Starting phenix.real_space_refine on Sat Jul 4 14:14:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zge_60076/07_2026/8zge_60076.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zge_60076/07_2026/8zge_60076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zge_60076/07_2026/8zge_60076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zge_60076/07_2026/8zge_60076.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zge_60076/07_2026/8zge_60076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zge_60076/07_2026/8zge_60076.map" } resolution = 3.4 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= 0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 6 7.51 5 Fe 2 7.16 5 P 12 5.49 5 S 100 5.16 5 C 13606 2.51 5 N 3718 2.21 5 O 3982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21426 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5756 Classifications: {'peptide': 706} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 662} Chain: "B" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5756 Classifications: {'peptide': 706} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 662} Chain: "U" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4801 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 549} Chain: "V" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4801 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 549} 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: "D" 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: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Ad-hoc single atom residues: {'FE2': 1, ' MN': 1} Unusual residues: {'AKG': 1, 'NAG': 2, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Ad-hoc single atom residues: {'FE2': 1, ' MN': 1} Unusual residues: {'AKG': 1, 'NAG': 2, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'GDU': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Chain: "V" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'GDU': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Time building chain proxies: 4.44, per 1000 atoms: 0.21 Number of scatterers: 21426 At special positions: 0 Unit cell: (179.3, 162.8, 199.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 Mn 6 24.99 S 100 16.00 P 12 15.00 O 3982 8.00 N 3718 7.00 C 13606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 385 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 385 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 698 " distance=2.03 Simple disulfide: pdb=" SG CYS U 228 " - pdb=" SG CYS U 283 " distance=2.05 Simple disulfide: pdb=" SG CYS V 228 " - pdb=" SG CYS V 283 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 801 " - " ASN A 63 " " NAG A 802 " - " ASN A 548 " " NAG B 801 " - " ASN B 63 " " NAG B 802 " - " ASN B 548 " " NAG C 1 " - " ASN U 184 " " NAG D 1 " - " ASN V 184 " Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 989.3 milliseconds 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4880 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 30 sheets defined 32.8% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 49 through 62 removed outlier: 3.819A pdb=" N PHE A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 98 removed outlier: 3.843A pdb=" N ARG A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 148 through 152 removed outlier: 4.281A pdb=" N GLU A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 191 through 201 removed outlier: 3.780A pdb=" N ASP A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 258 through 266 removed outlier: 3.675A pdb=" N LEU A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 319 removed outlier: 3.992A pdb=" N LEU A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 354 removed outlier: 3.509A pdb=" N ILE A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Proline residue: A 348 - end of helix Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.998A pdb=" N GLU A 364 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 401 through 410 removed outlier: 4.118A pdb=" N ASN A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 488 through 499 Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 548 through 555 Processing helix chain 'A' and resid 573 through 588 removed outlier: 3.517A pdb=" N CYS A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 588 " --> pdb=" O MET A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 618 removed outlier: 3.921A pdb=" N VAL A 617 " --> pdb=" O HIS A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 630 Processing helix chain 'A' and resid 630 through 639 removed outlier: 4.018A pdb=" N MET A 634 " --> pdb=" O TYR A 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 49 through 62 removed outlier: 3.819A pdb=" N PHE B 62 " --> pdb=" O SER B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 98 removed outlier: 3.842A pdb=" N ARG B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 148 through 152 removed outlier: 4.282A pdb=" N GLU B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.780A pdb=" N ASP B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 258 through 266 removed outlier: 3.675A pdb=" N LEU B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 319 removed outlier: 3.992A pdb=" N LEU B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 354 removed outlier: 3.509A pdb=" N ILE B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) Proline residue: B 348 - end of helix Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.999A pdb=" N GLU B 364 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 382 Processing helix chain 'B' and resid 401 through 410 removed outlier: 4.117A pdb=" N ASN B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 488 through 499 Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'B' and resid 573 through 588 removed outlier: 3.518A pdb=" N CYS B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY B 588 " --> pdb=" O MET B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 618 removed outlier: 3.922A pdb=" N VAL B 617 " --> pdb=" O HIS B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 630 Processing helix chain 'B' and resid 630 through 639 removed outlier: 4.018A pdb=" N MET B 634 " --> pdb=" O TYR B 630 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 76 removed outlier: 3.692A pdb=" N ARG U 76 " --> pdb=" O GLY U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 109 Processing helix chain 'U' and resid 136 through 156 Processing helix chain 'U' and resid 175 through 182 Processing helix chain 'U' and resid 217 through 222 Processing helix chain 'U' and resid 244 through 249 removed outlier: 3.732A pdb=" N ASN U 249 " --> pdb=" O ALA U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 276 removed outlier: 3.678A pdb=" N ALA U 270 " --> pdb=" O ILE U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 300 through 317 removed outlier: 3.605A pdb=" N GLU U 304 " --> pdb=" O THR U 300 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET U 316 " --> pdb=" O GLN U 312 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL U 317 " --> pdb=" O LEU U 313 " (cutoff:3.500A) Processing helix chain 'U' and resid 352 through 365 removed outlier: 3.626A pdb=" N GLU U 356 " --> pdb=" O GLN U 352 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG U 357 " --> pdb=" O ASP U 353 " (cutoff:3.500A) Processing helix chain 'U' and resid 381 through 386 Processing helix chain 'U' and resid 387 through 389 No H-bonds generated