Starting phenix.real_space_refine on Mon Oct 26 06:17:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vu0_65348/10_2026/9vu0_65348.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vu0_65348/10_2026/9vu0_65348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vu0_65348/10_2026/9vu0_65348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vu0_65348/10_2026/9vu0_65348.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vu0_65348/10_2026/9vu0_65348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vu0_65348/10_2026/9vu0_65348.map" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.054 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 126 5.16 5 C 12782 2.51 5 N 3086 2.21 5 O 3542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19544 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4903 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 591} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4768 Classifications: {'peptide': 591} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 574} Chain breaks: 6 Chain: "C" Number of atoms: 4770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4770 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 576} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 4695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4695 Classifications: {'peptide': 582} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 565} Chain breaks: 6 Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'POV': 1, 'YBG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'POV': 1, 'YBG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'POV': 1, 'YBG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'POV': 1, 'YBG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 4.23, per 1000 atoms: 0.22 Number of scatterers: 19544 At special positions: 0 Unit cell: (123.25, 123.25, 120.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 P 8 15.00 O 3542 8.00 N 3086 7.00 C 12782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.91 Conformation dependent library (CDL) restraints added in 725.8 milliseconds 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4478 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 4 sheets defined 66.2% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 118 through 124 Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.768A pdb=" N LYS A 150 " --> pdb=" O ASN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 165 Processing helix chain 'A' and resid 172 through 184 removed outlier: 3.954A pdb=" N LEU A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 214 through 224 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.642A pdb=" N LYS A 238 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 299 through 321 Processing helix chain 'A' and resid 325 through 329 removed outlier: 3.688A pdb=" N GLU A 328 " --> pdb=" O LYS A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 345 Processing helix chain 'A' and resid 346 through 355 removed outlier: 3.568A pdb=" N GLN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.546A pdb=" N VAL A 416 " --> pdb=" O MET A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 430 Processing helix chain 'A' and resid 431 through 455 Processing helix chain 'A' and resid 468 through 500 removed outlier: 4.192A pdb=" N TYR A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 509 removed outlier: 3.612A pdb=" N PHE A 507 " --> pdb=" O MET A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 531 removed outlier: 3.935A pdb=" N MET A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 533 No H-bonds generated for 'chain 'A' and resid 532 through 533' Processing helix chain 'A' and resid 534 through 535 No H-bonds generated for 'chain 'A' and resid 534 through 535' Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.725A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 547 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 removed outlier: 3.759A pdb=" N GLY A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.878A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.957A pdb=" N PHE A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 removed outlier: 3.515A pdb=" N PHE A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 690 removed outlier: 3.539A pdb=" N ILE A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 714 removed outlier: 3.924A pdb=" N LYS A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 717 No H-bonds generated for 'chain 'A' and resid 715 through 717' Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.610A pdb=" N LYS B 150 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 165 Processing helix chain 'B' and resid 172 through 181 removed outlier: 3.906A pdb=" N LEU B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 214 through 224 Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.622A pdb=" N LYS B 238 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 299 through 321 Processing helix chain 'B' and resid 325 through 329 removed outlier: 3.969A pdb=" N GLU B 328 " --> pdb=" O LYS B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 346 through 355 removed outlier: 3.595A pdb=" N GLN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 367 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.580A pdb=" N VAL B 416 " --> pdb=" O MET B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 430 Processing helix chain 'B' and resid 431 through 455 Processing helix chain 'B' and resid 469 through 500 removed outlier: 3.747A pdb=" N PHE B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 509 removed outlier: 3.800A pdb=" N PHE B 507 " --> pdb=" O MET B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 532 Processing helix chain 'B' and resid 536 through 552 removed outlier: 3.700A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 558 Processing helix chain 'B' and resid 559 through 599 removed outlier: 3.883A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.948A pdb=" N PHE B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 removed outlier: 3.524A pdb=" N PHE B 660 " --> pdb=" O PHE B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 690 removed outlier: 3.544A pdb=" N ILE B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 713 removed outlier: 3.918A pdb=" N LYS B 695 " --> pdb=" O ALA B 