Starting phenix.real_space_refine on Wed Jun 18 16:19:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zge_60076/06_2025/8zge_60076.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zge_60076/06_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_60076/06_2025/8zge_60076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zge_60076/06_2025/8zge_60076.map" model { file = "/net/cci-nas-00/data/ceres_data/8zge_60076/06_2025/8zge_60076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zge_60076/06_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-5710/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: 13.41, per 1000 atoms: 0.63 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: 5.38 Conformation dependent library (CDL) restraints added in 2.7 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: 2.44 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: 8.17 Time building geometry restraints manager: 6.29 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: 0.10 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: 3.820 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: 0.030 Extract box with map and model: 0.910 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 49.910 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.100 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.300 ------------------------------------------------------------------------------- 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 : 2.350 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: 0.3711 time to fit residues: 160.8217 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 : 2.332 ------------------------------------------------------------------------------- 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 = 0.4753 r_free = 0.4753 target = 0.223083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.190185 restraints weight = 37517.747| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 2.72 r_work: 0.3719 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22032 Z= 0.179 Angle : 0.646 11.344 29966 Z= 0.327 Chirality : 0.046 0.276 3166 Planarity : 0.005 0.056 3874 Dihedral : 8.582 54.932 3326 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.71 % Favored : 93.10 % Rotamer: Outliers : 3.47 % Allowed : 23.55 % Favored : 72.98 % 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: -1.70 (0.16), residues: 2578 helix: 1.20 (0.19), residues: 754 sheet: -2.23 (0.25), residues: 426 loop : -2.16 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP U 420 HIS 0.008 0.001 HIS A 421 PHE 0.020 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 0.00351 ( 6) link_NAG-ASN : angle 2.49900 ( 18) link_BETA1-4 : bond 0.00684 ( 2) link_BETA1-4 : angle 1.21125 ( 6) hydrogen bonds : bond 0.04802 ( 648) hydrogen bonds : angle 5.24628 ( 1842) SS BOND : bond 0.00973 ( 8) SS BOND : angle 2.56796 ( 16) covalent geometry : bond 0.00430 (22016) covalent geometry : angle 0.64073 (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 268 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 189 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 MET cc_start: 0.6281 (ptt) cc_final: 0.5225 (mmm) REVERT: A 696 TYR cc_start: 0.4665 (m-80) cc_final: 0.2381 (t80) REVERT: B 279 CYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6682 (t) REVERT: V 205 MET cc_start: 0.8526 (mtp) cc_final: 0.8312 (mtt) REVERT: V 428 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6916 (mp) REVERT: V 453 ARG cc_start: 0.8237 (tmm-80) cc_final: 0.7840 (mtm110) REVERT: V 544 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.8001 (mmt90) REVERT: V 587 ASP cc_start: 0.5676 (OUTLIER) cc_final: 0.5067 (p0) outliers start: 79 outliers final: 38 residues processed: 255 average time/residue: 0.3545 time to fit residues: 138.7147 Evaluate side-chains 213 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 2.815 ------------------------------------------------------------------------------- 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 497 PHE 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 736 VAL Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 155 ARG Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 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 544 ARG Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 190 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 224 optimal weight: 0.0000 chunk 176 optimal weight: 8.9990 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** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.221127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.187958 restraints weight = 37108.275| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 2.66 r_work: 0.3764 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2350 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= 