for 'chain 'U' and resid 387 through 389' Processing helix chain 'U' and resid 407 through 427 Processing helix chain 'U' and resid 443 through 459 Processing helix chain 'U' and resid 503 through 512 Processing helix chain 'U' and resid 520 through 525 Processing helix chain 'U' and resid 526 through 528 No H-bonds generated for 'chain 'U' and resid 526 through 528' Processing helix chain 'U' and resid 534 through 541 removed outlier: 4.192A pdb=" N LYS U 538 " --> pdb=" O VAL U 534 " (cutoff:3.500A) Processing helix chain 'U' and resid 597 through 601 Processing helix chain 'V' and resid 66 through 76 removed outlier: 3.692A pdb=" N ARG V 76 " --> pdb=" O GLY V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 109 Processing helix chain 'V' and resid 136 through 156 Processing helix chain 'V' and resid 175 through 182 Processing helix chain 'V' and resid 217 through 222 Processing helix chain 'V' and resid 244 through 249 removed outlier: 3.733A pdb=" N ASN V 249 " --> pdb=" O ALA V 246 " (cutoff:3.500A) Processing helix chain 'V' and resid 266 through 276 removed outlier: 3.678A pdb=" N ALA V 270 " --> pdb=" O ILE V 266 " (cutoff:3.500A) Processing helix chain 'V' and resid 300 through 317 removed outlier: 3.605A pdb=" N GLU V 304 " --> pdb=" O THR V 300 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET V 316 " --> pdb=" O GLN V 312 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL V 317 " --> pdb=" O LEU V 313 " (cutoff:3.500A) Processing helix chain 'V' and resid 352 through 365 removed outlier: 3.626A pdb=" N GLU V 356 " --> pdb=" O GLN V 352 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG V 357 " --> pdb=" O ASP V 353 " (cutoff:3.500A) Processing helix chain 'V' and resid 381 through 386 Processing helix chain 'V' and resid 387 through 389 No H-bonds generated for 'chain 'V' and resid 387 through 389' Processing helix chain 'V' and resid 407 through 427 Processing helix chain 'V' and resid 443 through 459 Processing helix chain 'V' and resid 503 through 512 Processing helix chain 'V' and resid 520 through 525 Processing helix chain 'V' and resid 526 through 528 No H-bonds generated for 'chain 'V' and resid 526 through 528' Processing helix chain 'V' and resid 534 through 541 removed outlier: 4.192A pdb=" N LYS V 538 " --> pdb=" O VAL V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 597 through 601 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 69 removed outlier: 8.156A pdb=" N ARG A 67 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 41 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU A 69 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR A 43 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 111 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL A 44 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 139 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N GLY A 167 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 11.770A pdb=" N LEU A 137 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.460A pdb=" N GLN A 220 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 229 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 274 removed outlier: 3.672A pdb=" N GLY A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 360 removed outlier: 6.583A pdb=" N PHE A 299 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU A 391 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ALA A 301 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 465 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 464 " --> pdb=" O PRO A 416 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 414 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 413 " --> pdb=" O HIS A 505 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N SER A 507 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 415 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 504 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 419 through 420 removed outlier: 6.673A pdb=" N SER A 419 " --> pdb=" O LEU A 515 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 428 through 429 removed outlier: 4.401A pdb=" N TYR A 460 " --> pdb=" O TRP A 429 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 431 through 432 Processing sheet with id=AA9, first strand: chain 'A' and resid 560 through 563 removed outlier: 7.612A pdb=" N VAL A 566 " --> pdb=" O PRO A 562 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N TRP A 707 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 678 " --> pdb=" O TRP A 707 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS A 711 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 673 " --> pdb=" O VAL A 736 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 736 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET A 650 " --> pdb=" O PHE A 735 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB2, first strand: chain 'A' and resid 698 through 699 Processing sheet with id=AB3, first strand: chain 'B' and resid 66 through 69 removed outlier: 8.157A pdb=" N ARG B 67 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 41 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU B 69 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR B 43 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 111 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL B 44 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 139 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N GLY B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 11.770A pdb=" N LEU B 137 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.460A pdb=" N GLN B 220 " --> pdb=" O HIS B 253 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 229 through 233 Processing sheet with id=AB6, first strand: chain 'B' and resid 273 through 274 removed outlier: 3.672A pdb=" N GLY B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 357 through 360 removed outlier: 6.583A pdb=" N PHE B 299 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU B 391 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ALA B 301 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 465 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 464 " --> pdb=" O PRO B 416 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 414 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 413 " --> pdb=" O HIS B 505 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N SER B 507 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA B 415 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU B 504 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 419 through 420 removed outlier: 6.674A pdb=" N SER B 419 " --> pdb=" O LEU B 515 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 428 through 429 removed outlier: 4.401A pdb=" N TYR B 460 " --> pdb=" O TRP B 429 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 431 through 432 Processing sheet with id=AC2, first strand: chain 'B' and resid 560 through 563 removed outlier: 7.612A pdb=" N VAL B 566 " --> pdb=" O PRO B 562 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N TRP B 707 " --> pdb=" O ALA B 678 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 678 " --> pdb=" O TRP B 707 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS B 711 " --> pdb=" O THR B 674 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 673 " --> pdb=" O VAL B 736 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 736 