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 146 through 150 removed outlier: 3.629A pdb=" N LYS C 150 " --> pdb=" O ASN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 165 Processing helix chain 'C' and resid 172 through 183 removed outlier: 3.902A pdb=" N LEU C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 214 through 224 Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.767A pdb=" N LYS C 238 " --> pdb=" O ASP C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 299 through 321 Processing helix chain 'C' and resid 325 through 329 removed outlier: 3.962A pdb=" N GLU C 328 " --> pdb=" O LYS C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 344 Processing helix chain 'C' and resid 346 through 355 removed outlier: 3.591A pdb=" N GLN C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 412 through 416 removed outlier: 3.512A pdb=" N VAL C 416 " --> pdb=" O MET C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 430 Processing helix chain 'C' and resid 430 through 455 removed outlier: 4.012A pdb=" N ILE C 434 " --> pdb=" O PHE C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 removed outlier: 4.155A pdb=" N TYR C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 509 removed outlier: 3.746A pdb=" N PHE C 507 " --> pdb=" O MET C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 532 removed outlier: 3.879A pdb=" N MET C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 552 removed outlier: 3.743A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 558 removed outlier: 3.534A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 599 removed outlier: 3.879A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.952A pdb=" N PHE C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 672 removed outlier: 3.542A pdb=" N PHE C 660 " --> pdb=" O PHE C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 690 removed outlier: 3.542A pdb=" N ILE C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 713 removed outlier: 3.914A pdb=" N LYS C 695 " --> pdb=" O ALA C 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'D' and resid 157 through 165 Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.921A pdb=" N LEU D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 204 through 212 Processing helix chain 'D' and resid 214 through 224 Processing helix chain 'D' and resid 234 through 238 removed outlier: 3.595A pdb=" N LYS D 238 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 259 Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 299 through 321 Processing helix chain 'D' and resid 325 through 329 removed outlier: 3.973A pdb=" N GLU D 328 " --> pdb=" O LYS D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 Processing helix chain 'D' and resid 346 through 355 removed outlier: 3.585A pdb=" N GLN D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 367 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 412 through 416 removed outlier: 3.525A pdb=" N VAL D 416 " --> pdb=" O MET D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 430 Processing helix chain 'D' and resid 431 through 455 Processing helix chain 'D' and resid 468 through 500 removed outlier: 4.197A pdb=" N TYR D 472 " --> pdb=" O LYS D 468 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE D 473 " --> pdb=" O THR D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 509 removed outlier: 3.729A pdb=" N PHE D 507 " --> pdb=" O MET D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 531 removed outlier: 3.749A pdb=" N MET D 514 " --> pdb=" O SER D 510 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 520 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 531 " --> pdb=" O VAL D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 533 No H-bonds generated for 'chain 'D' and resid 532 through 533' Processing helix chain 'D' and resid 534 through 535 No H-bonds generated for 'chain 'D' and resid 534 through 535' Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.740A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 558 Processing helix chain 'D' and resid 559 through 599 removed outlier: 3.878A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.954A pdb=" N PHE D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 672 removed outlier: 3.532A pdb=" N PHE D 660 " --> pdb=" O PHE D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 690 removed outlier: 3.545A pdb=" N ILE D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 712 removed outlier: 3.878A pdb=" N LYS D 695 " --> pdb=" O ALA D 691 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 375 removed outlier: 6.997A pdb=" N LYS A 369 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASP A 384 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR A 371 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 382 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TRP A 373 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP A 738 " --> pdb=" O VAL A 729 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 369 through 375 removed outlier: 7.009A pdb=" N LYS B 369 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP B 384 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N THR B 371 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B 382 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP B 373 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASP B 738 " --> pdb=" O VAL B 729 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 369 through 375 removed outlier: 6.996A pdb=" N LYS C 369 " --> pdb=" O ASP C 384 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP C 384 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N THR C 371 " --> pdb=" O LEU C 382 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 382 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP C 373 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP C 738 " --> pdb=" O VAL C 729 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 369 through 375 removed outlier: 7.052A pdb=" N LYS D 369 " --> pdb=" O ASP D 384 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP D 384 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N THR D 371 " --> pdb=" O LEU D 382 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU D 382 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP D 373 " --> pdb=" O SER D 380 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP D 738 " --> pdb=" O VAL D 729 " (cutoff:3.500A) 1078 hydrogen bonds defined for protein. 