0.213 Angle : 0.645 8.621 29966 Z= 0.327 Chirality : 0.046 0.261 3166 Planarity : 0.005 0.055 3874 Dihedral : 7.593 57.120 3309 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.41 % Favored : 92.44 % Rotamer: Outliers : 4.35 % Allowed : 22.54 % 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: -1.75 (0.16), residues: 2578 helix: 1.00 (0.19), residues: 776 sheet: -2.24 (0.24), residues: 432 loop : -2.15 (0.15), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP U 420 HIS 0.007 0.001 HIS B 719 PHE 0.021 0.002 PHE V 238 TYR 0.026 0.002 TYR U 494 ARG 0.005 0.000 ARG U 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 6) link_NAG-ASN : angle 2.23488 ( 18) link_BETA1-4 : bond 0.00581 ( 2) link_BETA1-4 : angle 1.62623 ( 6) hydrogen bonds : bond 0.04529 ( 648) hydrogen bonds : angle 5.03662 ( 1842) SS BOND : bond 0.00687 ( 8) SS BOND : angle 2.31187 ( 16) covalent geometry : bond 0.00513 (22016) covalent geometry : angle 0.64094 (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 279 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 180 time to evaluate : 3.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 MET cc_start: 0.6194 (ptt) cc_final: 0.5089 (mmm) REVERT: A 696 TYR cc_start: 0.4736 (m-80) cc_final: 0.1783 (t80) REVERT: B 106 MET cc_start: 0.7628 (mmm) cc_final: 0.7197 (mtp) REVERT: U 74 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7130 (tp) REVERT: U 392 MET cc_start: 0.4711 (ppp) cc_final: 0.4506 (ppp) REVERT: U 414 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6384 (tt) REVERT: U 449 MET cc_start: 0.6577 (tpt) cc_final: 0.6356 (tpp) REVERT: U 544 ARG cc_start: 0.2421 (OUTLIER) cc_final: 0.2064 (mmt-90) REVERT: U 577 TRP cc_start: 0.4302 (p-90) cc_final: 0.3700 (t60) REVERT: V 453 ARG cc_start: 0.8189 (tmm-80) cc_final: 0.7764 (mtm110) REVERT: V 544 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.8054 (mmt90) outliers start: 99 outliers final: 63 residues processed: 262 average time/residue: 0.3983 time to fit residues: 163.9653 Evaluate side-chains 227 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 160 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 49 LEU Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 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 280 MET Chi-restraints excluded: chain U residue 414 LEU Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 544 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 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 280 MET Chi-restraints excluded: chain V residue 282 VAL Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 493 SER Chi-restraints excluded: chain V residue 544 ARG 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: 0.9990 chunk 88 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 228 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.223273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.191242 restraints weight = 37871.471| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 2.62 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: 0.7730 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22032 Z= 0.130 Angle : 0.572 10.515 29966 Z= 0.289 Chirality : 0.043 0.226 3166 Planarity : 0.005 0.053 3874 Dihedral : 6.840 59.121 3308 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.90 % Favored : 93.91 % Rotamer: Outliers : 3.21 % Allowed : 24.34 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.52 (0.16), residues: 2578 helix: 1.12 (0.19), residues: 798 sheet: -1.99 (0.25), residues: 424 loop : -2.06 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP U 420 HIS 0.003 0.001 HIS V 310 PHE 0.020 0.001 PHE V 529 TYR 0.029 0.001 TYR V 211 ARG 0.006 0.000 ARG A 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 6) link_NAG-ASN : angle 1.73265 ( 18) link_BETA1-4 : bond 0.00612 ( 2) link_BETA1-4 : angle 1.53621 ( 6) hydrogen bonds : bond 0.03624 ( 648) hydrogen bonds : angle 4.85914 ( 1842) SS BOND : bond 0.02171 ( 8) SS BOND : angle 1.74589 ( 16) covalent geometry : bond 0.00301 (22016) covalent geometry : angle 0.56896 (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 247 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 174 time to evaluate : 2.011 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: 0.6494 (ptt) cc_final: 0.5389 (mmm) REVERT: A 696 TYR cc_start: 0.4900 (m-80) cc_final: 0.1952 (t80) REVERT: B 584 MET cc_start: 0.8224 (mmt) cc_final: 0.8007 (mmm) REVERT: U 343 VAL cc_start: 0.7092 (OUTLIER) cc_final: 0.6758 (m) REVERT: U 392 MET cc_start: 0.4600 (ppp) cc_final: 0.4317 (ppp) REVERT: U 544 ARG cc_start: 0.2893 (OUTLIER) cc_final: 0.1502 (mtt90) REVERT: U 577 TRP cc_start: 0.4424 (p-90) cc_final: 0.3887 (t60) REVERT: V 453 ARG cc_start: 0.8053 (tmm-80) cc_final: 0.7658 (mtm110) REVERT: V 544 