Starting phenix.real_space_refine on Wed May 21 12:36:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zge_60076/05_2025/8zge_60076.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zge_60076/05_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_60076/05_2025/8zge_60076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zge_60076/05_2025/8zge_60076.map" model { file = "/net/cci-nas-00/data/ceres_data/8zge_60076/05_2025/8zge_60076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zge_60076/05_2025/8zge_60076.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.28, per 1000 atoms: 0.62 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: 6.39 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.95 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: 8.67 Time building geometry restraints manager: 7.28 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: 0.12 Found NCS groups: ncs_group { reference = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 53.040 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.760 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP B 425 HIS 0.006 0.001 HIS A 527 PHE 0.020 0.002 PHE B 62 TYR 0.037 0.001 TYR B 64 ARG 0.007 0.000 ARG A 380 Details of bonding type rmsd link_NAG-ASN : bond 0.01259 ( 6) link_NAG-ASN : angle 5.16725 ( 18) link_BETA1-4 : bond 0.00328 ( 2) link_BETA1-4 : angle 1.28023 ( 6) hydrogen bonds : bond 0.20135 ( 648) hydrogen bonds : angle 6.78834 ( 1842) SS BOND : bond 0.01051 ( 8) SS BOND : angle 3.73735 ( 16) covalent geometry : bond 0.00560 (22016) covalent geometry : angle 0.90524 (29926) *********************** 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 : 2.453 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: 0.3677 time to fit residues: 159.2284 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 : 2.435 ------------------------------------------------------------------------------- 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 216 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 149 optimal weight: 30.0000 chunk 232 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.223539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.191473 restraints weight = 37757.782| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 2.59 r_work: 0.3871 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22032 Z= 0.180 Angle : 0.652 11.738 29966 Z= 0.329 Chirality : 0.046 0.275 3166 Planarity : 0.005 0.055 3874 Dihedral : 8.633 54.648 3326 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.56 % Favored : 93.25 % Rotamer: Outliers : 3.56 % Allowed : 23.33 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2578 helix: 1.18 (0.19), residues: 754 sheet: -2.24 (0.25), residues: 426 loop : -2.17 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP U 420 HIS 0.007 0.001 HIS A 421 PHE 0.021 0.002 PHE V 238 TYR 0.020 0.001 TYR B 64 ARG 0.005 0.000 ARG V 485 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 6) link_NAG-ASN : angle 2.49742 ( 18) link_BETA1-4 : bond 0.00426 ( 2) link_BETA1-4 : angle 1.26592 ( 6) hydrogen bonds : bond 0.04575 ( 648) hydrogen bonds : angle 5.22117 ( 1842) SS BOND : bond 0.00973 ( 8) SS BOND : angle 2.59173 ( 16) covalent geometry : bond 0.00429 (22016) covalent geometry : angle 0.64669 (29926) *********************** 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 269 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 188 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 MET cc_start: 0.5780 (ptt) cc_final: 0.4972 (mmm) REVERT: A 696 TYR cc_start: 0.4567 (m-80) cc_final: 0.2337 (t80) REVERT: B 279 CYS cc_start: 0.6765 (OUTLIER) cc_final: 0.6521 (t) REVERT: V 428 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6827 (mp) REVERT: V 453 ARG cc_start: 0.8218 (tmm-80) cc_final: 0.7842 (mtm110) REVERT: V 587 ASP cc_start: 0.5677 (OUTLIER) cc_final: 0.5287 (p0) outliers start: 81 outliers final: 40 residues processed: 256 average time/residue: 0.3491 time to fit residues: 136.1900 Evaluate side-chains 214 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 2.656 ------------------------------------------------------------------------------- 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 628 ARG 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 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 506 LEU 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 649 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 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 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 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 428 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 493 SER Chi-restraints excluded: chain V residue 587 ASP Chi-restraints excluded: chain V residue 602 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 