3108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3064 1.31 - 1.43: 5495 1.43 - 1.56: 11144 1.56 - 1.68: 47 1.68 - 1.81: 211 Bond restraints: 19961 Sorted by residual: bond pdb=" C21 YBG D 902 " pdb=" O3 YBG D 902 " ideal model delta sigma weight residual 1.329 1.429 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C21 YBG A 902 " pdb=" O3 YBG A 902 " ideal model delta sigma weight residual 1.329 1.428 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C21 YBG B 902 " pdb=" O3 YBG B 902 " ideal model delta sigma weight residual 1.329 1.427 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C21 YBG C 902 " pdb=" O3 YBG C 902 " ideal model delta sigma weight residual 1.329 1.426 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C18 YBG D 902 " pdb=" O2 YBG D 902 " ideal model delta sigma weight residual 1.331 1.415 -0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 19956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.61: 26898 5.61 - 11.22: 38 11.22 - 16.82: 10 16.82 - 22.43: 0 22.43 - 28.04: 4 Bond angle restraints: 26950 Sorted by residual: angle pdb=" C10 YBG B 902 " pdb=" C1 YBG B 902 " pdb=" C2 YBG B 902 " ideal model delta sigma weight residual 124.90 152.94 -28.04 3.00e+00 1.11e-01 8.74e+01 angle pdb=" C10 YBG C 902 " pdb=" C1 YBG C 902 " pdb=" C2 YBG C 902 " ideal model delta sigma weight residual 124.90 152.66 -27.76 3.00e+00 1.11e-01 8.56e+01 angle pdb=" C10 YBG A 902 " pdb=" C1 YBG A 902 " pdb=" C2 YBG A 902 " ideal model delta sigma weight residual 124.90 152.65 -27.75 3.00e+00 1.11e-01 8.56e+01 angle pdb=" C10 YBG D 902 " pdb=" C1 YBG D 902 " pdb=" C2 YBG D 902 " ideal model delta sigma weight residual 124.90 152.34 -27.44 3.00e+00 1.11e-01 8.37e+01 angle pdb=" C1 YBG B 902 " pdb=" C10 YBG B 902 " pdb=" C11 YBG B 902 " ideal model delta sigma weight residual 125.64 110.17 15.47 3.00e+00 1.11e-01 2.66e+01 ... (remaining 26945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 11399 35.04 - 70.08: 460 70.08 - 105.12: 84 105.12 - 140.16: 32 140.16 - 175.20: 4 Dihedral angle restraints: 11979 sinusoidal: 5028 harmonic: 6951 Sorted by residual: dihedral pdb=" C38 YBG B 902 " pdb=" O8 YBG B 902 " pdb=" P1 YBG B 902 " pdb=" O7 YBG B 902 " ideal model delta sinusoidal sigma weight residual -161.77 13.43 -175.20 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C38 YBG B 902 " pdb=" O8 YBG B 902 " pdb=" P1 YBG B 902 " pdb=" O5 YBG B 902 " ideal model delta sinusoidal sigma weight residual 85.25 -108.12 -166.63 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C38 YBG B 902 " pdb=" O8 YBG B 902 " pdb=" P1 YBG B 902 " pdb=" O6 YBG B 902 " ideal model delta sinusoidal sigma weight residual -28.19 133.22 -161.41 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 11976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.006: 3040 1.006 - 2.012: 0 2.012 - 3.018: 0 3.018 - 4.024: 0 4.024 - 5.030: 4 Chirality restraints: 3044 Sorted by residual: chirality pdb=" C38 YBG C 902 " pdb=" C39 YBG C 902 " pdb=" C43 YBG C 902 " pdb=" O8 YBG C 902 " both_signs ideal model delta sigma weight residual False 2.50 -2.53 5.03 2.00e-01 2.50e+01 6.32e+02 chirality pdb=" C38 YBG A 902 " pdb=" C39 YBG A 902 " pdb=" C43 YBG A 902 " pdb=" O8 YBG A 902 " both_signs ideal model delta sigma weight residual False 2.50 -2.53 5.03 2.00e-01 2.50e+01 6.31e+02 chirality pdb=" C38 YBG D 902 " pdb=" C39 YBG D 902 " pdb=" C43 YBG D 902 " pdb=" O8 YBG D 902 " both_signs ideal model delta sigma weight residual False 2.50 -2.52 5.02 2.00e-01 2.50e+01 6.30e+02 ... (remaining 3041 not shown) Planarity restraints: 3314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 554 " -0.008 2.00e-02 2.50e+03 1.64e-02 5.37e+00 pdb=" CG TYR D 554 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR D 554 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 554 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR D 554 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 554 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR D 554 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR D 554 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 544 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C SER C 544 " -0.034 2.00e-02 2.50e+03 pdb=" O SER C 544 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU C 545 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 546 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ALA C 546 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA C 546 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU C 547 " -0.010 2.00e-02 2.50e+03 ... (remaining 3311 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 427 2.71 - 3.26: 18309 3.26 - 3.80: 29594 3.80 - 4.35: 39378 4.35 - 4.90: 66265 Nonbonded interactions: 153973 Sorted by model distance: nonbonded pdb=" OH TYR B 200 " pdb=" O PRO D 764 " model vdw 2.162 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" O PRO B 764 " model vdw 2.181 3.040 nonbonded pdb=" O PRO A 764 " pdb=" OH TYR C 200 " model vdw 2.182 3.040 nonbonded pdb=" O PRO C 764 " pdb=" OH TYR D 200 " model vdw 2.221 3.040 nonbonded pdb=" NH2 ARG C 557 " pdb=" O7 YBG C 902 " model vdw 2.230 3.120 ... (remaining 153968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 118 through 128 or resid 144 through 178 or resid 187 thro \ ugh 391 or resid 394 through 712 or resid 722 through 752 or resid 760 through 7 \ 65 or resid 901 through 902)) selection = (chain 'B' and (resid 118 through 128 or resid 144 through 178 or resid 187 thro \ ugh 712 or resid 722 through 752 or resid 760 through 902)) selection = (chain 'C' and (resid 118 through 128 or resid 144 through 178 or resid 187 thro \ ugh 712 or resid 722 through 752 or resid 760 through 902)) selection = (chain 'D' and (resid 118 through 128 or resid 144 through 752 or resid 760 thro \ ugh 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.31 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.230 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 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 : 0.010 0.894 19968 Z= 0.908 Angle : 0.802 28.040 26950 Z= 0.357 Chirality : 0.183 5.030 3044 Planarity : 