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N MET B 650 " --> pdb=" O PHE B 735 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 686 through 687 Processing sheet with id=AC4, first strand: chain 'B' and resid 698 through 699 Processing sheet with id=AC5, first strand: chain 'U' and resid 115 through 117 removed outlier: 8.982A pdb=" N GLU U 116 " --> pdb=" O THR U 84 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU U 86 " --> pdb=" O GLU U 116 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU U 58 " --> pdb=" O TRP U 87 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA U 60 " --> pdb=" O ALA U 89 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU U 55 " --> pdb=" O LEU U 163 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE U 238 " --> pdb=" O PHE U 164 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL U 187 " --> pdb=" O TYR U 281 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N CYS U 283 " --> pdb=" O VAL U 187 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA U 189 " --> pdb=" O CYS U 283 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET U 280 " --> pdb=" O VAL U 231 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE U 229 " --> pdb=" O VAL U 282 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 170 through 171 Processing sheet with id=AC7, first strand: chain 'U' and resid 370 through 372 removed outlier: 5.450A pdb=" N VAL U 343 " --> pdb=" O ARG U 370 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL U 372 " --> pdb=" O VAL U 343 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N MET U 345 " --> pdb=" O VAL U 372 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE U 346 " --> pdb=" O PHE U 434 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR U 499 " --> pdb=" O VAL U 433 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR U 496 " --> pdb=" O ARG U 469 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ARG U 469 " --> pdb=" O THR U 496 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA U 498 " --> pdb=" O VAL U 467 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL U 467 " --> pdb=" O ALA U 498 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE U 465 " --> pdb=" O VAL U 500 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE U 549 " --> pdb=" O LEU U 464 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL U 551 " --> pdb=" O TYR U 466 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY U 468 " --> pdb=" O VAL U 551 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 438 through 440 removed outlier: 3.593A pdb=" N TYR U 557 " --> pdb=" O ARG U 439 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'V' and resid 115 through 117 removed outlier: 8.981A pdb=" N GLU V 116 " --> pdb=" O THR V 84 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU V 86 " --> pdb=" O GLU V 116 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU V 58 " --> pdb=" O TRP V 87 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA V 60 " --> pdb=" O ALA V 89 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU V 55 " --> pdb=" O LEU V 163 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE V 238 " --> pdb=" O PHE V 164 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL V 187 " --> pdb=" O TYR V 281 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N CYS V 283 " --> pdb=" O VAL V 187 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA V 189 " --> pdb=" O CYS V 283 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET V 280 " --> pdb=" O VAL V 231 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE V 229 " --> pdb=" O VAL V 282 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 170 through 171 Processing sheet with id=AD2, first strand: chain 'V' and resid 370 through 372 removed outlier: 5.450A pdb=" N VAL V 343 " --> pdb=" O ARG V 370 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL V 372 " --> pdb=" O VAL V 343 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N MET V 345 " --> pdb=" O VAL V 372 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE V 346 " --> pdb=" O PHE V 434 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR V 499 " --> pdb=" O VAL V 433 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR V 496 " --> pdb=" O ARG V 469 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ARG V 469 " --> pdb=" O THR V 496 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA V 498 " --> pdb=" O VAL V 467 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL V 467 " --> pdb=" O ALA V 498 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE V 465 " --> pdb=" O VAL V 500 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE V 549 " --> pdb=" O LEU V 464 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL V 551 " --> pdb=" O TYR V 466 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY V 468 " --> pdb=" O VAL V 551 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 438 through 440 removed outlier: 3.593A pdb=" N TYR V 557 " --> pdb=" O ARG V 439 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3512 1.31 - 1.45: 6326 1.45 - 1.59: 11994 1.59 - 1.73: 14 1.73 - 1.87: 170 Bond restraints: 22016 Sorted by residual: bond pdb=" O3A UDP B 805 " pdb=" PB UDP B 805 " ideal model delta sigma weight residual 1.584 1.716 -0.132 1.00e-02 1.00e+04 1.75e+02 bond pdb=" O3A UDP A 805 " pdb=" PB UDP A 805 " ideal model delta sigma weight residual 1.584 1.716 -0.132 1.00e-02 1.00e+04 1.74e+02 bond pdb=" O5' UDP B 805 " pdb=" PA UDP B 805 " ideal model delta sigma weight residual 1.581 1.766 -0.185 1.50e-02 4.44e+03 1.52e+02 bond pdb=" O5' UDP A 805 " pdb=" PA UDP A 805 " ideal model delta sigma weight residual 1.581 1.765 -0.184 1.50e-02 4.44e+03 1.51e+02 bond pdb=" O5' UDP B 805 " pdb=" C5' UDP B 805 " ideal model delta sigma weight residual 1.443 1.359 0.084 1.20e-02 6.94e+03 4.91e+01 ... (remaining 22011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.64: 29817 5.64 - 11.28: 98 11.28 - 16.92: 6 16.92 - 22.56: 3 22.56 - 28.20: 2 Bond angle restraints: 29926 Sorted by residual: angle pdb=" O1A UDP B 805 " pdb=" PA UDP B 805 " pdb=" O3A UDP B 805 " ideal model delta sigma weight residual 109.95 122.12 -12.17 1.00e+00 1.00e+00 1.48e+02 angle pdb=" O1A UDP A 805 " pdb=" PA UDP A 805 " pdb=" O3A UDP A 805 " ideal model delta sigma weight residual 109.95 122.07 -12.12 1.00e+00 1.00e+00 1.47e+02 angle pdb=" O5' UDP B 805 " pdb=" PA UDP B 805 " pdb=" O2A UDP B 805 " ideal model delta sigma weight residual 110.83 98.91 11.92 1.00e+00 1.00e+00 1.42e+02 angle pdb=" O5' UDP A 805 " pdb=" PA UDP A 805 " pdb=" O2A UDP A 805 " ideal model delta sigma weight residual 110.83 98.93 11.90 1.00e+00 1.00e+00 1.42e+02 angle pdb=" O3A UDP A 805 " pdb=" PB UDP A 805 " pdb=" O3B UDP A 805 " ideal model delta sigma weight residual 112.01 101.18 10.83 1.00e+00 1.00e+00 1.17e+02 ... (remaining 29921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11266 17.99 - 35.98: 1557 35.98 - 53.97: 481 53.97 - 71.97: 76 71.97 - 89.96: 28 Dihedral angle restraints: 13408 sinusoidal: 5834 harmonic: 7574 Sorted by residual: dihedral pdb=" C PHE U 38 " pdb=" N PHE U 38 " pdb=" CA PHE U 38 " pdb=" CB PHE U 38 " ideal model delta harmonic sigma weight residual -122.60 -156.73 34.13 0 2.50e+00 1.60e-01 1.86e+02 dihedral pdb=" N PHE U 38 " pdb=" C PHE U 38 " pdb=" CA PHE U 38 " pdb=" CB PHE U 38 " ideal model delta harmonic sigma weight residual 122.80 150.25 -27.45 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" C