Starting phenix.real_space_refine on Fri Sep 19 00:07:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zge_60076/09_2025/8zge_60076.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zge_60076/09_2025/8zge_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zge_60076/09_2025/8zge_60076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zge_60076/09_2025/8zge_60076.map" model { file = "/net/cci-nas-00/data/ceres_data/8zge_60076/09_2025/8zge_60076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zge_60076/09_2025/8zge_60076.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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, 65 Unusual residues: {' MN': 1, 'AKG': 1, 'FE2': 1, 'NAG': 2, 'UDP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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, 65 Unusual residues: {' MN': 1, 'AKG': 1, 'FE2': 1, 'NAG': 2, 'UDP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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, 63 Unusual residues: {' MN': 2, 'GDU': 1, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {' MN': 2, 'GDU': 1, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.97, per 1000 atoms: 0.19 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: 1.70 Conformation dependent library (CDL) restraints added in 944.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.86 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: 3.39 Time building geometry restraints manager: 2.27 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 2.320 nonbonded pdb=" OD2 ASP U 168 " pdb="MN MN U 703 " model vdw 2.077 2.320 nonbonded pdb=" O1B UDP V 702 " pdb="MN MN V 704 " model vdw 2.095 2.320 ... (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: 0.02 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.450 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 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 aren 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 covalent geometry : bond 0.00560 (22016) covalent geometry : angle 0.90524 (29926) SS BOND : bond 0.01051 ( 8) SS BOND : angle 3.73735 ( 16) hydrogen bonds : bond 0.20135 ( 648) hydrogen bonds : angle 6.78834 ( 1842) link_BETA1-4 : bond 0.00328 ( 2) link_BETA1-4 : angle 1.28023 ( 6) link_NAG-ASN : bond 0.01259 ( 6) link_NAG-ASN : angle 5.16725 ( 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 : 0.568 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: 0.1555 time to fit residues: 67.3567 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 : 0.769 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4770 r_free = 0.4770 target = 0.224833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.192703 restraints weight = 37653.080| |-----------------------------------------------------------------------------| r_work (start): 0.4418 rms_B_bonded: 2.51 r_work: 0.3747 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1511 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= 0.132 Angle : 0.616 11.183 29966 Z= 0.310 Chirality : 0.045 0.285 3166 Planarity : 0.005 0.053 3874 Dihedral : 8.565 54.969 3326 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.93 % Favored : 93.91 % Rotamer: Outliers : 2.94 % Allowed : 23.55 % Favored : 73.51 % 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 aren not related in a simple way. whole: -1.62 (0.16), residues: 2578 helix: 1.21 (0.19), residues: 766 sheet: -2.14 (0.25), residues: 422 loop : -2.13 (0.15), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 81 TYR 0.017 0.001 TYR V 211 PHE 0.018 0.001 PHE V 529 TRP 0.032 0.001 TRP U 420 HIS 0.009 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00303 (22016) covalent geometry : angle 0.61071 (29926) SS BOND : bond 0.00908 ( 8) SS BOND : angle 2.46543 ( 16) hydrogen bonds : bond 0.04424 ( 648) hydrogen bonds : angle 5.20459 ( 1842) link_BETA1-4 : bond 0.00525 ( 2) link_BETA1-4 : angle 1.16233 ( 6) link_NAG-ASN : bond 0.00377 ( 6) link_NAG-ASN : angle 2.50637 ( 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 259 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 192 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 MET cc_start: 0.6345 (ptt) cc_final: 0.5311 (mmm) REVERT: A 696 TYR cc_start: 0.4629 (m-80) cc_final: 0.2461 (t80) REVERT: B 279 CYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6504 (t) REVERT: B 634 MET cc_start: 0.8591 (ttm) cc_final: 0.8386 (ttm) REVERT: U 53 ARG cc_start: 0.6204 (OUTLIER) cc_final: 0.5259 (ptp-170) REVERT: U 420 TRP cc_start: 0.3831 (m-10) cc_final: 0.3605 (m-90) REVERT: V 453 ARG cc_start: 0.8109 (tmm-80) cc_final: 0.7713 (mtm110) REVERT: V 587 ASP cc_start: 0.5581 (OUTLIER) cc_final: 0.4930 (p0) outliers start: 67 outliers final: 27 residues processed: 248 average time/residue: 0.1446 time to fit residues: 54.8649 Evaluate side-chains 205 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 163 LEU 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 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: 0.3980 chunk 232 optimal weight: 1.9990 chunk 250 optimal weight: 0.0970 chunk 18 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 41 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4753 r_free = 0.4753 target = 0.223475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.190783 restraints weight = 38161.485| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 2.69 r_work: 0.4015 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22032 Z= 0.151 Angle : 0.591 7.917 29966 Z= 0.298 Chirality : 0.044 0.229 3166 Planarity : 0.005 0.148 3874 Dihedral : 7.492 51.562 3308 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.40 % Favored : 93.41 % Rotamer: Outliers : 3.34 % Allowed : 23.11 % Favored : 73.55 % 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 aren not related in a simple way. whole: -1.56 (0.16), residues: 2578 helix: 1.17 (0.19), residues: 784 sheet: -2.11 (0.24), residues: 434 loop : -2.07 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 602 TYR 0.024 0.001 TYR U 494 PHE 0.020 0.002 PHE A 493 TRP 0.027 0.001 TRP U 462 HIS 0.005 0.001 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00359 (22016) covalent geometry : angle 0.58704 (29926) SS BOND : bond 0.00873 ( 8) SS BOND : angle 2.10608 ( 16) hydrogen bonds : bond 0.03972 ( 648) hydrogen bonds : angle 4.94362 ( 1842) link_BETA1-4 : bond 0.00396 ( 2) link_BETA1-4 : angle 1.27233 ( 6) link_NAG-ASN : bond 0.00272 ( 6) link_NAG-ASN : angle 2.08693 ( 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 254 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 178 time to evaluate : 0.804 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: 0.5531 (ptt) cc_final: 0.4825 (mmm) REVERT: A 696 TYR cc_start: 0.4464 (m-80) cc_final: 0.1677 (t80) REVERT: B 279 CYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6933 (t) REVERT: U 544 ARG cc_start: 0.1840 (OUTLIER) cc_final: 0.1258 (mtt90) REVERT: V 144 MET cc_start: 0.8430 (mmm) cc_final: 0.8219 (mmm) REVERT: V 453 ARG cc_start: 0.8201 (tmm-80) cc_final: 0.7861 (mtm110) outliers start: 76 outliers final: 46 residues processed: 239 average time/residue: 0.1445 time to fit residues: 53.3036 Evaluate side-chains 213 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 617 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 247 SER 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 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 478 GLU Chi-restraints excluded: chain V residue 493 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 215 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 HIS ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 613 HIS ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 310 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.218701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.185770 restraints weight = 37649.619| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.59 r_work: 0.3643 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 22032 Z= 0.335 Angle : 0.738 9.231 29966 Z= 0.376 Chirality : 0.050 0.270 3166 Planarity : 0.006 0.116 3874 Dihedral : 7.407 59.226 3308 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.07 % Favored : 91.70 % Rotamer: Outliers : 4.61 % Allowed : 23.33 % 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 aren not related in a simple way. whole: -1.80 (0.16), residues: 2578 helix: 0.97 (0.19), residues: 774 sheet: -2.19 (0.25), residues: 422 loop : -2.23 (0.15), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 485 TYR 0.029 0.002 TYR V 211 PHE 0.036 0.003 PHE V 238 TRP 0.022 0.002 TRP A 623 HIS 0.010 0.001 HIS B 719 Details of bonding type rmsd covalent geometry : bond 0.00819 (22016) covalent geometry : angle 0.73389 (29926) SS BOND : bond 0.01013 ( 8) SS BOND : angle 2.28272 ( 16) hydrogen bonds : bond 0.05318 ( 648) hydrogen bonds : angle 5.14592 ( 1842) link_BETA1-4 : bond 0.00268 ( 2) link_BETA1-4 : angle 2.05783 ( 6) link_NAG-ASN : bond 0.00339 ( 6) link_NAG-ASN : angle 2.47700 ( 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 263 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 158 time to evaluate : 0.680 