190 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 117 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 224 optimal weight: 0.0050 chunk 176 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.223749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.191352 restraints weight = 37371.797| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.67 r_work: 0.3798 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22032 Z= 0.122 Angle : 0.567 7.673 29966 Z= 0.286 Chirality : 0.043 0.228 3166 Planarity : 0.005 0.141 3874 Dihedral : 7.550 55.338 3311 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.86 % Favored : 93.99 % Rotamer: Outliers : 3.12 % Allowed : 23.64 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.16), residues: 2578 helix: 1.17 (0.19), residues: 786 sheet: -2.10 (0.24), residues: 434 loop : -2.05 (0.15), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP U 420 HIS 0.004 0.001 HIS A 421 PHE 0.020 0.001 PHE V 529 TYR 0.025 0.001 TYR U 494 ARG 0.005 0.000 ARG U 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 6) link_NAG-ASN : angle 1.97576 ( 18) link_BETA1-4 : bond 0.00721 ( 2) link_BETA1-4 : angle 1.38838 ( 6) hydrogen bonds : bond 0.03642 ( 648) hydrogen bonds : angle 4.90010 ( 1842) SS BOND : bond 0.00762 ( 8) SS BOND : angle 2.05460 ( 16) covalent geometry : bond 0.00280 (22016) covalent geometry : angle 0.56341 (29926) *********************** 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 251 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 180 time to evaluate : 2.455 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: 0.6258 (ptt) cc_final: 0.5214 (mmm) REVERT: A 696 TYR cc_start: 0.4560 (m-80) cc_final: 0.1747 (t80) REVERT: B 279 CYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6514 (t) REVERT: U 449 MET cc_start: 0.6512 (tpt) cc_final: 0.6311 (tpp) REVERT: U 544 ARG cc_start: 0.2463 (OUTLIER) cc_final: 0.2117 (mtt90) REVERT: V 144 MET cc_start: 0.8147 (mmm) cc_final: 0.7933 (mmm) REVERT: V 183 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7345 (mt-10) REVERT: V 453 ARG cc_start: 0.8102 (tmm-80) cc_final: 0.7723 (mtm110) REVERT: V 587 ASP cc_start: 0.5520 (OUTLIER) cc_final: 0.4958 (p0) outliers start: 71 outliers final: 36 residues processed: 233 average time/residue: 0.3372 time to fit residues: 122.6055 Evaluate side-chains 207 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 2.558 ------------------------------------------------------------------------------- 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 628 ARG Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU 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 709 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 155 ARG Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 247 SER Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 280 MET Chi-restraints excluded: chain U residue 544 ARG 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 328 ILE Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 211 optimal weight: 1.9990 chunk 247 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 140 optimal weight: 0.1980 chunk 168 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 203 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 681 HIS ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 169 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 = 0.4764 r_free = 0.4764 target = 0.224433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.191658 restraints weight = 37907.059| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 2.75 r_work: 0.3724 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22032 Z= 0.114 Angle : 0.552 7.650 29966 Z= 0.276 Chirality : 0.043 0.221 3166 Planarity : 0.005 0.111 3874 Dihedral : 6.784 55.077 3308 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.78 % Favored : 94.03 % Rotamer: Outliers : 3.78 % Allowed : 22.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.16), residues: 2578 helix: 1.21 (0.19), residues: 800 sheet: -1.92 (0.25), residues: 424 loop : -2.00 (0.15), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP U 420 HIS 0.003 0.000 HIS V 310 PHE 0.019 0.001 PHE V 529 TYR 0.020 0.001 TYR V 211 ARG 0.007 0.000 ARG A 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 6) link_NAG-ASN : angle 1.62717 ( 18) link_BETA1-4 : bond 0.00452 ( 2) link_BETA1-4 : angle 1.42330 ( 6) hydrogen bonds : bond 0.03412 ( 648) hydrogen bonds : angle 4.78438 ( 1842) SS BOND : bond 0.01457 ( 8) SS BOND : angle 1.87382 ( 16) covalent geometry : bond 0.00261 (22016) covalent geometry : angle 0.54866 (29926) *********************** 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 269 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 183 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 MET cc_start: 0.6567 (ptt) cc_final: 0.5413 (mmm) REVERT: A 696 TYR cc_start: 0.4624 (m-80) cc_final: 0.1804 (t80) REVERT: B 79 ASP cc_start: 0.5773 (OUTLIER) cc_final: 0.5449 (t70) REVERT: B 279 CYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6568 (t) REVERT: U 74 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7065 (tp) REVERT: U 135 TRP cc_start: 0.5499 (m100) cc_final: 0.4941 (m-10) REVERT: U 345 MET cc_start: 0.7322 (ttm) cc_final: 0.6132 (mtm) REVERT: U 544 ARG cc_start: 0.2882 (OUTLIER) cc_final: 0.1465 (mtt90) REVERT: V 105 LEU cc_start: 0.8105 (mt) cc_final: 0.7902 (mt) REVERT: V 183 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7519 (mt-10) REVERT: V 453 ARG cc_start: 0.7975 (tmm-80) cc_final: 0.7622 (mtm110) outliers start: 86 outliers final: 52 residues processed: 251 average time/residue: 0.3359 time to fit residues: 132.1295 Evaluate side-chains 223 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 671 SER 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 79 ASP Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 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 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 247 SER Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 280 MET Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain U residue 544 ARG Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 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 317 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 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 85 optimal weight: 0.0870 chunk 176 optimal weight: 30.0000 chunk 143 optimal weight: 2.9990 chunk 215 optimal weight: 0.0470 chunk 13 optimal weight: 40.0000 chunk 135 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- 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** B 410 ASN ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 169 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 = 0.4746 r_free = 0.4746 target = 0.222881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.189765 restraints weight = 37775.761| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.72 r_work: 0.3685 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22032 Z= 0.141 Angle : 0.561 7.633 29966 Z= 0.281 Chirality : 0.044 0.215 3166 Planarity : 0.005 0.094 3874 Dihedral : 6.724 56.880 3308 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.17 % Favored : 93.68 % Rotamer: Outliers : 4.13 % Allowed : 22.63 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2578 helix: 1.23 (0.19), residues: 798 sheet: -1.70 (0.26), residues: 408 loop : -1.95 (0.15), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP U 420 HIS 0.004 0.001 HIS B 719 PHE 0.016 0.001 PHE V 308 TYR 0.016 0.001 TYR U 494 ARG 0.006 0.000 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 6) link_NAG-ASN : angle 1.65134 ( 18) link_BETA1-4 : bond 0.00502 ( 2) link_BETA1-4 : angle 1.48516 ( 6) hydrogen bonds : bond 0.03516 ( 648) hydrogen bonds : angle 4.70888 ( 1842) SS BOND : bond 0.00942 ( 8) SS BOND : angle 1.73593 ( 16) covalent geometry : bond 0.00338 (22016) covalent geometry : angle 0.55759 (29926) *********************** 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 261 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 167 time to evaluate : 2.423 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: 0.1537 (m-80) cc_final: 0.1207 (m-80) REVERT: A 584 MET cc_start: 0.6739 (ptt) cc_final: 0.5502 (mmm) REVERT: A 696 TYR cc_start: 0.4712 (m-80) cc_final: 0.1777 (t80) REVERT: A 732 MET cc_start: 0.3077 (tpp) cc_final: 0.2761 (tpp) REVERT: B 634 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8289 (tpp) REVERT: U 74 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7099 (tp) REVERT: U 205 MET cc_start: 0.5740 (mmm) cc_final: 0.4742 (tmm) REVERT: U 345 MET cc_start: 0.7330 (ttm) cc_final: 0.6122 (mtm) REVERT: U 392 MET cc_start: 0.4788 (ppp) cc_final: 0.4478 (ppp) REVERT: U 544 ARG cc_start: 0.2886 (OUTLIER) cc_final: 0.1517 (mtt90) REVERT: U 577 TRP cc_start: 0.4409 (p-90) cc_final: 0.3435 (t60) REVERT: V 105 LEU cc_start: 0.8182 (mt) cc_final: 0.7928 (mt) REVERT: V 453 ARG cc_start: 0.7988 (tmm-80) cc_final: 0.7616 (mtm110) REVERT: V 587 ASP cc_start: 0.5576 (OUTLIER) cc_final: 0.4892 (p0) outliers start: 94 outliers final: 60 residues processed: 243 average time/residue: 0.3268 time to fit residues: 124.3249 Evaluate side-chains 224 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 160 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 634 MET 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 87 TRP 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 346 ILE Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain U residue 544 ARG Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 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 410 