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.8070 (mmt90) outliers start: 73 outliers final: 46 residues processed: 231 average time/residue: 0.3583 time to fit residues: 128.5805 Evaluate side-chains 207 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 619 TYR 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 43 THR Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 37 TYR 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 343 VAL Chi-restraints excluded: chain U residue 544 ARG Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 280 MET Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 544 ARG 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: 0.9980 chunk 176 optimal weight: 30.0000 chunk 143 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 13 optimal weight: 0.0870 chunk 135 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 251 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- 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 ** V 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.222098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.188892 restraints weight = 37643.169| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 2.72 r_work: 0.3696 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22032 Z= 0.160 Angle : 0.580 9.845 29966 Z= 0.293 Chirality : 0.044 0.230 3166 Planarity : 0.005 0.057 3874 Dihedral : 6.656 56.782 3308 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.87 % Favored : 92.98 % Rotamer: Outliers : 4.13 % Allowed : 23.33 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.42 (0.16), residues: 2578 helix: 1.23 (0.19), residues: 796 sheet: -1.91 (0.25), residues: 424 loop : -2.03 (0.15), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 462 HIS 0.004 0.001 HIS B 719 PHE 0.016 0.001 PHE V 529 TYR 0.024 0.001 TYR U 494 ARG 0.013 0.000 ARG U 595 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 6) link_NAG-ASN : angle 1.81157 ( 18) link_BETA1-4 : bond 0.00344 ( 2) link_BETA1-4 : angle 1.59408 ( 6) hydrogen bonds : bond 0.03732 ( 648) hydrogen bonds : angle 4.76552 ( 1842) SS BOND : bond 0.01728 ( 8) SS BOND : angle 1.62421 ( 16) covalent geometry : bond 0.00384 (22016) covalent geometry : angle 0.57742 (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 248 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 154 time to evaluate : 2.673 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 144 CYS cc_start: -0.0131 (OUTLIER) cc_final: -0.1106 (p) REVERT: A 245 TYR cc_start: 0.1696 (m-80) cc_final: 0.1351 (m-80) REVERT: A 584 MET cc_start: 0.6635 (ptt) cc_final: 0.5380 (mmm) REVERT: B 106 MET cc_start: 0.7829 (mmm) cc_final: 0.7486 (ttm) REVERT: U 74 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7125 (tp) REVERT: U 343 VAL cc_start: 0.7123 (OUTLIER) cc_final: 0.6814 (m) REVERT: V 102 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7273 (ttm110) REVERT: V 105 LEU cc_start: 0.8187 (mt) cc_final: 0.7978 (mt) REVERT: V 453 ARG cc_start: 0.8159 (tmm-80) cc_final: 0.7737 (mtm110) REVERT: V 587 ASP cc_start: 0.5608 (OUTLIER) cc_final: 0.4872 (p0) REVERT: V 594 MET cc_start: 0.6330 (mpp) cc_final: 0.5878 (mtp) outliers start: 94 outliers final: 60 residues processed: 235 average time/residue: 0.3320 time to fit residues: 121.6652 Evaluate side-chains 211 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 146 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 631 VAL 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 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 638 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 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 343 VAL Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain U residue 544 ARG Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 94 MET Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 102 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 280 MET Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 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 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: 0.9980 chunk 223 optimal weight: 0.8980 chunk 218 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 252 optimal weight: 0.7980 chunk 242 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 chunk 99 optimal weight: 0.5980 chunk 69 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 310 HIS ** V 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.222556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.189535 restraints weight = 37566.865| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 2.73 r_work: 0.3683 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22032 Z= 0.125 Angle : 0.562 9.942 29966 Z= 0.283 Chirality : 0.043 0.259 3166 Planarity : 0.005 0.088 3874 Dihedral : 6.548 53.197 3308 