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: 0.6502 (ptt) cc_final: 0.5280 (mmm) REVERT: B 106 MET cc_start: 0.7721 (mmm) cc_final: 0.7472 (mtp) REVERT: B 327 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7292 (mtt-85) REVERT: B 446 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7942 (mm-30) REVERT: B 621 ASP cc_start: 0.8260 (t0) cc_final: 0.8057 (t0) REVERT: U 74 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7034 (tp) REVERT: U 316 MET cc_start: 0.7039 (mmp) cc_final: 0.6823 (mmp) REVERT: U 345 MET cc_start: 0.7284 (ttm) cc_final: 0.5981 (mtm) REVERT: U 472 MET cc_start: 0.3619 (pmm) cc_final: 0.2881 (ptp) REVERT: U 544 ARG cc_start: 0.2954 (OUTLIER) cc_final: 0.1368 (mtt90) REVERT: V 102 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7195 (ttm170) REVERT: V 128 ASP cc_start: 0.6102 (OUTLIER) cc_final: 0.5844 (p0) REVERT: V 417 TYR cc_start: 0.7951 (t80) cc_final: 0.7716 (t80) REVERT: V 453 ARG cc_start: 0.8056 (tmm-80) cc_final: 0.7630 (mtm110) REVERT: V 528 MET cc_start: 0.8115 (mmm) cc_final: 0.7908 (mmp) outliers start: 105 outliers final: 60 residues processed: 245 average time/residue: 0.1448 time to fit residues: 55.0346 Evaluate side-chains 212 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 147 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 619 TYR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 671 SER 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 248 LEU 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 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 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 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 280 MET 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 88 VAL Chi-restraints excluded: chain V residue 90 THR 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 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 328 ILE Chi-restraints excluded: chain V residue 372 VAL 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 Chi-restraints excluded: chain V residue 577 TRP 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: 9.9990 chunk 16 optimal weight: 8.9990 chunk 212 optimal weight: 0.7980 chunk 231 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 65 optimal weight: 30.0000 chunk 213 optimal weight: 0.8980 chunk 251 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 HIS B 410 ASN ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 HIS ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 256 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.217706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.184986 restraints weight = 37449.537| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 2.56 r_work: 0.3613 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 22032 Z= 0.339 Angle : 0.740 12.870 29966 Z= 0.377 Chirality : 0.050 0.260 3166 Planarity : 0.006 0.094 3874 Dihedral : 7.159 59.501 3308 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.42 % Favored : 91.35 % Rotamer: Outliers : 4.48 % Allowed : 23.51 % 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 aren not related in a simple way. whole: -1.96 (0.16), residues: 2578 helix: 0.79 (0.19), residues: 762 sheet: -2.26 (0.24), residues: 420 loop : -2.26 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 380 TYR 0.024 0.002 TYR U 161 PHE 0.040 0.002 PHE V 238 TRP 0.014 0.002 TRP B 590 HIS 0.008 0.001 HIS V 235 Details of bonding type rmsd covalent geometry : bond 0.00826 (22016) covalent geometry : angle 0.73551 (29926) SS BOND : bond 0.01557 ( 8) SS BOND : angle 2.30926 ( 16) hydrogen bonds : bond 0.05249 ( 648) hydrogen bonds : angle 5.16121 ( 1842) link_BETA1-4 : bond 0.00404 ( 2) link_BETA1-4 : angle 2.19545 ( 6) link_NAG-ASN : bond 0.00376 ( 6) link_NAG-ASN : angle 2.19141 ( 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 263 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 161 time to evaluate : 0.754 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: 0.1840 (m-80) cc_final: 0.1509 (m-80) REVERT: A 584 MET cc_start: 0.6244 (ptt) cc_final: 0.5088 (mmm) REVERT: A 605 GLU cc_start: 0.3438 (OUTLIER) cc_final: 0.1908 (tp30) REVERT: B 327 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7499 (mmt180) REVERT: B 621 ASP cc_start: 0.8677 (t0) cc_final: 0.8398 (t0) REVERT: B 645 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8569 (tttm) REVERT: U 74 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7165 (tp) REVERT: U 316 MET cc_start: 0.7067 (mmp) cc_final: 0.6760 (mmp) REVERT: U 345 MET cc_start: 0.7467 (ttm) cc_final: 0.6201 (mtm) REVERT: U 472 MET cc_start: 0.3613 (pmm) cc_final: 0.2893 (ptp) REVERT: V 102 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7628 (ttm170) REVERT: V 128 ASP cc_start: 0.6273 (OUTLIER) cc_final: 0.6038 (p0) REVERT: V 160 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.7596 (p0) REVERT: V 417 TYR cc_start: 0.8054 (t80) cc_final: 0.7796 (t80) REVERT: V 453 ARG cc_start: 0.8183 (tmm-80) cc_final: 0.7737 (mtm110) REVERT: V 464 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8564 (tt) REVERT: V 594 MET cc_start: 0.7392 (mpp) cc_final: 0.7013 (mtp) outliers start: 102 outliers final: 63 residues processed: 249 average time/residue: 0.1356 time to fit residues: 53.3106 Evaluate side-chains 216 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 146 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 605 GLU 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 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 327 ARG Chi-restraints excluded: chain B residue 396 VAL 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 609 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 694 LEU 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 47 SER Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 86 LEU 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 410 LEU Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain U residue 544 ARG Chi-restraints excluded: chain V residue 58 LEU 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 128 ASP Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 160 ASP 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 328 ILE Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 437 ASP 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 521 VAL Chi-restraints excluded: chain V residue 545 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 21 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 238 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 228 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 195 optimal weight: 0.3980 chunk 203 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 134 optimal weight: 0.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 ASN A 717 HIS ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 347 ASN V 352 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.220570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.187681 restraints weight = 37778.012| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 2.56 r_work: 0.3680 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22032 Z= 0.120 Angle : 0.578 12.700 29966 Z= 0.291 Chirality : 0.044 0.248 3166 Planarity : 0.005 0.073 3874 Dihedral : 6.644 59.872 3307 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.21 % Favored : 93.56 % Rotamer: Outliers : 2.94 % Allowed : 25.04 % 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 aren not related in a simple way. whole: -1.51 (0.16), residues: 2578 helix: 1.19 (0.19), residues: 762 sheet: -1.84 (0.26), residues: 404 loop : -2.08 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 411 TYR 0.015 0.001 TYR V 417 PHE 0.019 0.001 PHE V 529 TRP 0.013 0.001 TRP V 586 HIS 0.004 0.001 HIS B 668 Details of bonding type rmsd covalent geometry : bond 0.00279 (22016) covalent geometry : angle 0.57463 (29926) SS BOND : bond 0.01326 ( 8) SS BOND : angle 2.08964 ( 16) hydrogen bonds : bond 0.03460 ( 648) hydrogen bonds : angle 4.78701 ( 1842) link_BETA1-4 : bond 0.00454 ( 2) link_BETA1-4 : angle 1.70675 ( 6) link_NAG-ASN : bond 0.00293 ( 6) link_NAG-ASN : angle 1.58570 ( 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 229 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 162 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.1791 (m-80) cc_final: 0.1473 (m-80) REVERT: A 584 MET cc_start: 0.6316 (ptt) cc_final: 0.5153 (mmm) REVERT: A 650 MET cc_start: 0.4919 (ttt) cc_final: 0.4659 (ttt) REVERT: A 680 ASN cc_start: 0.2335 (OUTLIER) cc_final: 0.1440 (m110) REVERT: B 106 MET cc_start: 0.7871 (mmm) cc_final: 0.7615 (ttm) REVERT: B 137 LEU cc_start: 0.8634 (mp) cc_final: 0.8423 (mp) REVERT: B 327 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7307 (mtt-85) REVERT: B 554 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6309 (mt-10) REVERT: B 584 MET cc_start: 0.8075 (mmt) cc_final: 0.7858 (mmm) REVERT: B 621 ASP cc_start: 0.8220 (t0) cc_final: 0.8004 (t0) REVERT: B 645 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8519 (tttm) REVERT: B 698 CYS cc_start: 0.6040 (OUTLIER) cc_final: 0.5768 (t) REVERT: U 74 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7068 (tp) REVERT: U 144 MET cc_start: 0.6672 (mmm) cc_final: 0.6449 (mmm) REVERT: U 316 MET cc_start: 0.7037 (mmp) cc_final: 0.6734 (mmp) REVERT: U 345 MET cc_start: 0.7192 (ttm) cc_final: 0.6084 (mtm) REVERT: U 472 MET cc_start: 0.3535 (pmm) cc_final: 0.2869 (ptp) REVERT: V 128 ASP cc_start: 0.6354 (OUTLIER) cc_final: 0.6094 (p0) REVERT: V 183 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7557 (mt-10) REVERT: V 417 TYR cc_start: 0.7828 (t80) cc_final: 0.7576 (t80) REVERT: V 453 ARG cc_start: 0.8130 (tmm-80) cc_final: 0.7650 (mtm110) REVERT: V 594 MET cc_start: 0.7203 (mpp) cc_final: 0.6613 (mtm) outliers start: 67 outliers final: 41 residues processed: 216 average time/residue: 0.1424 time to fit residues: 47.5672 Evaluate side-chains 191 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 506 LEU Chi-restraints excluded: chain A residue 523 THR 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 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 327 ARG Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 566 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 37 TYR 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 155 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 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 108 VAL Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 280 MET Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 371 LEU 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 521 VAL Chi-restraints excluded: chain V residue 545 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 162 optimal weight: 0.0770 chunk 244 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 137 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 chunk 118 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 ASN ** V 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.218507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.182734 restraints weight = 36993.462| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 2.65 r_work: 0.3728 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22032 Z= 0.135 Angle : 0.581 13.002 29966 Z= 0.292 Chirality : 0.044 0.224 3166 Planarity : 0.005 0.067 3874 Dihedral : 6.580 58.711 3307 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.83 % Favored : 92.98 % Rotamer: Outliers : 2.94 % Allowed : 25.31 % Favored : 71.75 % 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 aren not related in a simple way. whole: -1.37 (0.16), residues: 2578 helix: 1.31 (0.20), residues: 760 sheet: -1.75 (0.26), residues: 404 loop : -1.98 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 594 TYR 0.014 0.001 TYR V 417 PHE 0.019 0.001 PHE V 529 TRP 0.012 0.001 TRP V 462 HIS 0.004 0.001 HIS V 310 Details of bonding type rmsd covalent geometry : bond 0.00323 (22016) covalent geometry : angle 0.57799 (29926) SS BOND : bond 0.01414 ( 8) SS BOND : angle 1.75063 ( 16) hydrogen bonds : bond 0.03484 ( 648) hydrogen bonds : angle 4.68146 ( 1842) link_BETA1-4 : bond 0.00478 ( 2) link_BETA1-4 : angle 1.66618 ( 6) link_NAG-ASN : bond 0.00387 ( 6) link_NAG-ASN : angle 1.66935 ( 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 212 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 145 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.3055 (tpt) cc_final: 0.2846 (mmm) REVERT: A 144 CYS cc_start: 0.0566 (OUTLIER) cc_final: -0.0661 (p) REVERT: A 245 TYR cc_start: 0.1754 (m-80) cc_final: 0.1525 (m-80) REVERT: A 584 MET cc_start: 0.6158 (ptt) cc_final: 0.4980 (mmm) REVERT: B 95 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7623 (tttt) REVERT: B 106 MET cc_start: 0.7855 (mmm) cc_final: 0.7650 (ttm) REVERT: B 327 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7315 (mtt-85) REVERT: B 554 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6232 (mt-10) REVERT: B 645 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8556 (tttm) REVERT: B 698 CYS cc_start: 0.6061 (OUTLIER) cc_final: 0.5790 (t) REVERT: U 74 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7110 (tp) REVERT: U 205 MET cc_start: 0.6420 (mmm) cc_final: 0.5419 (tmm) REVERT: U 316 MET cc_start: 0.7018 (mmp) cc_final: 0.6812 (mmp) REVERT: U 338 MET cc_start: 0.3764 (tpt) cc_final: 0.3553 (tpt) REVERT: U 472 MET cc_start: 0.3455 (pmm) cc_final: 0.2744 (ptp) REVERT: V 128 ASP cc_start: 0.6141 (OUTLIER) cc_final: 0.5907 (p0) REVERT: V 453 ARG cc_start: 0.8219 (tmm-80) cc_final: 0.7734 (mtm110) REVERT: V 464 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8536 (tt) REVERT: V 594 MET cc_start: 0.7136 (mpp) cc_final: 0.6711 (mtm) outliers start: 67 outliers final: 44 