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 545 ASN Chi-restraints excluded: chain V residue 577 TRP Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 133 optimal weight: 0.7980 chunk 223 optimal weight: 0.7980 chunk 218 optimal weight: 0.0030 chunk 204 optimal weight: 3.9990 chunk 252 optimal weight: 7.9990 chunk 242 optimal weight: 0.0070 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 99 optimal weight: 0.0980 chunk 69 optimal weight: 0.0770 chunk 57 optimal weight: 4.9990 overall best weight: 0.1966 ------------------------------------------------------------------------------- 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** B 410 ASN ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 169 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 = 0.4766 r_free = 0.4766 target = 0.224684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.192182 restraints weight = 37680.864| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 2.63 r_work: 0.3772 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 22032 Z= 0.095 Angle : 0.535 10.008 29966 Z= 0.267 Chirality : 0.042 0.211 3166 Planarity : 0.004 0.080 3874 Dihedral : 6.572 59.793 3308 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.62 % Favored : 94.30 % Rotamer: Outliers : 2.68 % Allowed : 24.43 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.16), residues: 2578 helix: 1.33 (0.19), residues: 798 sheet: -1.45 (0.26), residues: 400 loop : -1.88 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP U 420 HIS 0.002 0.000 HIS V 310 PHE 0.015 0.001 PHE V 529 TYR 0.023 0.001 TYR U 494 ARG 0.010 0.000 ARG A 551 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 6) link_NAG-ASN : angle 1.53943 ( 18) link_BETA1-4 : bond 0.00525 ( 2) link_BETA1-4 : angle 1.37409 ( 6) hydrogen bonds : bond 0.02973 ( 648) hydrogen bonds : angle 4.61255 ( 1842) SS BOND : bond 0.01590 ( 8) SS BOND : angle 1.92922 ( 16) covalent geometry : bond 0.00210 (22016) covalent geometry : angle 0.53207 (29926) *********************** 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 233 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 172 time to evaluate : 2.356 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: 0.1536 (m-80) cc_final: 0.1197 (m-80) REVERT: A 584 MET cc_start: 0.6563 (ptt) cc_final: 0.5430 (mmm) REVERT: A 696 TYR cc_start: 0.4602 (m-80) cc_final: 0.1721 (t80) REVERT: B 584 MET cc_start: 0.8115 (mmt) cc_final: 0.7897 (mmm) REVERT: B 634 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8129 (tpp) REVERT: V 453 ARG cc_start: 0.8009 (tmm-80) cc_final: 0.7660 (mtm110) REVERT: V 587 ASP cc_start: 0.5559 (OUTLIER) cc_final: 0.4851 (p0) outliers start: 61 outliers final: 40 residues processed: 217 average time/residue: 0.3395 time to fit residues: 115.0948 Evaluate side-chains 196 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 2.299 ------------------------------------------------------------------------------- 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 628 ARG 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 279 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 634 MET 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 47 SER Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 87 TRP Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 155 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 346 ILE Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain U residue 591 SER 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 121 GLU Chi-restraints excluded: chain V residue 311 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 577 TRP Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 225 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 527 HIS ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 613 HIS ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 169 ASN V 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.221383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.188163 restraints weight = 37435.671| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.63 r_work: 0.3945 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22032 Z= 0.205 Angle : 0.625 14.887 29966 Z= 0.315 Chirality : 0.046 0.440 3166 Planarity : 0.005 0.077 3874 Dihedral : 6.698 59.283 3308 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.21 % Favored : 92.67 % Rotamer: Outliers : 3.47 % Allowed : 23.37 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.16), residues: 2578 helix: 1.27 (0.19), residues: 786 sheet: -1.54 (0.27), residues: 388 loop : -1.91 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP U 420 HIS 0.007 0.001 HIS B 719 PHE 0.021 0.002 PHE V 238 TYR 0.016 0.001 TYR B 64 ARG 0.010 0.000 ARG B 411 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 6) link_NAG-ASN : angle 1.80558 ( 