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.86 % Favored : 94.03 % Rotamer: Outliers : 3.56 % Allowed : 23.95 % Favored : 72.50 % 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: 1.28 (0.19), residues: 798 sheet: -1.75 (0.25), residues: 418 loop : -1.97 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP V 462 HIS 0.003 0.001 HIS V 310 PHE 0.016 0.001 PHE V 529 TYR 0.018 0.001 TYR V 211 ARG 0.006 0.000 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 6) link_NAG-ASN : angle 1.62609 ( 18) link_BETA1-4 : bond 0.00462 ( 2) link_BETA1-4 : angle 1.52205 ( 6) hydrogen bonds : bond 0.03409 ( 648) hydrogen bonds : angle 4.70948 ( 1842) SS BOND : bond 0.01229 ( 8) SS BOND : angle 2.16221 ( 16) covalent geometry : bond 0.00295 (22016) covalent geometry : angle 0.55861 (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 235 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 154 time to evaluate : 2.512 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 144 CYS cc_start: 0.0486 (OUTLIER) cc_final: -0.0778 (p) REVERT: A 245 TYR cc_start: 0.1759 (m-80) cc_final: 0.1429 (m-80) REVERT: A 584 MET cc_start: 0.6552 (ptt) cc_final: 0.5362 (mmm) REVERT: A 605 GLU cc_start: 0.3203 (OUTLIER) cc_final: 0.1948 (tp30) REVERT: B 106 MET cc_start: 0.7811 (mmm) cc_final: 0.7503 (ttm) REVERT: B 624 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8200 (mt) REVERT: U 74 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7126 (tp) REVERT: U 205 MET cc_start: 0.5771 (mmm) cc_final: 0.4516 (tmm) REVERT: U 321 PRO cc_start: 0.6637 (Cg_exo) cc_final: 0.6406 (Cg_endo) REVERT: U 343 VAL cc_start: 0.7189 (OUTLIER) cc_final: 0.6903 (m) REVERT: V 102 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7298 (ttm110) REVERT: V 105 LEU cc_start: 0.8127 (mt) cc_final: 0.7903 (mt) REVERT: V 453 ARG cc_start: 0.8039 (tmm-80) cc_final: 0.7636 (mtm110) REVERT: V 594 MET cc_start: 0.6422 (mpp) cc_final: 0.5926 (mtp) outliers start: 81 outliers final: 60 residues processed: 222 average time/residue: 0.3378 time to fit residues: 116.9694 Evaluate side-chains 212 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 146 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 605 GLU 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 A residue 697 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 155 ARG Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 243 ARG Chi-restraints excluded: chain U residue 247 SER Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 283 CYS Chi-restraints excluded: chain U residue 343 VAL Chi-restraints excluded: chain U residue 410 LEU Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain U residue 544 ARG Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 102 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 280 MET Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 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 577 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 183 optimal weight: 50.0000 chunk 8 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 225 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 310 HIS V 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.220175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.188347 restraints weight = 37701.287| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 2.62 r_work: 0.3641 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22032 Z= 0.194 Angle : 0.602 11.865 29966 Z= 0.303 Chirality : 0.045 0.259 3166 Planarity : 0.005 0.062 3874 Dihedral : 6.617 53.084 3308 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.18 % Favored : 92.71 % Rotamer: Outliers : 3.91 % Allowed : 23.81 % Favored : 72.28 % 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: -1.36 (0.16), residues: 2578 helix: 1.27 (0.19), residues: 788 sheet: -1.76 (0.26), residues: 406 loop : -2.00 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP V 462 HIS 0.006 0.001 HIS B 719 PHE 0.020 0.002 PHE V 238 TYR 0.021 0.001 TYR V 211 ARG 0.006 0.000 ARG V 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 6) link_NAG-ASN : angle 1.75007 ( 18) link_BETA1-4 : bond 0.00294 ( 2) link_BETA1-4 : angle 1.70396 ( 6) hydrogen bonds : bond 0.03895 ( 648) hydrogen bonds : angle 4.73439 ( 1842) SS BOND : bond 0.01589 ( 8) SS BOND : angle 1.76930 ( 16) covalent geometry : bond 0.00473 (22016) covalent geometry : angle 0.59908 (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 236 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 147 time to evaluate : 2.579 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: 0.1914 (m-80) cc_final: 0.1600 (m-80) REVERT: A 584 MET cc_start: 0.6406 (ptt) cc_final: 0.5246 (mmm) REVERT: A 605 GLU cc_start: 0.3292 (OUTLIER) cc_final: 0.1961 (tp30) REVERT: B 95 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7218 (ttmt) REVERT: B 106 MET cc_start: 0.7826 (mmm) cc_final: 0.7520 (ttm) REVERT: B 397 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8438 (mp) REVERT: B 554 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6122 (mt-10) REVERT: U 74 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7136 (tp) REVERT: U 205 MET cc_start: 0.5963 (mmm) cc_final: 0.4609 (tmm) REVERT: U 321 PRO cc_start: 0.6499 (Cg_exo) cc_final: 0.6277 (Cg_endo) REVERT: U 343 VAL cc_start: 0.7377 (OUTLIER) cc_final: 0.7105 (m) REVERT: V 102 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7305 (ttm110) REVERT: V 453 ARG cc_start: 0.7890 (tmm-80) cc_final: 0.7488 (mtm110) REVERT: V 587 ASP cc_start: 0.5649 (OUTLIER) cc_final: 0.4800 (p0) REVERT: V 594 MET cc_start: 0.6584 (mpp) cc_final: 0.6107 (mtp) outliers start: 89 outliers final: 67 residues processed: 222 average time/residue: 0.3520 time to fit residues: 123.9198 Evaluate side-chains 216 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 141 time to evaluate : 2.700 ------------------------------------------------------------------------------- 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 279 CYS Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 631 VAL 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 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain U residue 49 LEU Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 155 ARG Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 243 ARG Chi-restraints excluded: chain U residue 247 SER Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 283 CYS Chi-restraints excluded: chain U residue 343 VAL Chi-restraints excluded: chain U residue 410 LEU Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain U residue 544 ARG Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 94 MET Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 102 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 280 MET Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 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: 1.9990 chunk 177 optimal weight: 40.0000 chunk 149 optimal weight: 20.0000 chunk 236 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 209 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 145 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 B 717 HIS ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.220532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.186289 restraints weight = 37736.681| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 2.71 r_work: 0.3691 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22032 Z= 0.171 Angle : 0.595 12.439 29966 Z= 0.300 Chirality : 0.045 0.281 3166 Planarity : 0.005 0.051 3874 Dihedral : 6.596 53.801 3308 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 3.82 % Allowed : 23.42 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.26 (0.19), residues: 776 sheet: -1.68 (0.26), residues: 404 loop : -1.93 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP V 462 HIS 0.004 0.001 HIS V 310 PHE 0.018 0.001 PHE V 238 TYR 0.013 0.001 TYR B 64 ARG 0.008 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 6) link_NAG-ASN : angle 1.65973 ( 18) link_BETA1-4 : bond 0.00395 ( 2) link_BETA1-4 : angle 1.68003 ( 6) hydrogen bonds : bond 0.03711 ( 648) hydrogen bonds : angle 4.68750 ( 1842) SS BOND : bond 0.01070 ( 8) SS BOND : angle 1.64069 ( 16) covalent geometry : bond 0.00416 (22016) covalent geometry : angle 0.59239 (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 231 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 144 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.0507 (OUTLIER) cc_final: -0.0771 (p) REVERT: A 245 TYR cc_start: 0.1952 (m-80) cc_final: 0.1706 (m-80) REVERT: A 584 MET cc_start: 0.6354 (ptt) cc_final: 0.5166 (mmm) REVERT: A 605 GLU cc_start: 0.3468 (OUTLIER) cc_final: 0.1982 (tp30) REVERT: B 95 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7243 (ttmt) REVERT: B 106 MET cc_start: 0.7916 (mmm) cc_final: 0.7690 (ttt) REVERT: B 397 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8361 (mp) REVERT: B 554 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6185 (mt-10) REVERT: B 624 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8223 (mt) REVERT: U 74 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7171 (tp) REVERT: U 205 MET cc_start: 0.6315 (mmm) cc_final: 0.4910 (tmm) REVERT: U 321 PRO cc_start: 0.6472 (Cg_exo) cc_final: 0.6213 (Cg_endo) REVERT: U 343 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.7153 (m) REVERT: V 102 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7633 (ttm110) REVERT: V 453 ARG cc_start: 0.8144 (tmm-80) cc_final: 0.7735 (mtm110) REVERT: V 587 ASP cc_start: 0.5706 (OUTLIER) cc_final: 0.4854 (p0) outliers start: 87 outliers final: 68 residues processed: 