residues processed: 200 average time/residue: 0.1349 time to fit residues: 43.1986 Evaluate side-chains 193 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 523 THR 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 227 ASP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 327 ARG 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 554 GLU 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 637 SER 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 722 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 155 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 88 VAL 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 243 ARG Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 464 LEU Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 521 VAL Chi-restraints excluded: chain V residue 545 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 233 optimal weight: 6.9990 chunk 246 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 232 optimal weight: 0.8980 chunk 133 optimal weight: 0.3980 chunk 221 optimal weight: 2.9990 chunk 183 optimal weight: 50.0000 chunk 148 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS B 410 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.219719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.186256 restraints weight = 37597.607| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 2.66 r_work: 0.3746 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22032 Z= 0.157 Angle : 0.596 12.508 29966 Z= 0.299 Chirality : 0.044 0.230 3166 Planarity : 0.005 0.066 3874 Dihedral : 6.574 58.548 3307 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.14 % Favored : 92.67 % Rotamer: Outliers : 3.25 % Allowed : 25.26 % Favored : 71.49 % 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 aren not related in a simple way. whole: -1.33 (0.16), residues: 2578 helix: 1.29 (0.20), residues: 762 sheet: -1.77 (0.26), residues: 404 loop : -1.91 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 595 TYR 0.015 0.001 TYR B 64 PHE 0.019 0.001 PHE V 529 TRP 0.019 0.001 TRP V 462 HIS 0.006 0.001 HIS V 310 Details of bonding type rmsd covalent geometry : bond 0.00379 (22016) covalent geometry : angle 0.59184 (29926) SS BOND : bond 0.01279 ( 8) SS BOND : angle 2.56941 ( 16) hydrogen bonds : bond 0.03749 ( 648) hydrogen bonds : angle 4.68949 ( 1842) link_BETA1-4 : bond 0.00381 ( 2) link_BETA1-4 : angle 1.67622 ( 6) link_NAG-ASN : bond 0.00220 ( 6) link_NAG-ASN : angle 1.70172 ( 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 221 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 147 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.0658 (OUTLIER) cc_final: -0.0559 (p) REVERT: A 605 GLU cc_start: 0.3166 (OUTLIER) cc_final: 0.2057 (tp30) REVERT: B 95 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7580 (tttt) REVERT: B 106 MET cc_start: 0.7988 (mmm) cc_final: 0.7741 (ttm) REVERT: B 327 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7287 (mtt-85) REVERT: B 397 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8450 (mp) REVERT: B 554 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6273 (mt-10) REVERT: B 584 MET cc_start: 0.7996 (mmt) cc_final: 0.7788 (mmm) REVERT: B 624 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8167 (mt) REVERT: B 645 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8507 (tttm) REVERT: B 698 CYS cc_start: 0.6061 (OUTLIER) cc_final: 0.5782 (t) REVERT: U 74 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7133 (tp) REVERT: U 205 MET cc_start: 0.6351 (mmm) cc_final: 0.5391 (tmm) REVERT: U 472 MET cc_start: 0.3380 (pmm) cc_final: 0.2689 (ptp) REVERT: V 128 ASP cc_start: 0.6411 (OUTLIER) cc_final: 0.6159 (p0) REVERT: V 453 ARG cc_start: 0.8236 (tmm-80) cc_final: 0.7746 (mtm110) REVERT: V 464 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8532 (tt) outliers start: 74 outliers final: 49 residues processed: 209 average time/residue: 0.1351 time to fit residues: 44.6402 Evaluate side-chains 199 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 279 CYS 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 610 VAL 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 227 ASP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 397 LEU 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 481 VAL 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 554 GLU 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 637 SER 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 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 155 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 