18) link_BETA1-4 : bond 0.00413 ( 2) link_BETA1-4 : angle 1.60580 ( 6) hydrogen bonds : bond 0.04032 ( 648) hydrogen bonds : angle 4.69528 ( 1842) SS BOND : bond 0.01751 ( 8) SS BOND : angle 3.20795 ( 16) covalent geometry : bond 0.00498 (22016) covalent geometry : angle 0.61937 (29926) *********************** 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 231 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 152 time to evaluate : 2.457 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: 0.1430 (m-80) cc_final: 0.1224 (m-10) REVERT: A 584 MET cc_start: 0.5965 (ptt) cc_final: 0.5049 (mmm) REVERT: B 95 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7238 (ttmt) REVERT: B 106 MET cc_start: 0.7963 (mmm) cc_final: 0.7696 (ttm) REVERT: B 624 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8219 (mt) REVERT: U 74 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.6960 (tp) REVERT: U 205 MET cc_start: 0.5664 (mmm) cc_final: 0.4442 (tmm) REVERT: V 102 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7702 (ttm110) REVERT: V 211 TYR cc_start: 0.8790 (t80) cc_final: 0.8578 (t80) REVERT: V 453 ARG cc_start: 0.8200 (tmm-80) cc_final: 0.7801 (mtm110) REVERT: V 587 ASP cc_start: 0.5619 (OUTLIER) cc_final: 0.5293 (p0) REVERT: V 594 MET cc_start: 0.6578 (mpp) cc_final: 0.6008 (mtp) outliers start: 79 outliers final: 59 residues processed: 220 average time/residue: 0.3359 time to fit residues: 117.5481 Evaluate side-chains 207 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 143 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 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 628 ARG Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 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 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 346 ILE Chi-restraints excluded: chain U residue 410 LEU Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain U residue 591 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 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 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 311 VAL Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 493 SER Chi-restraints excluded: chain V residue 545 ASN Chi-restraints excluded: chain V residue 577 TRP Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 26 optimal weight: 0.0040 chunk 177 optimal weight: 40.0000 chunk 149 optimal weight: 20.0000 chunk 236 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 167 optimal weight: 30.0000 chunk 145 optimal weight: 0.0370 overall best weight: 0.7672 ------------------------------------------------------------------------------- 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** B 410 ASN U 310 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.222654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.189366 restraints weight = 37638.950| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 2.72 r_work: 0.3917 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22032 Z= 0.123 Angle : 0.572 11.962 29966 Z= 0.287 Chirality : 0.044 0.401 3166 Planarity : 0.005 0.069 3874 Dihedral : 6.578 58.142 3308 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.13 % Favored : 93.75 % Rotamer: Outliers : 3.08 % Allowed : 23.73 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.16), residues: 2578 helix: 1.43 (0.20), residues: 772 sheet: -1.39 (0.27), residues: 388 loop : -1.86 (0.15), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP V 462 HIS 0.003 0.001 HIS V 310 PHE 0.017 0.001 PHE V 529 TYR 0.016 0.001 TYR V 417 ARG 0.005 0.000 ARG A 551 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 6) link_NAG-ASN : angle 1.55064 ( 18) link_BETA1-4 : bond 0.00433 ( 2) link_BETA1-4 : angle 1.46619 ( 6) hydrogen bonds : bond 0.03330 ( 648) hydrogen bonds : angle 4.60072 ( 1842) SS BOND : bond 0.01140 ( 8) SS BOND : angle 3.38614 ( 16) covalent geometry : bond 0.00290 (22016) covalent geometry : angle 0.56568 (29926) *********************** 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 218 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 148 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.1518 (m-80) cc_final: 0.1235 (m-10) REVERT: A 584 MET cc_start: 0.6133 (ptt) cc_final: 0.5115 (mmm) REVERT: A 605 GLU cc_start: 0.3738 (OUTLIER) cc_final: 0.1824 (tp30) REVERT: B 95 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7200 (ttmt) REVERT: B 584 MET cc_start: 0.8337 (mmt) cc_final: 0.8112 (mmm) REVERT: U 74 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7004 (tp) REVERT: U 205 MET cc_start: 0.5821 (mmm) cc_final: 0.4600 (tmm) REVERT: V 453 ARG cc_start: 0.8210 (tmm-80) cc_final: 0.7808 (mtm110) REVERT: V 587 ASP cc_start: 0.5603 (OUTLIER) cc_final: 0.5213 (p0) REVERT: V 594 MET cc_start: 0.6650 (mpp) cc_final: 0.6040 (mtp) outliers start: 70 outliers