0.004 0.040 3314 Dihedral : 20.691 175.197 7501 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.68 % Favored : 98.28 % Rotamer: Outliers : 1.53 % Allowed : 15.88 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.17), residues: 2324 helix: 1.81 (0.14), residues: 1399 sheet: 1.65 (0.60), residues: 72 loop : -1.02 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 499 TYR 0.030 0.002 TYR D 554 PHE 0.019 0.002 PHE D 305 TRP 0.012 0.002 TRP C 698 HIS 0.006 0.001 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.24 (19961) covalent geometry : angle 0.80161 / 0.36 (26950) hydrogen bonds : bond 0.14907 / 10.05 ( 1078) hydrogen bonds : angle 4.77001 / 3.36 ( 3108) Misc. bond : bond 0.46859 / 20.32 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 0.651 Fit side-chains REVERT: A 305 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.6833 (t80) REVERT: A 433 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7675 (mtt90) REVERT: A 467 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: A 500 ARG cc_start: 0.7862 (mtt180) cc_final: 0.7481 (mtp85) REVERT: A 725 LYS cc_start: 0.8694 (mttt) cc_final: 0.7979 (mtpp) REVERT: B 163 MET cc_start: 0.7759 (tpp) cc_final: 0.7295 (mmp) REVERT: B 305 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.6893 (t80) REVERT: B 328 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7489 (mm-30) REVERT: B 433 ARG cc_start: 0.8227 (mtt180) cc_final: 0.7707 (mtt90) REVERT: B 500 ARG cc_start: 0.8010 (mtt180) cc_final: 0.7703 (mtp-110) REVERT: B 692 GLN cc_start: 0.7745 (tp40) cc_final: 0.7461 (tp40) REVERT: B 722 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7262 (ttt180) REVERT: B 725 LYS cc_start: 0.8718 (tttt) cc_final: 0.8040 (mtpp) REVERT: C 163 MET cc_start: 0.7711 (tpp) cc_final: 0.7235 (mmp) REVERT: C 305 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.6903 (t80) REVERT: C 328 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7612 (mm-30) REVERT: C 429 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7606 (mtt-85) REVERT: C 433 ARG cc_start: 0.8363 (mtt180) cc_final: 0.7790 (mtt90) REVERT: C 466 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7501 (mtm) REVERT: C 500 ARG cc_start: 0.8004 (mtt180) cc_final: 0.7666 (mtp-110) REVERT: C 553 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8033 (mp) REVERT: C 725 LYS cc_start: 0.8671 (mttt) cc_final: 0.7983 (mtpp) REVERT: D 274 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.6839 (tm-30) REVERT: D 328 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7617 (mm-30) REVERT: D 433 ARG cc_start: 0.8290 (mtt180) cc_final: 0.7764 (mtt90) REVERT: D 500 ARG cc_start: 0.7956 (mtt180) cc_final: 0.7513 (mtp85) REVERT: D 725 LYS cc_start: 0.8575 (mttt) cc_final: 0.8056 (mtpp) outliers start: 32 outliers final: 14 residues processed: 267 average time/residue: 0.7148 time to fit residues: 211.5950 Evaluate side-chains 261 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 722 ARG Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 429 ARG Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 723 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0060 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 8.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN B 170 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 HIS ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 GLN D 214 ASN ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.152807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.109023 restraints weight = 19901.861| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.47 r_work: 0.2826 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19968 Z= 0.136 Angle : 0.545 9.534 26950 Z= 0.279 Chirality : 0.039 0.317 3044 Planarity : 0.004 0.047 3314 Dihedral : 14.977 150.812 3058 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.19 % Favored : 97.76 % Rotamer: Outliers : 2.78 % Allowed : 13.62 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.17), residues: 2324 helix: 2.11 (0.14), residues: 1426 sheet: 1.64 (0.59), residues: 72 loop : -0.98 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 557 TYR 0.024 0.001 TYR D 554 PHE 0.017 0.001 PHE D 305 TRP 0.011 0.001 TRP D 698 HIS 0.005 0.001 HIS B 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (19961) covalent geometry : angle 0.54477 / 0.28 (26950) hydrogen bonds : bond 0.06499 / 4.32 ( 1078) hydrogen bonds : angle 3.88904 / 2.75 ( 3108) Misc. bond : bond 0.00476 / 0.23 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 245 time to evaluate : 0.774 Fit side-chains REVERT: A 274 GLN cc_start: 0.7758 (tp-100) cc_final: 0.7544 (mm-40) REVERT: A 305 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7345 (t80) REVERT: A 500 ARG cc_start: 0.7807 (mtt180) cc_final: 0.7441 (mtp85) REVERT: A 725 LYS cc_start: 0.8636 (mttt) cc_final: 0.7945 (mtpp) REVERT: B 305 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7441 (t80) REVERT: B 328 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7593 (mm-30) REVERT: B 500 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7595 (mtp85) REVERT: B 575 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7942 (mtt180) REVERT: B 692 GLN cc_start: 0.7763 (tp40) cc_final: 0.7432 (tp40) REVERT: B 725 LYS cc_start: 0.8644 (tttt) cc_final: 0.7993 (mtpp) REVERT: C 305 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7429 (t80) REVERT: C 433 ARG cc_start: 0.8285 (mtt180) cc_final: 0.7710 (mtt90) REVERT: C 500 ARG cc_start: 0.8010 (mtt180) cc_final: 0.7664 (mtp-110) REVERT: C 553 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7928 (mp) REVERT: C 725 LYS cc_start: 0.8579 (mttt) cc_final: 0.7898 (mtpp) REVERT: D 274 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: D 500 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7422 (mtp85) REVERT: D 725 LYS cc_start: 0.8566 (mttt) cc_final: 0.8036 (mtpp) outliers start: 58 outliers final: 19 residues processed: 288 average time/residue: 0.6561 time to fit residues: 211.6098 Evaluate side-chains 267 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 553 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [55, 117, 182, 234, 9, 57, 31, 233, 176, 219, 92] chunk 55 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 234 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 