TYR U 37 " pdb=" N TYR U 37 " pdb=" CA TYR U 37 " pdb=" CB TYR U 37 " ideal model delta harmonic sigma weight residual -122.60 -141.27 18.67 0 2.50e+00 1.60e-01 5.58e+01 ... (remaining 13405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 3156 0.270 - 0.540: 8 0.540 - 0.810: 1 0.810 - 1.080: 0 1.080 - 1.350: 1 Chirality restraints: 3166 Sorted by residual: chirality pdb=" CA PHE U 38 " pdb=" N PHE U 38 " pdb=" C PHE U 38 " pdb=" CB PHE U 38 " both_signs ideal model delta sigma weight residual False 2.51 1.16 1.35 2.00e-01 2.50e+01 4.56e+01 chirality pdb=" CA TYR U 37 " pdb=" N TYR U 37 " pdb=" C TYR U 37 " pdb=" CB TYR U 37 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" C1D GDU U 701 " pdb=" C2D GDU U 701 " pdb=" N1 GDU U 701 " pdb=" O4D GDU U 701 " both_signs ideal model delta sigma weight residual False 2.21 2.58 -0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 3163 not shown) Planarity restraints: 3880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 801 " -0.091 2.00e-02 2.50e+03 7.44e-02 6.92e+01 pdb=" C7 NAG B 801 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG B 801 " -0.070 2.00e-02 2.50e+03 pdb=" N2 NAG B 801 " 0.116 2.00e-02 2.50e+03 pdb=" O7 NAG B 801 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 801 " -0.091 2.00e-02 2.50e+03 7.43e-02 6.90e+01 pdb=" C7 NAG A 801 " 0.025 2.00e-02 2.50e+03 pdb=" C8 NAG A 801 " -0.069 2.00e-02 2.50e+03 pdb=" N2 NAG A 801 " 0.116 2.00e-02 2.50e+03 pdb=" O7 NAG A 801 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP U 437 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.64e+00 pdb=" C ASP U 437 " 0.054 2.00e-02 2.50e+03 pdb=" O ASP U 437 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU U 438 " -0.019 2.00e-02 2.50e+03 ... (remaining 3877 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 124 2.48 - 3.09: 14088 3.09 - 3.69: 30717 3.69 - 4.30: 43245 4.30 - 4.90: 74920 Nonbonded interactions: 163094 Sorted by model distance: nonbonded pdb=" OG1 THR A 716 " pdb=" OD2 ASP B 565 " model vdw 1.877 3.040 nonbonded pdb=" OD2 ASP A 565 " pdb=" OG1 THR B 716 " model vdw 1.978 3.040 nonbonded pdb=" OD2 ASP V 168 " pdb="MN MN V 703 " model vdw 2.077 3.060 nonbonded pdb=" OD2 ASP U 168 " pdb="MN MN U 703 " model vdw 2.077 3.060 nonbonded pdb=" O1B UDP V 702 " pdb="MN MN V 704 " model vdw 2.095 3.060 ... (remaining 163089 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.530 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 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 : 0.006 0.185 22032 Z= 0.331 Angle : 0.918 28.197 29966 Z= 0.530 Chirality : 0.058 1.350 3166 Planarity : 0.006 0.074 3874 Dihedral : 17.965 89.957 8504 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.53 % Favored : 92.24 % Rotamer: Outliers : 0.75 % Allowed : 25.44 % Favored : 73.81 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 2.50 % 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: -1.79 (0.16), residues: 2578 helix: 1.04 (0.20), residues: 738 sheet: -2.26 (0.25), residues: 402 loop : -2.16 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 380 TYR 0.037 0.001 TYR B 64 PHE 0.020 0.002 PHE B 62 TRP 0.009 0.001 TRP B 425 HIS 0.006 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.33 (22016) covalent geometry : angle 0.90524 / 0.53 (29926) SS BOND : bond 0.01051 / 0.30 ( 8) SS BOND : angle 3.73735 / 2.70 ( 16) hydrogen bonds : bond 0.20135 / 13.17 ( 648) hydrogen bonds : angle 6.78834 / 4.77 ( 1842) link_BETA1-4 : bond 0.00328 / 0.23 ( 2) link_BETA1-4 : angle 1.28023 / 0.63 ( 6) link_NAG-ASN : bond 0.01259 / 0.73 ( 6) link_NAG-ASN : angle 5.16725 / 3.25 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 280 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 696 TYR cc_start: 0.4205 (m-80) cc_final: 0.2192 (t80) REVERT: B 106 MET cc_start: 0.7328 (mmm) cc_final: 0.7111 (mtt) REVERT: B 634 MET cc_start: 0.8101 (ttm) cc_final: 0.7797 (ttm) REVERT: U 53 ARG cc_start: 0.5415 (mtt180) cc_final: 0.4404 (mtt90) REVERT: U 242 LEU cc_start: 0.7348 (mt) cc_final: 0.6526 (mt) REVERT: U 577 TRP cc_start: 0.2856 (p-90) cc_final: 0.2502 (t60) REVERT: V 378 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7451 (mmtt) outliers start: 17 outliers final: 9 residues processed: 291 average time/residue: 0.1739 time to fit residues: 76.2155 Evaluate side-chains 196 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 40 GLU Chi-restraints excluded: chain U residue 42 ARG Chi-restraints excluded: chain U residue 156 ASP Chi-restraints excluded: chain V residue 156 ASP Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 378 LYS Chi-restraints excluded: chain V residue 437 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 HIS A 214 HIS ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 HIS U 134 HIS U 169 ASN U 597 GLN V 134 HIS V 169 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.223350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.189763 restraints weight = 37296.328| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 2.69 r_work: 0.3858 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22032 Z= 0.133 Angle : 0.614 11.215 29966 Z= 0.311 Chirality : 0.045 0.269 3166 Planarity : 0.005 0.053 3874 Dihedral : 8.789 58.391 3326 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.05 % Favored : 93.75 % Rotamer: Outliers : 2.86 % Allowed : 23.86 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.59 (0.16), residues: 2578 helix: 1.23 (0.19), residues: 766 sheet: -2.04 (0.25), residues: 412 loop : -2.14 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 81 TYR 0.017 0.001 TYR U 37 PHE 0.018 0.001 PHE V 529 TRP 0.035 0.001 TRP U 420 HIS 0.008 0.001 HIS A 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (22016) covalent geometry : angle 0.60885 / 0.31 (29926) SS BOND : bond 0.00893 / 0.27 ( 8) SS BOND : angle 2.45872 / 1.81 ( 16) hydrogen bonds : bond 0.04596 / 3.07 ( 648) hydrogen bonds : angle 5.23188 / 3.73 ( 1842) link_BETA1-4 : bond 0.00643 / 0.45 ( 2) link_BETA1-4 : angle 0.94497 / 0.43 ( 6) link_NAG-ASN : bond 0.00340 / 0.22 ( 6) link_NAG-ASN : angle 2.56961 / 1.59 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 191 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 MET cc_start: 0.5948 (ptt) cc_final: 0.5051 (mmm) REVERT: A 696 TYR cc_start: 0.4518 (m-80) cc_final: 0.2408 (t80) REVERT: B 279 CYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6477 (t) REVERT: B 634 MET cc_start: 0.8514 (ttm) cc_final: 0.8301 (ttm) REVERT: U 53 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.5205 (ptp-170) REVERT: V 453 ARG cc_start: 0.8184 (tmm-80) cc_final: 0.7790 (mtm110) REVERT: V 587 ASP cc_start: 0.5536 (OUTLIER) cc_final: 0.5172 (p0) outliers start: 65 outliers final: 27 residues processed: 246 average time/residue: 0.1647 time to fit residues: 62.2313 Evaluate side-chains 201 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 155 ARG Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 247 SER Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 280 MET Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 428 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 587 ASP Chi-restraints excluded: chain V residue 602 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 138 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 232 optimal weight: 0.2980 chunk 250 optimal weight: 1.9990 chunk 18 optimal weight: 40.0000 chunk 42 optimal