final: 56 residues processed: 205 average time/residue: 0.3137 time to fit residues: 102.5444 Evaluate side-chains 207 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 147 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 628 ARG 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 95 LYS 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 410 ASN Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 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 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 346 ILE Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain U residue 591 SER 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 121 GLU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 371 LEU Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 419 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 Chi-restraints excluded: chain V residue 545 ASN Chi-restraints excluded: chain V residue 577 TRP Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 121 optimal weight: 0.5980 chunk 250 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 49 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 223 optimal weight: 1.9990 chunk 96 optimal weight: 0.0070 chunk 76 optimal weight: 2.9990 chunk 189 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- 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** B 410 ASN U 310 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.222081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.189039 restraints weight = 37620.035| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 2.71 r_work: 0.3961 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22032 Z= 0.146 Angle : 0.584 14.007 29966 Z= 0.293 Chirality : 0.044 0.392 3166 Planarity : 0.005 0.066 3874 Dihedral : 6.574 58.555 3308 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.67 % Favored : 93.21 % Rotamer: Outliers : 2.94 % Allowed : 23.77 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2578 helix: 1.45 (0.20), residues: 762 sheet: -1.41 (0.27), residues: 388 loop : -1.82 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP V 462 HIS 0.004 0.001 HIS V 310 PHE 0.017 0.001 PHE V 529 TYR 0.016 0.001 TYR V 417 ARG 0.005 0.000 ARG V 595 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 6) link_NAG-ASN : angle 1.55173 ( 18) link_BETA1-4 : bond 0.00537 ( 2) link_BETA1-4 : angle 1.56019 ( 6) hydrogen bonds : bond 0.03442 ( 648) hydrogen bonds : angle 4.60012 ( 1842) SS BOND : bond 0.01185 ( 8) SS BOND : angle 3.63666 ( 16) covalent geometry : bond 0.00350 (22016) covalent geometry : angle 0.57687 (29926) *********************** 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 216 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 149 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 GLU cc_start: 0.3835 (OUTLIER) cc_final: 0.2113 (tp30) REVERT: B 95 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7250 (ttmt) REVERT: B 106 MET cc_start: 0.8164 (mmm) cc_final: 0.7910 (ttm) REVERT: U 74 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.6988 (tp) REVERT: U 205 MET cc_start: 0.5907 (mmm) cc_final: 0.4764 (tmm) REVERT: V 358 MET cc_start: 0.8073 (tpp) cc_final: 0.7709 (mmm) REVERT: V 453 ARG cc_start: 0.8186 (tmm-80) cc_final: 0.7793 (mtm110) REVERT: V 594 MET cc_start: 0.6804 (mpp) cc_final: 0.6086 (mtp) outliers start: 67 outliers final: 57 residues processed: 201 average time/residue: 0.3118 time to fit residues: 100.1269 Evaluate side-chains 204 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 144 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 619 TYR 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 95 LYS 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 419 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 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 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 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 346 ILE Chi-restraints excluded: chain U residue 410 LEU Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain U residue 591 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 121 GLU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 371 LEU Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 419 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 Chi-restraints excluded: chain V residue 545 ASN Chi-restraints excluded: chain V residue 577 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 35 optimal weight: 30.0000 chunk 11 optimal weight: 0.5980 chunk 94 optimal weight: 0.1980 chunk 139 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 253 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 561 GLN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN U 310 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.223126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.190856 