233 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 92 optimal weight: 0.0020 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 HIS ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 GLN D 128 GLN D 214 ASN ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS D 692 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.149818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.106418 restraints weight = 20088.656| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.93 r_work: 0.2798 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19968 Z= 0.187 Angle : 0.596 9.714 26950 Z= 0.304 Chirality : 0.040 0.274 3044 Planarity : 0.004 0.044 3314 Dihedral : 14.053 152.993 3034 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.81 % Favored : 98.15 % Rotamer: Outliers : 3.21 % Allowed : 13.62 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.17), residues: 2324 helix: 2.10 (0.13), residues: 1408 sheet: 1.56 (0.58), residues: 72 loop : -0.89 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 499 TYR 0.024 0.002 TYR D 554 PHE 0.020 0.002 PHE D 305 TRP 0.014 0.002 TRP D 698 HIS 0.006 0.001 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (19961) covalent geometry : angle 0.59606 / 0.30 (26950) hydrogen bonds : bond 0.07650 / 5.10 ( 1078) hydrogen bonds : angle 3.90054 / 2.76 ( 3108) Misc. bond : bond 0.00501 / 0.24 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 245 time to evaluate : 0.839 Fit side-chains REVERT: A 274 GLN cc_start: 0.7731 (tp-100) cc_final: 0.7485 (mm-40) REVERT: A 305 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7375 (t80) REVERT: A 433 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7636 (mtt90) REVERT: A 500 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7444 (mtp85) REVERT: A 725 LYS cc_start: 0.8602 (mttt) cc_final: 0.7903 (mtpp) REVERT: B 272 SER cc_start: 0.7632 (OUTLIER) cc_final: 0.7405 (t) REVERT: B 305 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7394 (t80) REVERT: B 433 ARG cc_start: 0.8224 (mtt180) cc_final: 0.7674 (mtt90) REVERT: B 500 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7586 (mtp85) REVERT: B 575 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7963 (mtt180) REVERT: B 692 GLN cc_start: 0.7794 (tp40) cc_final: 0.7592 (tp40) REVERT: B 725 LYS cc_start: 0.8672 (tttt) cc_final: 0.8015 (mtpp) REVERT: C 305 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7483 (t80) REVERT: C 433 ARG cc_start: 0.8319 (mtt180) cc_final: 0.7733 (mtt90) REVERT: C 500 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7662 (mtp-110) REVERT: C 553 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7885 (mp) REVERT: C 725 LYS cc_start: 0.8578 (mttt) cc_final: 0.7909 (mtpp) REVERT: D 274 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6543 (tm-30) REVERT: D 433 ARG cc_start: 0.8265 (mtt180) cc_final: 0.7737 (mtt90) REVERT: D 500 ARG cc_start: 0.7845 (mtt180) cc_final: 0.7432 (mtp85) REVERT: D 725 LYS cc_start: 0.8587 (mttt) cc_final: 0.8021 (mtpp) outliers start: 67 outliers final: 26 residues processed: 289 average time/residue: 0.6814 time to fit residues: 219.0954 Evaluate side-chains 270 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 721 PHE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 553 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [63, 158, 107, 140, 163, 141, 144, 81, 178, 146, 110] chunk 63 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 178 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN B 411 HIS C 359 GLN D 128 GLN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS D 692 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.152007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.107339 restraints weight = 20067.828| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.01 r_work: 0.2821 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19968 Z= 0.142 Angle : 0.529 10.049 26950 Z= 0.274 Chirality : 0.038 0.234 3044 Planarity : 0.003 0.042 3314 Dihedral : 13.720 149.146 3032 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.11 % Favored : 97.85 % Rotamer: Outliers : 2.83 % Allowed : 14.20 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.17), residues: 2324 helix: 2.25 (0.13), residues: 1408 sheet: 1.55 (0.58), residues: 72 loop : -0.85 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 557 TYR 0.020 0.002 TYR D 554 PHE 0.017 0.001 PHE D 305 TRP 0.013 0.001 TRP D 698 HIS 0.005 0.001 HIS A 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (19961) covalent geometry : angle 0.52927 / 0.27 (26950) hydrogen bonds : bond 0.06480 / 4.31 ( 1078) hydrogen bonds : angle 3.78103 / 2.67 ( 3108) Misc. bond : bond 0.00393 / 0.19 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 234 time to evaluate : 0.726 Fit side-chains REVERT: A 274 GLN cc_start: 0.7705 (tp-100) cc_final: 0.7471 (mm-40) REVERT: A 305 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7273 (t80) REVERT: A 500 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7426 (mtp85) REVERT: A 725 LYS cc_start: 0.8589 (mttt) cc_final: 0.7873 (mtpp) REVERT: B 305 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7330 (t80) REVERT: B 500 ARG cc_start: 0.7987 (mtt180) cc_final: 0.7583 (mtp85) REVERT: B 575 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7963 (mtt180) REVERT: B 692 GLN cc_start: 0.7755 (tp40) cc_final: 0.7470 (tp40) REVERT: B 725 LYS cc_start: 0.8622 (tttt) cc_final: 0.7949 (mtpp) REVERT: C 305 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7357 (t80) REVERT: C 328 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7528 (mm-30) REVERT: C 433 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7695 (mtt90) REVERT: C 500 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7663 (mtp-110) REVERT: C 553 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7733 (mp) REVERT: C 575 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7916 (mtt180) REVERT: C 725 LYS cc_start: 0.8556 (mttt) cc_final: 0.7852 (mtpp) REVERT: D 274 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.6384 (tm-30) REVERT: D 324 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7793 (tm) REVERT: D 328 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7576 (mm-30) REVERT: D 500 ARG cc_start: 0.7843 (mtt180) cc_final: 0.7432 (mtp85) REVERT: D 725 LYS cc_start: 0.8561 (mttt) cc_final: 0.7994 (mtpp) outliers start: 59 outliers final: 25 residues processed: 277 average time/residue: 0.6598 time to fit residues: 204.0089 Evaluate side-chains 266 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 553 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [186, 152, 165, 9, 99, 196, 220, 48, 224, 100, 88] chunk 186 optimal weight: 8.9990 chunk 152 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 224 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 HIS ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 GLN D 128 GLN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS D 692 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.149802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106166 restraints weight = 19988.017| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.93 r_work: 0.2798 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19968 Z= 0.193 Angle : 0.594 10.300 26950 Z= 0.304 Chirality : 0.041 0.264 3044 Planarity : 0.004 0.043 3314 Dihedral : 13.788 149.938 3032 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.98 % Favored : 97.98 % Rotamer: Outliers : 3.45 % Allowed : 14.15 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.17), residues: 2324 helix: 2.08 (0.13), residues: 1410 sheet: 1.55 (0.59), residues: 72 loop : -0.94 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 557 TYR 0.024 0.002 TYR D 554 PHE 0.020 0.002 PHE A 305 TRP 0.014 0.002 TRP A 698 HIS 0.006 0.001 HIS A 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (19961) covalent geometry : angle 0.59444 / 0.30 (26950) hydrogen bonds : bond 0.07604 / 5.07 ( 1078) hydrogen bonds : angle 3.85431 / 2.72 ( 3108) Misc. bond : bond 0.00500 / 0.24 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 236 time to evaluate : 0.729 Fit side-chains REVERT: A 274 GLN cc_start: 0.7711 (tp-100) cc_final: 0.7461 (mm-40) REVERT: A 305 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.7160 (t80) REVERT: A 433 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7646 (mtt90) REVERT: A 500 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7422 (mtp85) REVERT: A 575 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7955 (mtt180) REVERT: A 725 LYS cc_start: 0.8606 (mttt) cc_final: 0.7887 (mtpp) REVERT: B 272 SER cc_start: 0.7598 (OUTLIER) cc_final: 0.7394 (t) REVERT: B 305 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7147 (t80) REVERT: B 328 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7580 (mm-30) REVERT: B 433 ARG cc_start: 0.8229 (mtt180) cc_final: 0.7679 (mtt90) REVERT: B 500 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7593 (mtp85) REVERT: B 575 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7960 (mtt180) REVERT: B 725 LYS cc_start: 0.8664 (tttt) cc_final: 0.7994 (mtpp) REVERT: C 305 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7136 (t80) REVERT: C 433 ARG cc_start: 0.8340 (mtt180) cc_final: 0.7758 (mtt90) REVERT: C 500 ARG cc_start: 0.7999 (mtt180) cc_final: 0.7648 (mtp-110) REVERT: C 553 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7799 (mp) REVERT: C 725 LYS cc_start: 0.8586 (mttt) cc_final: 0.7912 (mtpp) REVERT: D 274 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.6157 (tm-30) REVERT: D 433 ARG cc_start: 0.8260 (mtt180) cc_final: 0.7723 (mtt90) REVERT: D 500 ARG cc_start: 0.7846 (mtt180) cc_final: 0.7425 (mtp85) REVERT: D 725 LYS cc_start: 0.8593 (mttt) cc_final: 0.8039 (mtpp) outliers start: 72 outliers final: 38 residues processed: 285 average time/residue: 0.6811 time to fit residues: 216.1726 Evaluate side-chains 280 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 721 PHE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 553 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [173, 70, 220, 170, 40, 131, 187, 143, 183, 9, 77] chunk 173 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 187 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 411 HIS C 359 GLN D 128 GLN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS D 692 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.151873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.109034 restraints weight = 19908.457| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.61 r_work: 0.2840 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19968 Z= 0.134 Angle : 0.516 9.756 26950 Z= 0.268 Chirality : 0.038 0.236 3044 Planarity : 0.003 0.042 3314 Dihedral : 13.440 147.064 3032 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.94 % Favored : 98.02 % Rotamer: Outliers : 3.12 % Allowed : 14.58 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.17), residues: 2324 helix: 2.30 (0.13), residues: 1408 sheet: 1.64 (0.59), residues: 72 loop : -0.83 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 557 TYR 0.019 0.002 TYR D 554 PHE 0.017 0.001 PHE C 305 TRP 0.013 0.001 TRP D 698 HIS 0.005 0.001 HIS B 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (19961) covalent geometry : angle 0.51632 / 0.27 (26950) hydrogen bonds : bond 0.06199 / 4.12 ( 1078) hydrogen bonds : angle 3.72477 / 2.63 ( 3108) Misc. bond : bond 0.00411 / 0.20 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 235 time to evaluate : 0.730 Fit side-chains REVERT: A 274 GLN cc_start: 0.7711 (tp-100) cc_final: 0.7469 (mm-40) REVERT: A 305 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7021 (t80) REVERT: A 500 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7441 (mtp85) REVERT: A 575 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7938 (mtt180) REVERT: A 725 LYS cc_start: 0.8574 (mttt) cc_final: 0.7868 (mtpp) REVERT: B 305 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7024 (t80) REVERT: B 319 LYS cc_start: 0.7545 (mttm) cc_final: 0.7342 (mtpp) REVERT: B 328 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7567 (mm-30) REVERT: B 500 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7600 (mtp85) REVERT: B 575 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7949 (mtt180) REVERT: B 725 LYS cc_start: 0.8631 (tttt) cc_final: 0.7973 (mtpp) REVERT: C 163 MET cc_start: 0.7834 (tpp) cc_final: 0.7344 (mmp) REVERT: C 305 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7040 (t80) REVERT: C 328 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7537 (mm-30) REVERT: C 433 ARG cc_start: 0.8260 (mtt180) cc_final: 