weight: 40.0000 chunk 93 optimal weight: 0.0370 chunk 0 optimal weight: 40.0000 chunk 41 optimal weight: 10.0000 overall best weight: 1.0664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.223204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.190014 restraints weight = 38204.536| |-----------------------------------------------------------------------------| r_work (start): 0.4411 rms_B_bonded: 2.75 r_work: 0.3736 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22032 Z= 0.151 Angle : 0.590 7.963 29966 Z= 0.298 Chirality : 0.044 0.232 3166 Planarity : 0.005 0.150 3874 Dihedral : 7.622 57.997 3308 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.32 % Favored : 93.48 % Rotamer: Outliers : 3.38 % Allowed : 23.29 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.56 (0.16), residues: 2578 helix: 1.21 (0.19), residues: 772 sheet: -2.11 (0.24), residues: 434 loop : -2.06 (0.15), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 349 TYR 0.032 0.001 TYR U 494 PHE 0.020 0.001 PHE V 529 TRP 0.053 0.001 TRP U 420 HIS 0.005 0.001 HIS B 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (22016) covalent geometry : angle 0.58628 / 0.30 (29926) SS BOND : bond 0.01204 / 0.37 ( 8) SS BOND : angle 2.08406 / 1.39 ( 16) hydrogen bonds : bond 0.03950 / 2.60 ( 648) hydrogen bonds : angle 4.95836 / 3.55 ( 1842) link_BETA1-4 : bond 0.00217 / 0.14 ( 2) link_BETA1-4 : angle 1.24432 / 0.57 ( 6) link_NAG-ASN : bond 0.00292 / 0.19 ( 6) link_NAG-ASN : angle 2.07700 / 1.27 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 179 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 MET cc_start: 0.6367 (ptt) cc_final: 0.5284 (mmm) REVERT: A 696 TYR cc_start: 0.4628 (m-80) cc_final: 0.1781 (t80) REVERT: B 279 CYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6598 (t) REVERT: U 316 MET cc_start: 0.6876 (mmp) cc_final: 0.6667 (mmp) REVERT: U 449 MET cc_start: 0.6455 (tpt) cc_final: 0.6252 (tpp) REVERT: U 544 ARG cc_start: 0.2671 (OUTLIER) cc_final: 0.2461 (mtt90) REVERT: V 144 MET cc_start: 0.8252 (mmm) cc_final: 0.8032 (mmm) REVERT: V 453 ARG cc_start: 0.8093 (tmm-80) cc_final: 0.7714 (mtm110) REVERT: V 587 ASP cc_start: 0.5439 (OUTLIER) cc_final: 0.4927 (p0) outliers start: 77 outliers final: 46 residues processed: 239 average time/residue: 0.1607 time to fit residues: 59.4831 Evaluate side-chains 215 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 42 ARG Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 155 ARG Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 243 ARG Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 544 ARG Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 280 MET Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 493 SER Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 215 optimal weight: 1.9990 chunk 161 optimal weight: 0.0370 chunk 245 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 26 optimal weight: 30.0000 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** 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 = 0.4728 r_free = 0.4728 target = 0.221144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.183535 restraints weight = 37634.354| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.62 r_work: 0.3638 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22032 Z= 0.214 Angle : 0.631 8.436 29966 Z= 0.319 Chirality : 0.046 0.205 3166 Planarity : 0.005 0.108 3874 Dihedral : 7.075 59.506 3308 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.18 % Favored : 92.63 % Rotamer: Outliers : 4.48 % Allowed : 22.98 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.55 (0.16), residues: 2578 helix: 1.18 (0.19), residues: 786 sheet: -2.07 (0.25), residues: 422 loop : -2.09 (0.15), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG V 485 TYR 0.028 0.002 TYR V 211 PHE 0.022 0.002 PHE V 238 TRP 0.026 0.001 TRP A 623 HIS 0.007 0.001 HIS B 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.21 (22016) covalent geometry : angle 0.62678 / 0.32 (29926) SS BOND : bond 0.01155 / 0.38 ( 8) SS BOND : angle 2.19102 / 1.31 ( 16) hydrogen bonds : bond 0.04322 / 2.87 ( 648) hydrogen bonds : angle 4.92260 / 3.52 ( 1842) link_BETA1-4 : bond 0.00576 / 0.41 ( 2) link_BETA1-4 : angle 1.69554 / 0.75 ( 6) link_NAG-ASN : bond 0.00266 / 0.16 ( 6) link_NAG-ASN : angle 2.04055 / 1.27 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 168 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 MET cc_start: 0.6492 (ptt) cc_final: 0.5381 (mmm) REVERT: A 696 TYR cc_start: 0.4780 (m-80) cc_final: 0.1719 (t80) REVERT: B 106 MET cc_start: 0.7679 (mmm) cc_final: 0.7253 (mtp) REVERT: B 327 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7214 (mtt-85) REVERT: U 74 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7003 (tp) REVERT: U 316 MET cc_start: 0.6870 (mmp) cc_final: 0.6542 (mmp) REVERT: U 472 MET cc_start: 0.3507 (pmm) cc_final: 0.2765 (ptp) REVERT: U 544 ARG cc_start: 0.2797 (OUTLIER) cc_final: 0.1400 (mtt90) REVERT: U 577 TRP cc_start: 0.4452 (p-90) cc_final: 0.3790 (t60) REVERT: V 128 ASP cc_start: 0.5987 (OUTLIER) cc_final: 0.5768 (p0) REVERT: V 417 TYR cc_start: 0.7888 (t80) cc_final: 0.7610 (t80) REVERT: V 453 ARG cc_start: 0.8234 (tmm-80) cc_final: 0.7785 (mtm110) outliers start: 102 outliers final: 63 residues processed: 251 average time/residue: 0.1630 time to fit residues: 63.8592 Evaluate side-chains 226 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 159 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 42 ARG Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 49 LEU Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 155 ARG Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 243 ARG Chi-restraints excluded: chain U residue 247 SER Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 543 LEU Chi-restraints excluded: chain U residue 544 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 264 ASP Chi-restraints excluded: chain V residue 280 MET Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 493 SER Chi-restraints excluded: chain V residue 545 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 176 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 212 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 36 optimal weight: 50.0000 chunk 65 optimal weight: 20.0000 chunk 213 optimal weight: 0.7980 chunk 251 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 310 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.221694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.188203 restraints weight = 37521.218| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 2.64 r_work: 0.3677 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22032 Z= 0.169 Angle : 0.591 10.045 29966 Z= 0.299 Chirality : 0.044 0.236 3166 Planarity : 0.005 0.096 3874 Dihedral : 6.706 57.552 3308 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.63 % Favored : 93.17 % Rotamer: Outliers : 3.82 % Allowed : 23.42 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.51 (0.16), residues: 2578 helix: 1.09 (0.19), residues: 798 sheet: -1.94 (0.25), residues: 424 loop : -2.05 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 628 TYR 0.025 0.001 TYR V 211 PHE 0.017 0.001 PHE V 238 TRP 0.017 0.001 TRP U 420 HIS 0.004 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (22016) covalent geometry : angle 0.58712 / 0.30 (29926) SS BOND : bond 0.01456 / 0.77 ( 8) SS BOND : angle 2.26394 / 1.32 ( 16) hydrogen bonds : bond 0.03870 / 2.64 ( 648) hydrogen bonds : angle 4.83865 / 3.45 ( 1842) link_BETA1-4 : bond 0.00342 / 0.23 ( 2) link_BETA1-4 : angle 1.65839 / 0.76 ( 6) link_NAG-ASN : bond 0.00423 / 0.29 ( 6) link_NAG-ASN : angle 1.85941 / 1.