ( 659) hydrogen bonds : angle 4.27880 ( 1935) Misc. bond : bond 0.00008 ( 1) link_ALPHA1-2 : bond 0.00642 ( 1) link_ALPHA1-2 : angle 4.33030 ( 3) link_ALPHA1-3 : bond 0.01290 ( 2) link_ALPHA1-3 : angle 2.17330 ( 6) link_ALPHA1-6 : bond 0.00866 ( 1) link_ALPHA1-6 : angle 2.15986 ( 3) link_BETA1-4 : bond 0.00995 ( 10) link_BETA1-4 : angle 3.18332 ( 30) link_NAG-ASN : bond 0.00484 ( 12) link_NAG-ASN : angle 4.06567 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7212 (tm-30) REVERT: B 380 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8743 (mt-10) REVERT: B 398 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8082 (tppt) REVERT: B 430 TRP cc_start: 0.9058 (t60) cc_final: 0.8821 (t60) REVERT: B 442 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8957 (mp) REVERT: C 35 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8101 (mm-30) REVERT: C 429 ARG cc_start: 0.8239 (tpp-160) cc_final: 0.7889 (mmp80) REVERT: C 678 ARG cc_start: 0.9026 (mtm-85) cc_final: 0.8762 (ttm-80) REVERT: A 35 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8289 (mp0) REVERT: A 63 ASP cc_start: 0.9279 (m-30) cc_final: 0.9038 (m-30) REVERT: A 270 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8157 (tpp) REVERT: A 325 GLU cc_start: 0.8772 (tt0) cc_final: 0.8416 (tp30) REVERT: A 429 ARG cc_start: 0.8275 (tpp-160) cc_final: 0.7903 (tpp-160) REVERT: A 430 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: A 637 ASP cc_start: 0.8914 (m-30) cc_final: 0.8666 (m-30) REVERT: A 723 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: D 352 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8025 (tm-30) REVERT: D 398 LYS cc_start: 0.8651 (tppp) cc_final: 0.8419 (tppp) REVERT: D 452 GLN cc_start: 0.7981 (pm20) cc_final: 0.7671 (pm20) outliers start: 38 outliers final: 22 residues processed: 165 average time/residue: 0.7194 time to fit residues: 129.4915 Evaluate side-chains 157 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN C 98 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.087369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.054309 restraints weight = 29581.966| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.82 r_work: 0.2583 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14691 Z= 0.235 Angle : 0.654 12.275 19959 Z= 0.314 Chirality : 0.046 0.523 2129 Planarity : 0.004 0.042 2524 Dihedral : 6.671 56.650 2416 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.91 % Allowed : 20.03 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.21), residues: 1675 helix: 1.61 (0.18), residues: 886 sheet: 0.18 (0.46), residues: 115 loop : -0.55 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 600 TYR 0.018 0.002 TYR A 385 PHE 0.020 0.002 PHE A 523 TRP 0.029 0.002 TRP D 430 HIS 0.007 0.002 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00544 (14656) covalent geometry : angle 0.61528 (19865) SS BOND : bond 0.00588 ( 8) SS BOND : angle 0.80721 ( 16) hydrogen bonds : bond 0.04814 ( 659) hydrogen bonds : angle 4.33802 ( 1935) Misc. bond : bond 0.00016 ( 1) link_ALPHA1-2 : bond 0.00655 ( 1) link_ALPHA1-2 : angle 4.28230 ( 3) link_ALPHA1-3 : bond 0.01112 ( 2) link_ALPHA1-3 : angle 1.89833 ( 6) link_ALPHA1-6 : bond 0.00836 ( 1) link_ALPHA1-6 : angle 1.98925 ( 3) link_BETA1-4 : bond 0.00923 ( 10) link_BETA1-4 : angle 3.25720 ( 30) link_NAG-ASN : bond 0.00495 ( 12) link_NAG-ASN : angle 4.12059 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7107 (tm-30) REVERT: B 379 ASP cc_start: 0.8971 (t0) cc_final: 0.8753 (p0) REVERT: B 380 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: B 398 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8054 (tppt) REVERT: B 430 TRP cc_start: 0.9080 (t60) cc_final: 0.8836 (t60) REVERT: B 442 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8976 (mp) REVERT: C 35 GLU cc_start: 0.8763 (tp30) cc_final: 0.8148 (mm-30) REVERT: C 678 ARG cc_start: 0.9026 (mtm-85) cc_final: 0.8762 (ttm-80) REVERT: A 35 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8325 (mp0) REVERT: A 63 ASP cc_start: 0.9314 (m-30) cc_final: 0.9041 (m-30) REVERT: A 270 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8312 (tpp) REVERT: A 325 GLU cc_start: 0.8777 (tt0) cc_final: 0.8412 (tp30) REVERT: A 637 ASP cc_start: 0.8915 (m-30) cc_final: 0.8670 (m-30) REVERT: A 678 ARG cc_start: 0.8873 (ttm-80) cc_final: 0.8618 (ttm-80) REVERT: A 723 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: D 352 GLN cc_start: 0.8586 (tp-100) cc_final: 0.8047 (tm-30) REVERT: D 398 LYS cc_start: 0.8669 (tppp) cc_final: 0.8292 (tppp) REVERT: D 452 GLN cc_start: 0.7964 (pm20) cc_final: 0.7665 (pm20) outliers start: 44 outliers final: 20 residues processed: 166 average time/residue: 0.6419 time to fit residues: 116.3428 Evaluate side-chains 153 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 137 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.056699 restraints weight = 29249.954| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.82 r_work: 0.2655 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14691 Z= 0.123 Angle : 0.598 11.780 19959 Z= 0.284 Chirality : 0.043 0.485 2129 Planarity : 0.004 0.037 2524 Dihedral : 6.327 56.839 2411 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.38 % Allowed : 20.22 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.21), residues: 1675 helix: 1.83 (0.18), residues: 878 sheet: 0.08 (0.49), residues: 103 loop : -0.51 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 600 TYR 0.016 0.001 TYR A 385 PHE 0.013 0.001 PHE A 523 TRP 0.029 0.001 TRP D 430 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00270 (14656) covalent geometry : angle 0.55761 (19865) SS BOND : bond 0.00227 ( 8) SS BOND : angle 0.66602 ( 16) hydrogen bonds : bond 0.04049 ( 659) hydrogen bonds : angle 4.26034 ( 1935) Misc. bond : bond 0.00016 ( 1) link_ALPHA1-2 : bond 0.00644 ( 1) link_ALPHA1-2 : angle 4.33302 ( 3) link_ALPHA1-3 : bond 0.01180 ( 2) link_ALPHA1-3 : angle 1.87285 ( 6) link_ALPHA1-6 : bond 0.00829 ( 1) link_ALPHA1-6 : angle 1.90986 ( 3) link_BETA1-4 : bond 0.01031 ( 10) link_BETA1-4 : angle 3.13812 ( 30) link_NAG-ASN : bond 0.00523 ( 12) link_NAG-ASN : angle 3.98593 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7042 (tm-30) REVERT: B 380 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: B 398 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8077 (tppt) REVERT: B 430 TRP cc_start: 0.9079 (t60) cc_final: 0.8833 (t60) REVERT: B 442 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8976 (mp) REVERT: C 35 GLU cc_start: 0.8739 (tp30) cc_final: 0.8141 (mm-30) REVERT: C 678 ARG cc_start: 0.9011 (mtm-85) cc_final: 0.8712 (ttm-80) REVERT: A 35 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8223 (mp0) REVERT: A 63 ASP cc_start: 0.9289 (m-30) cc_final: 0.9014 (m-30) REVERT: A 270 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8070 (tpp) REVERT: A 325 GLU cc_start: 0.8773 (tt0) cc_final: 0.8423 (tp30) REVERT: A 429 ARG cc_start: 0.8215 (tpp-160) cc_final: 0.7803 (tpp-160) REVERT: A 430 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: A 637 ASP cc_start: 0.8907 (m-30) cc_final: 0.8651 (m-30) REVERT: A 678 ARG cc_start: 0.8856 (ttm-80) cc_final: 0.8608 (ttm-80) REVERT: A 723 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: D 352 GLN cc_start: 0.8601 (tp-100) cc_final: 0.8071 (tm-30) REVERT: D 398 LYS cc_start: 0.8703 (tppp) cc_final: 0.8311 (tppp) REVERT: D 452 GLN cc_start: 0.7985 (pm20) cc_final: 0.7632 (pm20) outliers start: 36 outliers final: 23 residues processed: 161 average time/residue: 0.6500 time to fit residues: 114.3521 Evaluate side-chains 161 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 93 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.088267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.055302 restraints weight = 29561.013| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.83 r_work: 0.2611 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14691 Z= 0.167 Angle : 0.620 11.905 19959 Z= 0.295 Chirality : 0.044 0.494 2129 Planarity : 0.004 0.040 2524 Dihedral : 6.284 56.739 2411 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.05 % Allowed : 20.22 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1675 helix: 1.83 (0.18), residues: 880 sheet: 0.06 (0.49), residues: 103 loop : -0.47 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 429 TYR 0.017 0.001 TYR C 385 PHE 0.017 0.001 PHE A 523 TRP 0.024 0.001 TRP D 430 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00381 (14656) covalent geometry : angle 0.58089 (19865) SS BOND : bond 0.00252 ( 8) SS BOND : angle 0.73274 ( 16) hydrogen bonds : bond 0.04307 ( 659) hydrogen bonds : angle 4.27391 ( 1935) Misc. bond : bond 0.00003 ( 1) link_ALPHA1-2 : bond 0.00651 ( 1) link_ALPHA1-2 : angle 4.30491 ( 3) link_ALPHA1-3 : bond 0.01078 ( 2) link_ALPHA1-3 : angle 1.87287 ( 6) link_ALPHA1-6 : bond 0.00834 ( 1) link_ALPHA1-6 : angle 1.94426 ( 3) link_BETA1-4 : bond 0.00984 ( 10) link_BETA1-4 : angle 3.13877 ( 30) link_NAG-ASN : bond 0.00497 ( 12) link_NAG-ASN : angle 3.98967 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7469 (tp40) REVERT: B 377 ARG cc_start: 0.8387 (mtp180) cc_final: 0.7995 (mtp-110) REVERT: B 380 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8247 (mt-10) REVERT: B 398 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8073 (tppt) REVERT: B 430 TRP cc_start: 0.9089 (t60) cc_final: 0.8834 (t60) REVERT: B 442 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8966 (mp) REVERT: C 35 GLU cc_start: 0.8765 (tp30) cc_final: 0.8197 (mm-30) REVERT: C 429 ARG cc_start: 0.8277 (tpp-160) cc_final: 0.7906 (mmp80) REVERT: C 678 ARG cc_start: 0.9014 (mtm-85) cc_final: 0.8717 (ttm-80) REVERT: A 35 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8274 (mp0) REVERT: A 63 ASP cc_start: 0.9291 (m-30) cc_final: 0.9035 (m-30) REVERT: A 270 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8126 (tpp) REVERT: A 325 GLU cc_start: 0.8824 (tt0) cc_final: 0.8464 (tp30) REVERT: A 429 ARG cc_start: 0.8274 (tpp-160) cc_final: 0.7664 (mmp80) REVERT: A 430 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: A 637 ASP cc_start: 0.8898 (m-30) cc_final: 0.8634 (m-30) REVERT: A 678 ARG cc_start: 0.8877 (ttm-80) cc_final: 0.8549 (ttm-80) REVERT: A 723 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7401 (OUTLIER) REVERT: D 352 GLN cc_start: 0.8600 (tp-100) cc_final: 0.8079 (tm-30) REVERT: D 398 LYS cc_start: 0.8689 (tppp) cc_final: 0.8298 (tppp) REVERT: D 452 GLN cc_start: 0.7959 (pm20) cc_final: 0.7648 (pm20) outliers start: 31 outliers final: 25 residues processed: 156 average time/residue: 0.6996 time to fit residues: 118.9290 Evaluate side-chains 157 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 147 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056720 restraints weight = 29335.795| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.82 r_work: 0.2656 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14691 Z= 0.130 Angle : 0.607 12.758 19959 Z= 0.289 Chirality : 0.043 0.479 2129 Planarity : 0.004 0.041 2524 Dihedral : 6.193 57.552 2411 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.05 % Allowed : 20.22 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.21), residues: 1675 helix: 1.90 (0.18), residues: 878 sheet: 0.05 (0.49), residues: 103 loop : -0.49 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 429 TYR 0.015 0.001 TYR A 385 PHE 0.013 0.001 PHE A 523 TRP 0.022 0.001 TRP D 430 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00289 (14656) covalent geometry : angle 0.56849 (19865) SS BOND : bond 0.00211 ( 8) SS BOND : angle 0.66693 ( 16) hydrogen bonds : bond 0.03994 ( 659) hydrogen bonds : angle 4.23337 ( 1935) Misc. bond : bond 0.00020 ( 1) link_ALPHA1-2 : bond 0.00662 ( 1) link_ALPHA1-2 : angle 4.32203 ( 3) link_ALPHA1-3 : bond 0.01048 ( 2) link_ALPHA1-3 : angle 1.87396 ( 6) link_ALPHA1-6 : bond 0.00832 ( 1) link_ALPHA1-6 : angle 1.89934 ( 3) link_BETA1-4 : bond 0.01045 ( 10) link_BETA1-4 : angle 3.10574 ( 30) link_NAG-ASN : bond 0.00504 ( 12) link_NAG-ASN : angle 3.91657 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7247 (t80) REVERT: B 352 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7497 (tp40) REVERT: B 377 ARG cc_start: 0.8483 (mtp180) cc_final: 0.8108 (mtp-110) REVERT: B 379 ASP cc_start: 0.8591 (p0) cc_final: 0.8219 (p0) REVERT: B 380 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8578 (mt-10) REVERT: B 398 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8068 (tppt) REVERT: B 430 TRP cc_start: 0.9094 (t60) cc_final: 0.8833 (t60) REVERT: C 35 GLU cc_start: 0.8735 (tp30) cc_final: 0.8173 (mm-30) REVERT: C 429 ARG cc_start: 0.8294 (tpp-160) cc_final: 0.7939 (mmp80) REVERT: C 678 ARG cc_start: 0.8989 (mtm-85) cc_final: 0.8699 (ttm-80) REVERT: A 35 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8350 (mp0) REVERT: A 63 ASP cc_start: 0.9276 (m-30) cc_final: 0.9021 (m-30) REVERT: A 325 GLU cc_start: 0.8818 (tt0) cc_final: 0.8457 (tp30) REVERT: A 429 ARG cc_start: 0.8250 (tpp-160) cc_final: 0.7654 (mmp80) REVERT: A 430 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: A 678 ARG cc_start: 0.8861 (ttm-80) cc_final: 0.8570 (ttm-80) REVERT: A 723 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7363 (OUTLIER) REVERT: D 352 GLN cc_start: 0.8594 (tp-100) cc_final: 0.8065 (tm-30) REVERT: D 380 GLU cc_start: 0.9061 (pt0) cc_final: 0.8454 (pm20) REVERT: D 398 LYS cc_start: 0.8714 (tppp) cc_final: 0.8313 (tppp) REVERT: D 452 GLN cc_start: 0.7953 (pm20) cc_final: 0.7587 (pm20) outliers start: 31 outliers final: 23 residues processed: 160 average time/residue: 0.6500 time to fit residues: 113.7873 Evaluate side-chains 157 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 48 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 150 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.089516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.057092 restraints weight = 29246.939| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.77 r_work: 0.2667 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14691 Z= 0.122 Angle : 0.605 11.510 19959 Z= 0.287 Chirality : 0.043 0.471 2129 Planarity : 0.004 0.042 2524 Dihedral : 6.086 58.210 2411 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.78 % Allowed : 20.56 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.25 (0.21), residues: 1675 helix: 1.95 (0.18), residues: 878 sheet: 0.12 (0.49), residues: 103 loop : -0.49 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 429 TYR 0.016 0.001 TYR A 385 PHE 0.012 0.001 PHE A 369 TRP 0.021 0.001 TRP D 430 HIS 0.004 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00271 (14656) covalent geometry : angle 0.56815 (19865) SS BOND : bond 0.00201 ( 8) SS BOND : angle 0.66321 ( 16) hydrogen bonds : bond 0.03866 ( 659) hydrogen bonds : angle 4.20540 ( 1935) Misc. bond : bond 0.00017 ( 1) link_ALPHA1-2 : bond 0.00664 ( 1) link_ALPHA1-2 : angle 4.31476 ( 3) link_ALPHA1-3 : bond 0.01079 ( 2) link_ALPHA1-3 : angle 1.89036 ( 6) link_ALPHA1-6 : bond 0.00839 ( 1) link_ALPHA1-6 : angle 1.88287 ( 3) link_BETA1-4 : bond 0.00999 ( 10) link_BETA1-4 : angle 2.99581 ( 30) link_NAG-ASN : bond 0.00495 ( 12) link_NAG-ASN : angle 3.84593 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.7369 (t80) REVERT: B 352 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7612 (tp40) REVERT: B 377 ARG cc_start: 0.8507 (mtp180) cc_final: 0.7912 (mtp-110) REVERT: B 380 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8098 (mt-10) REVERT: B 398 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8102 (tppt) REVERT: B 430 TRP cc_start: 0.9093 (t60) cc_final: 0.8833 (t60) REVERT: C 35 GLU cc_start: 0.8724 (tp30) cc_final: 0.8147 (mm-30) REVERT: C 429 ARG cc_start: 0.8291 (tpp-160) cc_final: 0.7934 (mmp80) REVERT: C 678 ARG cc_start: 0.8986 (mtm-85) cc_final: 0.8696 (ttm-80) REVERT: A 35 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8124 (mp0) REVERT: A 63 ASP cc_start: 0.9278 (m-30) cc_final: 0.9030 (m-30) REVERT: A 270 MET cc_start: 0.8395 (tpp) cc_final: 0.8011 (tpp) REVERT: A 325 GLU cc_start: 0.8808 (tt0) cc_final: 0.8449 (tp30) REVERT: A 429 ARG cc_start: 0.8212 (tpp-160) cc_final: 0.7630 (mmp80) REVERT: A 430 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: A 678 ARG cc_start: 0.8854 (ttm-80) cc_final: 0.8575 (ttm-80) REVERT: A 723 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: D 352 GLN cc_start: 0.8614 (tp-100) cc_final: 0.8066 (tm-30) REVERT: D 379 ASP cc_start: 0.8014 (p0) cc_final: 0.7573 (p0) REVERT: D 380 GLU cc_start: 0.8938 (pt0) cc_final: 0.8260 (pm20) REVERT: D 398 LYS cc_start: 0.8688 (tppp) cc_final: 0.8298 (tppp) REVERT: D 452 GLN cc_start: 0.7974 (pm20) cc_final: 0.7608 (pm20) outliers start: 27 outliers final: 22 residues processed: 154 average time/residue: 0.6557 time to fit residues: 110.3827 Evaluate side-chains 156 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 4 optimal weight: 3.9990 chunk 150 optimal weight: 0.0070 chunk 101 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 158 optimal weight: 0.0040 overall best weight: 0.9612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.056551 restraints weight = 29414.118| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.84 r_work: 0.2659 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14691 Z= 0.127 Angle : 0.599 11.470 19959 Z= 0.284 Chirality : 0.043 0.471 2129 Planarity : 0.004 0.044 2524 Dihedral : 6.036 58.369 2411 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.98 % Allowed : 20.49 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.21), residues: 1675 helix: 1.96 (0.18), residues: 878 sheet: 0.16 (0.49), residues: 103 loop : -0.48 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 429 TYR 0.016 0.001 TYR A 385 PHE 0.013 0.001 PHE A 523 TRP 0.019 0.001 TRP D 430 HIS 0.005 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00284 (14656) covalent geometry : angle 0.56160 (19865) SS BOND : bond 0.00207 ( 8) SS BOND : angle 0.65883 ( 16) hydrogen bonds : bond 0.03900 ( 659) hydrogen bonds : angle 4.20430 ( 1935) Misc. bond : bond 0.00008 ( 1) link_ALPHA1-2 : bond 0.00660 ( 1) link_ALPHA1-2 : angle 4.31608 ( 3) link_ALPHA1-3 : bond 0.01016 ( 2) link_ALPHA1-3 : angle 1.89627 ( 6) link_ALPHA1-6 : bond 0.00837 ( 1) link_ALPHA1-6 : angle 1.87348 ( 3) link_BETA1-4 : bond 0.00997 ( 10) link_BETA1-4 : angle 2.98170 ( 30) link_NAG-ASN : bond 0.00491 ( 12) link_NAG-ASN : angle 3.81817 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6333.47 seconds wall clock time: 108 minutes 32.06 seconds (6512.06 seconds total)