0.7683 (mtt90) REVERT: C 500 ARG cc_start: 0.8004 (mtt180) cc_final: 0.7663 (mtp-110) REVERT: C 553 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7711 (mp) REVERT: C 575 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7945 (mtt180) REVERT: C 725 LYS cc_start: 0.8566 (mttt) cc_final: 0.7869 (mtpp) REVERT: D 274 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.6092 (tm-30) REVERT: D 328 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7583 (mm-30) REVERT: D 500 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7457 (mtp85) REVERT: D 725 LYS cc_start: 0.8534 (mttt) cc_final: 0.7984 (mtpp) outliers start: 65 outliers final: 30 residues processed: 281 average time/residue: 0.6763 time to fit residues: 211.7858 Evaluate side-chains 271 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 721 PHE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 553 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [162, 215, 216, 93, 145, 197, 226, 114, 24, 154, 219] chunk 162 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 145 optimal weight: 0.0370 chunk 197 optimal weight: 4.9990 chunk 226 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 GLN B 411 HIS D 128 GLN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS D 692 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.154382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111686 restraints weight = 20081.944| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.45 r_work: 0.2858 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 19968 Z= 0.104 Angle : 0.466 9.145 26950 Z= 0.244 Chirality : 0.036 0.211 3044 Planarity : 0.003 0.041 3314 Dihedral : 13.073 144.501 3032 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.94 % Favored : 98.02 % Rotamer: Outliers : 2.88 % Allowed : 14.82 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.17), residues: 2324 helix: 2.52 (0.13), residues: 1407 sheet: 1.66 (0.58), residues: 72 loop : -0.71 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 557 TYR 0.017 0.001 TYR D 554 PHE 0.014 0.001 PHE C 305 TRP 0.012 0.001 TRP D 698 HIS 0.005 0.001 HIS B 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (19961) covalent geometry : angle 0.46589 / 0.24 (26950) hydrogen bonds : bond 0.05029 / 3.34 ( 1078) hydrogen bonds : angle 3.57768 / 2.52 ( 3108) Misc. bond : bond 0.00304 / 0.14 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 244 time to evaluate : 0.763 Fit side-chains REVERT: A 274 GLN cc_start: 0.7715 (tp-100) cc_final: 0.7498 (mm-40) REVERT: A 305 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.6847 (t80) REVERT: A 500 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7398 (mtp85) REVERT: A 575 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7918 (mtt180) REVERT: A 725 LYS cc_start: 0.8571 (mttt) cc_final: 0.7874 (mtpp) REVERT: B 305 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.6833 (t80) REVERT: B 500 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7551 (mtp85) REVERT: B 575 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7897 (mtt180) REVERT: B 725 LYS cc_start: 0.8570 (tttt) cc_final: 0.7929 (mtpp) REVERT: C 305 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.6878 (t80) REVERT: C 328 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7549 (mm-30) REVERT: C 500 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7610 (mtp85) REVERT: C 553 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7639 (mp) REVERT: C 575 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7888 (mtt180) REVERT: C 725 LYS cc_start: 0.8550 (mttt) cc_final: 0.7863 (mtpp) REVERT: D 274 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6033 (tm-30) REVERT: D 328 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7565 (mm-30) REVERT: D 500 ARG cc_start: 0.7808 (mtt180) cc_final: 0.7377 (mtp85) REVERT: D 725 LYS cc_start: 0.8524 (mttt) cc_final: 0.7975 (mtpp) outliers start: 60 outliers final: 23 residues processed: 289 average time/residue: 0.6615 time to fit residues: 213.1058 Evaluate side-chains 271 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 675 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [226, 105, 233, 81, 9, 34, 132, 125, 65, 99, 20] chunk 226 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 411 HIS B 692 GLN C 359 GLN D 128 GLN D 411 HIS D 692 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.152685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107662 restraints weight = 19884.793| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.03 r_work: 0.2840 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19968 Z= 0.140 Angle : 0.521 9.565 26950 Z= 0.269 Chirality : 0.038 0.227 3044 Planarity : 0.003 0.042 3314 Dihedral : 13.133 143.373 3029 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.02 % Favored : 97.93 % Rotamer: Outliers : 2.59 % Allowed : 15.25 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.17), residues: 2324 helix: 2.37 (0.13), residues: 1415 sheet: 1.62 (0.59), residues: 72 loop : -0.80 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 557 TYR 0.017 0.002 TYR D 554 PHE 0.018 0.001 PHE A 305 TRP 0.012 0.001 TRP D 698 HIS 0.005 0.001 HIS A 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (19961) covalent geometry : angle 0.52083 / 0.27 (26950) hydrogen bonds : bond 0.06115 / 4.07 ( 1078) hydrogen bonds : angle 3.64458 / 2.57 ( 3108) Misc. bond : bond 0.00393 / 0.19 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 238 time to evaluate : 0.768 Fit side-chains REVERT: A 274 GLN cc_start: 0.7670 (tp-100) cc_final: 0.7434 (mm-40) REVERT: A 305 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7009 (t80) REVERT: A 467 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: A 500 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7383 (mtp85) REVERT: A 575 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7879 (mtt180) REVERT: A 725 LYS cc_start: 0.8568 (mttt) cc_final: 0.7858 (mtpp) REVERT: B 305 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.6969 (t80) REVERT: B 328 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7560 (mm-30) REVERT: B 500 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7577 (mtp85) REVERT: B 575 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7896 (mtt180) REVERT: B 725 LYS cc_start: 0.8586 (tttt) cc_final: 