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 160 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.1718 (m-80) cc_final: 0.1287 (m-10) REVERT: A 584 MET cc_start: 0.6410 (ptt) cc_final: 0.5250 (mmm) REVERT: B 137 LEU cc_start: 0.8756 (mp) cc_final: 0.8553 (mp) REVERT: B 621 ASP cc_start: 0.8236 (t0) cc_final: 0.8036 (t0) REVERT: U 74 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7059 (tp) REVERT: U 144 MET cc_start: 0.6714 (mmm) cc_final: 0.6489 (mmm) REVERT: U 316 MET cc_start: 0.6974 (mmp) cc_final: 0.6660 (mmp) REVERT: U 472 MET cc_start: 0.3408 (pmm) cc_final: 0.2709 (ptp) REVERT: V 102 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7091 (ttm110) REVERT: V 128 ASP cc_start: 0.6190 (OUTLIER) cc_final: 0.5939 (p0) REVERT: V 453 ARG cc_start: 0.8064 (tmm-80) cc_final: 0.7642 (mtm110) outliers start: 87 outliers final: 59 residues processed: 232 average time/residue: 0.1479 time to fit residues: 54.5254 Evaluate side-chains 212 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 150 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 155 ARG Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 243 ARG Chi-restraints excluded: chain U residue 247 SER Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 283 CYS Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain U residue 544 ARG Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 94 MET Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 102 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 280 MET Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 545 ASN Chi-restraints excluded: chain V residue 577 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 21 optimal weight: 20.0000 chunk 117 optimal weight: 0.7980 chunk 238 optimal weight: 0.7980 chunk 37 optimal weight: 30.0000 chunk 245 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 195 optimal weight: 20.0000 chunk 203 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 310 HIS ** V 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 592 GLN ** 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 = 0.4739 r_free = 0.4739 target = 0.222169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.188214 restraints weight = 37739.589| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 2.71 r_work: 0.3686 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22032 Z= 0.125 Angle : 0.553 10.127 29966 Z= 0.279 Chirality : 0.043 0.266 3166 Planarity : 0.005 0.082 3874 Dihedral : 6.553 53.764 3308 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.40 % Favored : 93.48 % Rotamer: Outliers : 3.51 % Allowed : 24.12 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.35 (0.16), residues: 2578 helix: 1.27 (0.19), residues: 786 sheet: -1.76 (0.25), residues: 418 loop : -1.98 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 411 TYR 0.017 0.001 TYR V 417 PHE 0.017 0.001 PHE V 529 TRP 0.023 0.001 TRP V 462 HIS 0.004 0.001 HIS V 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (22016) covalent geometry : angle 0.55024 / 0.28 (29926) SS BOND : bond 0.01062 / 0.52 ( 8) SS BOND : angle 1.70548 / 1.03 ( 16) hydrogen bonds : bond 0.03391 / 2.32 ( 648) hydrogen bonds : angle 4.69109 / 3.34 ( 1842) link_BETA1-4 : bond 0.00326 / 0.22 ( 2) link_BETA1-4 : angle 1.52351 / 0.70 ( 6) link_NAG-ASN : bond 0.00274 / 0.18 ( 6) link_NAG-ASN : angle 1.67102 / 0.98 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 159 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 PHE cc_start: 0.4242 (m-10) cc_final: 0.3977 (m-80) REVERT: A 245 TYR cc_start: 0.1747 (m-80) cc_final: 0.1432 (m-80) REVERT: A 584 MET cc_start: 0.6516 (ptt) cc_final: 0.5354 (mmm) REVERT: B 106 MET cc_start: 0.7878 (mmm) cc_final: 0.7577 (ttm) REVERT: B 137 LEU cc_start: 0.8661 (mp) cc_final: 0.8427 (mp) REVERT: B 584 MET cc_start: 0.8217 (mmt) cc_final: 0.8015 (mmm) REVERT: B 624 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8202 (mt) REVERT: U 205 MET cc_start: 0.5529 (mmp) cc_final: 0.4035 (tmm) REVERT: U 316 MET cc_start: 0.6952 (mmp) cc_final: 0.6635 (mmp) REVERT: U 472 MET cc_start: 0.3489 (pmm) cc_final: 0.2813 (ptp) REVERT: V 102 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7374 (ttm110) REVERT: V 128 ASP cc_start: 0.6334 (OUTLIER) cc_final: 0.6084 (p0) REVERT: V 417 TYR cc_start: 0.7875 (t80) cc_final: 0.7568 (t80) REVERT: V 453 ARG cc_start: 0.8125 (tmm-80) cc_final: 0.7690 (mtm110) REVERT: V 594 MET cc_start: 0.6633 (mpp) cc_final: 0.5958 (mtp) outliers start: 80 outliers final: 57 residues processed: 223 average time/residue: 0.1467 time to fit residues: 52.1743 Evaluate side-chains 212 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 152 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 155 ARG Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 243 ARG Chi-restraints excluded: chain U residue 247 SER Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 283 CYS Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain U residue 544 ARG Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 94 MET Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 102 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 280 MET Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 545 ASN Chi-restraints excluded: chain V residue 577 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 162 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 137 optimal weight: 0.7980 chunk 131 optimal weight: 0.4980 chunk 124 optimal weight: 0.5980 chunk 181 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN U 310 HIS ** V 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 401 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 = 0.4742 r_free = 0.4742 target = 0.222343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.189301 restraints weight = 37664.706| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 2.66 r_work: 0.3666 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22032 Z= 0.120 Angle : 0.555 11.003 29966 Z= 0.280 Chirality : 0.043 0.220 3166 Planarity : 0.004 0.072 3874 Dihedral : 6.358 52.899 3306 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.21 % Favored : 93.68 % Rotamer: Outliers : 3.08 % Allowed : 24.47 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.24 (0.16), residues: 2578 helix: 1.33 (0.20), residues: 786 sheet: -1.63 (0.26), residues: 406 loop : -1.92 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 595 TYR 0.018 0.001 TYR V 211 PHE 0.018 0.001 PHE V 529 TRP 0.030 0.001 TRP V 462 HIS 0.003 0.001 HIS V 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (22016) covalent geometry : angle 0.55120 / 0.28 (29926) SS BOND : bond 0.01243 / 0.65 ( 8) SS BOND : angle 2.28164 / 1.81 ( 16) hydrogen bonds : bond 0.03306 / 2.30 ( 648) hydrogen bonds : angle 4.63392 / 3.30 ( 1842) link_BETA1-4 : bond 0.00519 / 0.35 ( 2) link_BETA1-4 : angle 1.49389 / 0.67 ( 6) link_NAG-ASN : bond 0.00270 / 0.17 ( 6) link_NAG-ASN : angle 1.57428 / 0.