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 108 VAL Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 464 LEU Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 545 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 158 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 chunk 239 optimal weight: 0.0670 chunk 111 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN B 410 ASN ** V 401 HIS ** 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 = 0.4720 r_free = 0.4720 target = 0.220116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.188436 restraints weight = 37416.694| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.46 r_work: 0.3813 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22032 Z= 0.140 Angle : 0.593 11.835 29966 Z= 0.298 Chirality : 0.044 0.307 3166 Planarity : 0.005 0.064 3874 Dihedral : 6.539 58.094 3307 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.94 % Favored : 92.90 % Rotamer: Outliers : 2.64 % Allowed : 25.92 % Favored : 71.44 % 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 aren not related in a simple way. whole: -1.26 (0.16), residues: 2578 helix: 1.33 (0.20), residues: 762 sheet: -1.70 (0.26), residues: 404 loop : -1.86 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 544 TYR 0.017 0.001 TYR A 245 PHE 0.017 0.001 PHE V 529 TRP 0.016 0.001 TRP V 462 HIS 0.004 0.001 HIS V 310 Details of bonding type rmsd covalent geometry : bond 0.00337 (22016) covalent geometry : angle 0.58919 (29926) SS BOND : bond 0.01139 ( 8) SS BOND : angle 2.39034 ( 16) hydrogen bonds : bond 0.03509 ( 648) hydrogen bonds : angle 4.63465 ( 1842) link_BETA1-4 : bond 0.00368 ( 2) link_BETA1-4 : angle 1.65200 ( 6) link_NAG-ASN : bond 0.00244 ( 6) link_NAG-ASN : angle 1.55572 ( 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 205 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 145 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.0602 (OUTLIER) cc_final: -0.0584 (p) REVERT: A 605 GLU cc_start: 0.3188 (OUTLIER) cc_final: 0.2066 (tp30) REVERT: B 95 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7580 (tttt) REVERT: B 397 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8408 (mp) REVERT: B 554 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6174 (mt-10) REVERT: B 584 MET cc_start: 0.7848 (mmt) cc_final: 0.7646 (mmm) REVERT: B 645 LYS cc_start: 0.8719 (mmmt) cc_final: 0.8501 (tttm) REVERT: B 698 CYS cc_start: 0.5981 (OUTLIER) cc_final: 0.5705 (t) REVERT: U 74 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7133 (tp) REVERT: U 205 MET cc_start: 0.6573 (mmm) cc_final: 0.5675 (tmm) REVERT: U 472 MET cc_start: 0.3293 (pmm) cc_final: 0.2609 (ptp) REVERT: V 128 ASP cc_start: 0.6246 (OUTLIER) cc_final: 0.6021 (p0) REVERT: V 183 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7418 (mt-10) REVERT: V 453 ARG cc_start: 0.8198 (tmm-80) cc_final: 0.7719 (mtm110) outliers start: 60 outliers final: 49 residues processed: 195 average time/residue: 0.1394 time to fit residues: 43.3860 Evaluate side-chains 196 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 279 CYS 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 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 288 THR Chi-restraints excluded: chain B residue 397 LEU 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 554 GLU 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 609 THR Chi-restraints excluded: chain B residue 637 SER 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 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 155 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 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 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 315 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 372 VAL 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 594 MET 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: 20.0000 chunk 196 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 163 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 255 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN A 613 HIS A 717 HIS B 410 ASN U 169 ASN ** V 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.216276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.182666 restraints weight = 37467.083| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 2.57 r_work: 0.3881 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.097 22032 Z= 0.374 Angle : 0.779 13.957 29966 Z= 0.393 Chirality : 0.052 0.304 3166 Planarity : 0.007 0.084 3874 Dihedral : 7.042 58.831 3307 