218 average time/residue: 0.3184 time to fit residues: 110.7651 Evaluate side-chains 217 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 139 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 637 SER 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 343 VAL Chi-restraints excluded: chain U residue 410 LEU Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 94 MET Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 102 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 280 MET Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 317 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 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: 0.7980 chunk 250 optimal weight: 0.0570 chunk 141 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 223 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 189 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 ** V 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.221353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.188910 restraints weight = 37810.277| |-----------------------------------------------------------------------------| r_work (start): 0.4394 rms_B_bonded: 2.70 r_work: 0.3680 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22032 Z= 0.116 Angle : 0.564 12.824 29966 Z= 0.282 Chirality : 0.043 0.268 3166 Planarity : 0.005 0.051 3874 Dihedral : 6.473 55.460 3308 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.56 % Favored : 93.37 % Rotamer: Outliers : 3.08 % Allowed : 24.30 % Favored : 72.63 % 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: -1.20 (0.16), residues: 2578 helix: 1.31 (0.20), residues: 776 sheet: -1.58 (0.26), residues: 404 loop : -1.85 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP V 462 HIS 0.003 0.000 HIS V 310 PHE 0.017 0.001 PHE V 529 TYR 0.012 0.001 TYR V 494 ARG 0.007 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 6) link_NAG-ASN : angle 1.50593 ( 18) link_BETA1-4 : bond 0.00428 ( 2) link_BETA1-4 : angle 1.55599 ( 6) hydrogen bonds : bond 0.03190 ( 648) hydrogen bonds : angle 4.61309 ( 1842) SS BOND : bond 0.01048 ( 8) SS BOND : angle 1.53119 ( 16) covalent geometry : bond 0.00272 (22016) covalent geometry : angle 0.56170 (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 215 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 145 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.0578 (OUTLIER) cc_final: -0.0794 (p) REVERT: A 245 TYR cc_start: 0.1751 (m-80) cc_final: 0.1519 (m-80) REVERT: A 584 MET cc_start: 0.6479 (ptt) cc_final: 0.5237 (mmm) REVERT: A 605 GLU cc_start: 0.3266 (OUTLIER) cc_final: 0.1947 (tp30) REVERT: B 95 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7149 (ttmt) REVERT: B 106 MET cc_start: 0.7952 (mmm) cc_final: 0.7722 (ttt) REVERT: B 584 MET cc_start: 0.7703 (mtt) cc_final: 0.7475 (mtm) REVERT: B 624 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8250 (mt) REVERT: U 74 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7117 (tp) REVERT: U 205 MET cc_start: 0.6432 (mmm) cc_final: 0.5000 (tmm) REVERT: U 321 PRO cc_start: 0.6489 (Cg_exo) cc_final: 0.6254 (Cg_endo) REVERT: U 343 VAL cc_start: 0.7286 (OUTLIER) cc_final: 0.7038 (m) REVERT: V 102 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7328 (ttm170) REVERT: V 183 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7604 (mt-10) REVERT: V 453 ARG cc_start: 0.8074 (tmm-80) cc_final: 0.7639 (mtm110) REVERT: V 587 ASP cc_start: 0.5578 (OUTLIER) cc_final: 0.4713 (p0) outliers start: 70 outliers final: 57 residues processed: 204 average time/residue: 0.3166 time to fit residues: 103.0841 Evaluate side-chains 206 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 141 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 337 VAL 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 610 VAL Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 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 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 635 THR 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 343 VAL Chi-restraints excluded: chain U residue 410 LEU Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 94 MET Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 102 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 214 THR 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 372 VAL Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 545 ASN Chi-restraints excluded: chain V residue 577 TRP Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 160 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 171 optimal weight: 7.9990 chunk 253 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 ** V 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.220955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.188392 restraints weight = 