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 158 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.1824 (m-80) cc_final: 0.1497 (m-80) REVERT: A 584 MET cc_start: 0.6634 (ptt) cc_final: 0.5346 (mmm) REVERT: A 605 GLU cc_start: 0.3236 (OUTLIER) cc_final: 0.1957 (tp30) REVERT: B 106 MET cc_start: 0.7806 (mmm) cc_final: 0.7532 (ttm) REVERT: B 137 LEU cc_start: 0.8732 (mp) cc_final: 0.8496 (mp) REVERT: B 584 MET cc_start: 0.8164 (mmt) cc_final: 0.7953 (mmm) REVERT: B 624 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8201 (mt) REVERT: U 74 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7184 (tp) REVERT: U 205 MET cc_start: 0.5464 (mmp) cc_final: 0.4085 (tmm) REVERT: U 316 MET cc_start: 0.7019 (mmp) cc_final: 0.6706 (mmp) REVERT: U 472 MET cc_start: 0.3277 (pmm) cc_final: 0.2640 (ptp) REVERT: V 102 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7406 (ttm110) REVERT: V 183 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7546 (mt-10) REVERT: V 453 ARG cc_start: 0.7977 (tmm-80) cc_final: 0.7581 (mtm110) REVERT: V 594 MET cc_start: 0.6654 (mpp) cc_final: 0.6244 (mtp) outliers start: 70 outliers final: 57 residues processed: 214 average time/residue: 0.1540 time to fit residues: 52.2596 Evaluate side-chains 210 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 149 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 155 ARG Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 243 ARG Chi-restraints excluded: chain U residue 247 SER Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 283 CYS Chi-restraints excluded: chain U residue 410 LEU Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain U residue 544 ARG Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 94 MET Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 102 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 280 MET Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 493 SER Chi-restraints excluded: chain V residue 545 ASN Chi-restraints excluded: chain V residue 577 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 233 optimal weight: 0.0010 chunk 246 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 131 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 232 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 221 optimal weight: 1.9990 chunk 183 optimal weight: 50.0000 chunk 148 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN U 310 HIS ** V 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 401 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 = 0.4746 r_free = 0.4746 target = 0.222675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.188437 restraints weight = 37661.486| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 2.68 r_work: 0.3663 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22032 Z= 0.110 Angle : 0.544 11.396 29966 Z= 0.274 Chirality : 0.043 0.210 3166 Planarity : 0.004 0.064 3874 Dihedral : 6.288 55.341 3306 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.97 % Favored : 93.95 % Rotamer: Outliers : 3.12 % Allowed : 24.78 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.10 (0.16), residues: 2578 helix: 1.52 (0.20), residues: 762 sheet: -1.55 (0.26), residues: 404 loop : -1.83 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 411 TYR 0.017 0.001 TYR V 417 PHE 0.017 0.001 PHE V 529 TRP 0.034 0.001 TRP V 462 HIS 0.003 0.000 HIS V 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (22016) covalent geometry : angle 0.54121 / 0.27 (29926) SS BOND : bond 0.01276 / 0.55 ( 8) SS BOND : angle 1.90741 / 1.49 ( 16) hydrogen bonds : bond 0.03115 / 2.16 ( 648) hydrogen bonds : angle 4.55430 / 3.24 ( 1842) link_BETA1-4 : bond 0.00438 / 0.30 ( 2) link_BETA1-4 : angle 1.45801 / 0.65 ( 6) link_NAG-ASN : bond 0.00289 / 0.18 ( 6) link_NAG-ASN : angle 1.46797 / 0.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 152 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.1906 (m-80) cc_final: 0.1608 (m-80) REVERT: A 584 MET cc_start: 0.6548 (ptt) cc_final: 0.5299 (mmm) REVERT: A 605 GLU cc_start: 0.3232 (OUTLIER) cc_final: 0.1698 (tp30) REVERT: B 95 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7219 (ttmt) REVERT: B 106 MET cc_start: 0.7899 (mmm) cc_final: 0.7631 (ttm) REVERT: B 137 LEU cc_start: 0.8690 (mp) cc_final: 0.8454 (mp) REVERT: B 584 MET cc_start: 0.8152 (mmt) cc_final: 0.7925 (mmm) REVERT: B 624 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8199 (mt) REVERT: U 74 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7243 (tp) REVERT: U 205 MET cc_start: 0.5456 (OUTLIER) cc_final: 0.4254 (tmm) REVERT: U 316 MET cc_start: 0.7075 (mmp) cc_final: 0.6752 (mmp) REVERT: U 449 MET cc_start: 0.6384 (tpt) cc_final: 0.5530 (tpt) REVERT: U 472 MET cc_start: 0.3293 (pmm) cc_final: 0.2625 (ptp) REVERT: V 102 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7402 (ttm110) REVERT: V 128 ASP cc_start: 0.6271 (OUTLIER) cc_final: 0.6014 (p0) REVERT: V 453 ARG cc_start: 0.8060 (tmm-80) cc_final: 0.7649 (mtm110) REVERT: V 464 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8557 (tt) REVERT: V 594 MET cc_start: 0.6701 (mpp) cc_final: 0.6228 (mtm) outliers start: 71 outliers final: 54 residues processed: 210 average time/residue: 0.1552 time to fit residues: 51.4048 Evaluate side-chains 207 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 145 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 49 LEU Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 155 ARG Chi-restraints excluded: chain U residue 205 MET Chi-restraints excluded: chain U residue 243 ARG Chi-restraints excluded: chain U residue 247 SER Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 283 CYS Chi-restraints excluded: chain U residue 410 LEU Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 102 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 464 LEU Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 493 SER Chi-restraints excluded: chain V residue 545 ASN Chi-restraints excluded: chain V residue 577 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 158 optimal weight: 9.9990 chunk 131 optimal weight: 0.6980 chunk 239 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 232 optimal weight: 2.9990 chunk 168 optimal weight: 0.0010 chunk 200 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 15 optimal weight: 0.0870 chunk 2 optimal weight: 20.0000 chunk 175 optimal weight: 9.9990 overall best weight: 0.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 HIS A 561 GLN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN U 310 HIS V 347 ASN ** V 401 HIS ** 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 = 0.4749 r_free = 0.4749 target = 0.223074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.190463 restraints weight = 37532.938| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 2.67 r_work: 0.3989 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22032 Z= 0.105 Angle : 0.543 10.410 29966 Z= 0.273 Chirality : 0.043 0.278 3166 Planarity : 0.005 0.112 3874 Dihedral : 6.257 56.817 3306 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.91 % Rotamer: Outliers : 3.16 % Allowed : 24.82 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.07 (0.17), residues: 2578 helix: 1.42 (0.20), residues: 776 sheet: -1.48 (0.26), residues: 404 loop : -1.77 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 595 TYR 0.017 0.001 TYR V 417 PHE 0.017 0.001 PHE U 529 TRP 0.040 0.001 TRP V 462 HIS 0.005 0.000 HIS V 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (22016) covalent geometry : angle 0.54014 / 0.27 (29926) SS BOND : bond 0.00963 / 0.42 ( 8) SS BOND : angle 1.69775 / 1.29 ( 16) hydrogen bonds : bond 0.02959 / 2.04 ( 648) hydrogen bonds : angle 4.49743 / 3.20 ( 1842) link_BETA1-4 : bond 0.00472 / 0.32 ( 2) link_BETA1-4 : angle 1.45764 / 0.64 ( 6) link_NAG-ASN : bond 0.00292 / 0.18 ( 6) link_NAG-ASN : angle 1.38573 / 0.