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.23 % Favored : 90.57 % Rotamer: Outliers : 2.99 % Allowed : 25.62 % Favored : 71.40 % 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 aren not related in a simple way. whole: -1.61 (0.16), residues: 2578 helix: 1.06 (0.20), residues: 744 sheet: -1.99 (0.25), residues: 404 loop : -2.03 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 695 TYR 0.023 0.002 TYR B 64 PHE 0.040 0.003 PHE V 413 TRP 0.015 0.002 TRP V 462 HIS 0.011 0.002 HIS V 235 Details of bonding type rmsd covalent geometry : bond 0.00912 (22016) covalent geometry : angle 0.77493 (29926) SS BOND : bond 0.01365 ( 8) SS BOND : angle 2.68395 ( 16) hydrogen bonds : bond 0.05423 ( 648) hydrogen bonds : angle 4.98987 ( 1842) link_BETA1-4 : bond 0.00277 ( 2) link_BETA1-4 : angle 2.26739 ( 6) link_NAG-ASN : bond 0.00312 ( 6) link_NAG-ASN : angle 2.12661 ( 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 214 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 146 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.0585 (OUTLIER) cc_final: -0.0422 (p) REVERT: B 327 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7585 (mtt-85) REVERT: B 397 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8412 (mp) REVERT: B 554 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6613 (mt-10) REVERT: B 621 ASP cc_start: 0.8317 (t0) cc_final: 0.8073 (t0) REVERT: B 698 CYS cc_start: 0.6492 (OUTLIER) cc_final: 0.6241 (t) REVERT: U 74 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7100 (tp) REVERT: U 205 MET cc_start: 0.6527 (mmm) cc_final: 0.5637 (tmm) REVERT: U 472 MET cc_start: 0.3265 (pmm) cc_final: 0.2483 (ptp) REVERT: V 128 ASP cc_start: 0.6237 (OUTLIER) cc_final: 0.5983 (p0) REVERT: V 453 ARG cc_start: 0.8346 (tmm-80) cc_final: 0.7808 (mtm110) REVERT: V 464 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8487 (tt) outliers start: 68 outliers final: 53 residues processed: 204 average time/residue: 0.1359 time to fit residues: 44.2759 Evaluate side-chains 199 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 138 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 610 VAL 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 227 ASP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 481 VAL 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 554 GLU 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 609 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 637 SER 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 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 155 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 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 214 THR Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 424 VAL Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 464 LEU Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 545 ASN Chi-restraints excluded: chain V residue 594 MET 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: 0.9980 chunk 66 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 224 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 223 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 717 HIS ** V 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.219589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.186433 restraints weight = 37784.802| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.67 r_work: 0.3642 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22032 Z= 0.132 Angle : 0.602 12.450 29966 Z= 0.302 Chirality : 0.044 0.260 3166 Planarity : 0.005 0.061 3874 Dihedral : 6.639 56.653 3307 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.59 % Favored : 93.25 % Rotamer: Outliers : 2.33 % Allowed : 26.01 % Favored : 71.66 % 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 aren not related in a simple way. whole: -1.30 (0.16), residues: 2578 helix: 1.29 (0.20), residues: 746 sheet: -1.72 (0.25), residues: 404 loop : -1.85 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 411 TYR 0.014 0.001 TYR V 494 PHE 0.016 0.001 PHE V 529 TRP 0.021 0.001 TRP V 462 HIS 0.004 0.001 HIS V 310 Details of bonding type rmsd covalent geometry : bond 0.00313 (22016) covalent geometry : angle 0.59745 (29926) SS BOND : bond 0.01129 ( 8) SS BOND : angle 2.44263 ( 16) hydrogen bonds : bond 0.03474 ( 648) hydrogen bonds : angle 4.67084 ( 1842) link_BETA1-4 : bond 0.00087 ( 2) link_BETA1-4 : angle 1.77043 ( 6) link_NAG-ASN : bond 0.00274 ( 6) link_NAG-ASN : angle 1.61945 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5130.91 seconds wall clock time: 88 minutes 23.31 seconds (5303.31 seconds total)