37838.501| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 2.75 r_work: 0.3797 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22032 Z= 0.138 Angle : 0.583 12.623 29966 Z= 0.290 Chirality : 0.044 0.257 3166 Planarity : 0.005 0.051 3874 Dihedral : 6.456 55.844 3308 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.83 % Favored : 93.10 % Rotamer: Outliers : 3.12 % Allowed : 24.30 % Favored : 72.58 % 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: -1.19 (0.17), residues: 2578 helix: 1.31 (0.20), residues: 776 sheet: -1.58 (0.26), residues: 404 loop : -1.83 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP V 462 HIS 0.004 0.001 HIS V 310 PHE 0.017 0.001 PHE V 529 TYR 0.012 0.001 TYR B 64 ARG 0.007 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 6) link_NAG-ASN : angle 1.51643 ( 18) link_BETA1-4 : bond 0.00430 ( 2) link_BETA1-4 : angle 1.61121 ( 6) hydrogen bonds : bond 0.03361 ( 648) hydrogen bonds : angle 4.60210 ( 1842) SS BOND : bond 0.00996 ( 8) SS BOND : angle 1.47937 ( 16) covalent geometry : bond 0.00333 (22016) covalent geometry : angle 0.58118 (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 211 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 140 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: -0.1714 (tpp) cc_final: -0.2874 (tpt) REVERT: A 144 CYS cc_start: 0.0560 (OUTLIER) cc_final: -0.0569 (p) REVERT: A 605 GLU cc_start: 0.3369 (OUTLIER) cc_final: 0.1956 (tp30) REVERT: B 95 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7203 (ttmt) REVERT: B 106 MET cc_start: 0.7912 (mmm) cc_final: 0.7680 (ttt) REVERT: B 624 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8174 (mt) REVERT: U 74 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7036 (tp) REVERT: U 205 MET cc_start: 0.6387 (mmm) cc_final: 0.5051 (tmm) REVERT: U 321 PRO cc_start: 0.6417 (Cg_exo) cc_final: 0.6199 (Cg_endo) REVERT: U 338 MET cc_start: 0.3091 (tpt) cc_final: 0.2881 (tpt) REVERT: U 343 VAL cc_start: 0.7247 (OUTLIER) cc_final: 0.6907 (m) REVERT: V 102 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7538 (ttm110) REVERT: V 453 ARG cc_start: 0.8193 (tmm-80) cc_final: 0.7746 (mtm110) REVERT: V 587 ASP cc_start: 0.5624 (OUTLIER) cc_final: 0.4970 (p0) outliers start: 71 outliers final: 59 residues processed: 202 average time/residue: 0.3182 time to fit residues: 103.4071 Evaluate side-chains 202 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 135 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 337 VAL 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 631 VAL Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 637 SER 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 343 VAL Chi-restraints excluded: chain U residue 542 SER Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 102 ARG Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 121 GLU Chi-restraints excluded: chain V residue 214 THR 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 372 VAL Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 478 GLU Chi-restraints excluded: chain V residue 545 ASN Chi-restraints excluded: chain V residue 577 TRP Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 165 optimal weight: 6.9990 chunk 207 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 184 optimal weight: 0.0040 chunk 236 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 229 optimal weight: 0.4980 chunk 150 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 252 optimal weight: 5.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.222404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.189354 restraints weight = 37744.673| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 2.71 r_work: 0.3655 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3708 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= 0.112 Angle : 0.565 12.964 29966 Z= 0.280 Chirality : 0.043 0.261 3166 Planarity : 0.004 0.051 3874 Dihedral : 6.387 56.631 3308 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.90 % Allowed : 24.65 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.07 (0.17), residues: 2578 helix: 1.35 (0.20), residues: 776 sheet: -1.38 (0.27), residues: 388 loop : -1.77 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP V 462 HIS 0.003 0.000 HIS V 310 PHE 0.016 0.001 PHE V 529 TYR 0.015 0.001 TYR A 245 ARG 0.006 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 6) link_NAG-ASN : angle 1.40643 ( 18) link_BETA1-4 : bond 0.00526 ( 2) link_BETA1-4 : angle 1.55895 ( 6) hydrogen bonds : bond 0.03064 ( 648) hydrogen bonds : angle 4.54867 ( 1842) SS BOND : bond 0.00961 ( 8) SS BOND : angle 1.40101 ( 16) covalent geometry : bond 0.00265 (22016) covalent geometry : angle 0.56266 (29926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11959.85 seconds wall clock time: 207 minutes 33.50 seconds (12453.50 seconds total)