restraints weight = 37731.653| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 2.66 r_work: 0.3735 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22032 Z= 0.116 Angle : 0.565 12.650 29966 Z= 0.282 Chirality : 0.043 0.344 3166 Planarity : 0.004 0.063 3874 Dihedral : 6.503 59.734 3308 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.86 % Allowed : 23.95 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.16), residues: 2578 helix: 1.45 (0.20), residues: 762 sheet: -1.39 (0.27), residues: 388 loop : -1.74 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP V 462 HIS 0.003 0.000 HIS V 310 PHE 0.017 0.001 PHE U 529 TYR 0.017 0.001 TYR V 417 ARG 0.013 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 6) link_NAG-ASN : angle 1.37828 ( 18) link_BETA1-4 : bond 0.00413 ( 2) link_BETA1-4 : angle 1.49543 ( 6) hydrogen bonds : bond 0.03123 ( 648) hydrogen bonds : angle 4.55176 ( 1842) SS BOND : bond 0.00872 ( 8) SS BOND : angle 3.41042 ( 16) covalent geometry : bond 0.00274 (22016) covalent geometry : angle 0.55859 (29926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5156 Ramachandran restraints generated. 2578 Oldfield, 0 Emsley, 2578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 147 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 GLU cc_start: 0.3332 (OUTLIER) cc_final: 0.1967 (tp30) REVERT: B 95 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7093 (ttmt) REVERT: B 106 MET cc_start: 0.7914 (mmm) cc_final: 0.7648 (ttt) REVERT: B 584 MET cc_start: 0.8148 (mmt) cc_final: 0.7939 (mmm) REVERT: B 624 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8188 (mt) REVERT: U 74 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7037 (tp) REVERT: U 205 MET cc_start: 0.6127 (mmm) cc_final: 0.4759 (tmm) REVERT: V 358 MET cc_start: 0.7614 (tpp) cc_final: 0.7268 (mmm) REVERT: V 453 ARG cc_start: 0.8042 (tmm-80) cc_final: 0.7656 (mtm110) REVERT: V 594 MET cc_start: 0.6650 (mpp) cc_final: 0.6043 (mtp) outliers start: 65 outliers final: 58 residues processed: 200 average time/residue: 0.3132 time to fit residues: 101.3319 Evaluate side-chains 207 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 145 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 619 TYR 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 95 LYS 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 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 539 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 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 247 SER Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 283 CYS Chi-restraints excluded: chain U residue 410 LEU Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain U residue 591 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 121 GLU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 264 ASP 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 371 LEU Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 419 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 Chi-restraints excluded: chain V residue 545 ASN Chi-restraints excluded: chain V residue 577 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 165 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 184 optimal weight: 20.0000 chunk 236 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 229 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** B 410 ASN U 310 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.223075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.191268 restraints weight = 37814.811| |-----------------------------------------------------------------------------| r_work (start): 0.4420 rms_B_bonded: 2.62 r_work: 0.3832 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 22032 Z= 0.182 Angle : 0.729 59.200 29966 Z= 0.405 Chirality : 0.044 0.353 3166 Planarity : 0.005 0.073 3874 Dihedral : 6.517 59.722 3308 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.21 % Favored : 93.64 % Rotamer: Outliers : 2.86 % Allowed : 23.73 % Favored : 73.42 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.16), residues: 2578 helix: 1.45 (0.20), residues: 762 sheet: -1.38 (0.27), residues: 388 loop : -1.74 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP V 462 HIS 0.003 0.001 HIS V 310 PHE 0.017 0.001 PHE U 529 TYR 0.016 0.001 TYR V 417 ARG 0.009 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 6) link_NAG-ASN : angle 1.37786 ( 18) link_BETA1-4 : bond 0.00411 ( 2) link_BETA1-4 : angle 1.53395 ( 6) hydrogen bonds : bond 0.03223 ( 648) hydrogen bonds : angle 4.55138 ( 1842) SS BOND : bond 0.00767 ( 8) SS BOND : angle 3.24250 ( 16) covalent geometry : bond 0.00386 (22016) covalent geometry : angle 0.72414 (29926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11597.28 seconds wall clock time: 201 minutes 9.67 seconds (12069.67 seconds total)