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 147 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 GLU cc_start: 0.3752 (OUTLIER) cc_final: 0.1813 (tp30) REVERT: B 95 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7236 (ttmt) REVERT: B 106 MET cc_start: 0.7839 (mmm) cc_final: 0.7594 (ttm) REVERT: B 584 MET cc_start: 0.7872 (mmt) cc_final: 0.7665 (mmm) REVERT: B 624 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8020 (mt) REVERT: B 634 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7994 (tpp) REVERT: U 74 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.6989 (tp) REVERT: U 205 MET cc_start: 0.4982 (OUTLIER) cc_final: 0.4213 (tmm) REVERT: U 472 MET cc_start: 0.3038 (pmm) cc_final: 0.2220 (ptp) REVERT: V 128 ASP cc_start: 0.5684 (OUTLIER) cc_final: 0.5438 (p0) REVERT: V 453 ARG cc_start: 0.8104 (tmm-80) cc_final: 0.7720 (mtm110) REVERT: V 464 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8464 (tt) REVERT: V 594 MET cc_start: 0.6683 (mpp) cc_final: 0.5925 (mtm) outliers start: 72 outliers final: 59 residues processed: 203 average time/residue: 0.1451 time to fit residues: 47.4175 Evaluate side-chains 209 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 142 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 49 LEU Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 155 ARG Chi-restraints excluded: chain U residue 205 MET Chi-restraints excluded: chain U residue 243 ARG Chi-restraints excluded: chain U residue 247 SER Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 283 CYS Chi-restraints excluded: chain U residue 410 LEU Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 280 MET Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 464 LEU Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 493 SER Chi-restraints excluded: chain V residue 545 ASN Chi-restraints excluded: chain V residue 577 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 6 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 196 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 217 optimal weight: 0.0060 chunk 129 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 chunk 255 optimal weight: 9.9990 overall best weight: 4.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS A 561 GLN A 613 HIS A 680 ASN B 253 HIS B 410 ASN B 613 HIS B 717 HIS ** V 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.216597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.183540 restraints weight = 37496.140| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 2.54 r_work: 0.3753 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.118 22032 Z= 0.447 Angle : 0.844 12.015 29966 Z= 0.427 Chirality : 0.055 0.328 3166 Planarity : 0.007 0.081 3874 Dihedral : 7.103 57.203 3306 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.15 % Favored : 90.69 % Rotamer: Outliers : 2.94 % Allowed : 25.00 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.70 (0.16), residues: 2578 helix: 0.85 (0.19), residues: 762 sheet: -1.99 (0.25), residues: 402 loop : -2.06 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 411 TYR 0.026 0.003 TYR U 37 PHE 0.055 0.003 PHE V 238 TRP 0.043 0.002 TRP V 462 HIS 0.011 0.002 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.01090 / 0.45 (22016) covalent geometry : angle 0.84056 / 0.43 (29926) SS BOND : bond 0.01486 / 0.58 ( 8) SS BOND : angle 2.07552 / 1.42 ( 16) hydrogen bonds : bond 0.05994 / 3.96 ( 648) hydrogen bonds : angle 5.09362 / 3.64 ( 1842) link_BETA1-4 : bond 0.00270 / 0.18 ( 2) link_BETA1-4 : angle 2.38998 / 1.22 ( 6) link_NAG-ASN : bond 0.00387 / 0.22 ( 6) link_NAG-ASN : angle 2.38734 / 1.49 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 145 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: -0.1810 (tpp) cc_final: -0.2929 (tpt) REVERT: A 605 GLU cc_start: 0.3226 (OUTLIER) cc_final: 0.1936 (tp30) REVERT: A 680 ASN cc_start: 0.2505 (OUTLIER) cc_final: 0.1493 (m110) REVERT: B 106 MET cc_start: 0.7842 (mmm) cc_final: 0.7544 (mtp) REVERT: B 327 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7403 (mtt-85) REVERT: B 576 MET cc_start: 0.8559 (ttt) cc_final: 0.7864 (ttt) REVERT: U 74 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7417 (tp) REVERT: U 205 MET cc_start: 0.5356 (OUTLIER) cc_final: 0.4097 (tmm) REVERT: U 472 MET cc_start: 0.3301 (pmm) cc_final: 0.2456 (ptp) REVERT: V 102 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7419 (ttm170) REVERT: V 128 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5937 (p0) REVERT: V 417 TYR cc_start: 0.7816 (t80) cc_final: 0.7567 (t80) REVERT: V 464 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8435 (tt) REVERT: V 594 MET cc_start: 0.7370 (mpp) cc_final: 0.6893 (mtp) outliers start: 67 outliers final: 45 residues processed: 200 average time/residue: 0.1504 time to fit residues: 47.4756 Evaluate side-chains 188 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 49 LEU Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 155 ARG Chi-restraints excluded: chain U residue 205 MET Chi-restraints excluded: chain U residue 243 ARG Chi-restraints excluded: chain U residue 247 SER Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 283 CYS Chi-restraints excluded: chain U residue 410 LEU Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 102 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 464 LEU Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 493 SER Chi-restraints excluded: chain V residue 545 ASN Chi-restraints excluded: chain V residue 577 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 255 optimal weight: 3.9990 chunk 235 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 54 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 55 optimal weight: 20.0000 chunk 223 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 352 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.217285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.184472 restraints weight = 37633.956| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 2.56 r_work: 0.3799 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.232 22032 Z= 0.353 Angle : 0.963 59.188 29966 Z= 0.529 Chirality : 0.060 1.595 3166 Planarity : 0.007 0.154 3874 Dihedral : 7.098 57.036 3306 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.92 % Favored : 90.92 % Rotamer: Outliers : 2.59 % Allowed : 25.13 % Favored : 72.28 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.50 % 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: -1.72 (0.16), residues: 2578 helix: 0.83 (0.19), residues: 762 sheet: -1.98 (0.25), residues: 404 loop : -2.08 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 411 TYR 0.023 0.002 TYR U 37 PHE 0.045 0.003 PHE V 238 TRP 0.039 0.002 TRP V 462 HIS 0.008 0.001 HIS V 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00855 / 0.35 (22016) covalent geometry : angle 0.96011 / 0.53 (29926) SS BOND : bond 0.01077 / 0.44 ( 8) SS BOND : angle 2.10705 / 1.40 ( 16) hydrogen bonds : bond 0.05524 / 3.66 ( 648) hydrogen bonds : angle 5.08046 / 3.63 ( 1842) link_BETA1-4 : bond 0.00394 / 0.28 ( 2) link_BETA1-4 : angle 2.35530 / 1.20 ( 6) link_NAG-ASN : bond 0.00367 / 0.22 ( 6) link_NAG-ASN : angle 2.41372 / 1.50 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5336.99 seconds wall clock time: 92 minutes 8.13 seconds (5528.13 seconds total)