0.7928 (mtpp) REVERT: C 305 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7025 (t80) REVERT: C 429 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7403 (mtt-85) REVERT: C 433 ARG cc_start: 0.8293 (mtt180) cc_final: 0.7714 (mtt90) REVERT: C 500 ARG cc_start: 0.7995 (mtt180) cc_final: 0.7582 (mtp85) REVERT: C 553 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7670 (mp) REVERT: C 575 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7863 (mtt180) REVERT: C 725 LYS cc_start: 0.8570 (mttt) cc_final: 0.7853 (mtpp) REVERT: D 274 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.5916 (tm-30) REVERT: D 328 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7578 (mm-30) REVERT: D 500 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7345 (mtp85) REVERT: D 725 LYS cc_start: 0.8543 (mttt) cc_final: 0.7985 (mtpp) outliers start: 54 outliers final: 26 residues processed: 277 average time/residue: 0.6699 time to fit residues: 206.5906 Evaluate side-chains 273 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 429 ARG Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 723 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [195, 174, 228, 40, 125, 9, 230, 64, 234, 2, 30] chunk 195 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 234 optimal weight: 0.1980 chunk 2 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 HIS B 692 GLN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS D 692 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.150641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105797 restraints weight = 19765.593| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.93 r_work: 0.2790 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19968 Z= 0.178 Angle : 0.584 10.130 26950 Z= 0.298 Chirality : 0.040 0.258 3044 Planarity : 0.004 0.044 3314 Dihedral : 13.249 144.778 3029 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.73 % Allowed : 15.25 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.17), residues: 2324 helix: 2.12 (0.13), residues: 1423 sheet: 1.61 (0.59), residues: 72 loop : -0.98 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 557 TYR 0.022 0.002 TYR D 554 PHE 0.020 0.002 PHE C 305 TRP 0.013 0.002 TRP C 698 HIS 0.006 0.001 HIS A 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (19961) covalent geometry : angle 0.58386 / 0.30 (26950) hydrogen bonds : bond 0.07310 / 4.87 ( 1078) hydrogen bonds : angle 3.77913 / 2.67 ( 3108) Misc. bond : bond 0.00474 / 0.23 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 0.786 Fit side-chains REVERT: A 433 ARG cc_start: 0.8230 (mtt180) cc_final: 0.7685 (mtt90) REVERT: A 467 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: A 500 ARG cc_start: 0.7783 (mtt180) cc_final: 0.7383 (mtp85) REVERT: A 575 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7945 (mtt180) REVERT: A 725 LYS cc_start: 0.8599 (mttt) cc_final: 0.7898 (mtpp) REVERT: B 272 SER cc_start: 0.7557 (OUTLIER) cc_final: 0.7348 (t) REVERT: B 328 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7521 (mm-30) REVERT: B 433 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7665 (mtt90) REVERT: B 500 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7588 (mtp85) REVERT: B 575 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7966 (mtt180) REVERT: B 725 LYS cc_start: 0.8643 (tttt) cc_final: 0.7981 (mtpp) REVERT: C 328 GLU cc_start: 0.8538 (mt-10) cc_final: 0.7589 (mm-30) REVERT: C 429 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7805 (mtt-85) REVERT: C 433 ARG cc_start: 0.8363 (mtt180) cc_final: 0.7792 (mtt90) REVERT: C 500 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7643 (mtp-110) REVERT: C 553 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7741 (mp) REVERT: C 575 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7930 (mtt180) REVERT: C 725 LYS cc_start: 0.8648 (mttt) cc_final: 0.7932 (mtpp) REVERT: D 274 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.5961 (tm-30) REVERT: D 433 ARG cc_start: 0.8293 (mtt180) cc_final: 0.7721 (mtt90) REVERT: D 500 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7408 (mtp85) REVERT: D 725 LYS cc_start: 0.8587 (mttt) cc_final: 0.8039 (mtpp) outliers start: 57 outliers final: 34 residues processed: 280 average time/residue: 0.7023 time to fit residues: 218.2812 Evaluate side-chains 275 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 429 ARG Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 723 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [97, 27, 1, 162, 103, 207, 46, 203, 115, 202, 25] chunk 97 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 HIS B 692 GLN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 GLN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS D 692 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.149610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104505 restraints weight = 19875.812| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.87 r_work: 0.2791 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19968 Z= 0.214 Angle : 0.635 11.406 26950 Z= 0.322 Chirality : 0.042 0.295 3044 Planarity : 0.004 0.044 3314 Dihedral : 13.429 144.941 3029 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.45 % Allowed : 15.68 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.17), residues: 2324 helix: 1.94 (0.13), residues: 1423 sheet: 1.47 (0.59), residues: 72 loop : -1.09 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 499 TYR 0.026 0.002 TYR D 554 PHE 0.021 0.002 PHE C 305 TRP 0.015 0.002 TRP D 698 HIS 0.007 0.001 HIS A 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.21 (19961) covalent geometry : angle 0.63465 / 0.32 (26950) hydrogen bonds : bond 0.08012 / 5.33 ( 1078) hydrogen bonds : angle 3.85960 / 2.72 ( 3108) Misc. bond : bond 0.00545 / 0.26 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 0.769 Fit side-chains REVERT: A 433 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7686 (mtt90) REVERT: A 467 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: A 500 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7427 (mtp85) REVERT: A 575 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7950 (mtt180) REVERT: A 725 LYS cc_start: 0.8614 (mttt) cc_final: 0.7898 (mtpp) REVERT: B 272 SER cc_start: 0.7585 (OUTLIER) cc_final: 0.7367 (t) REVERT: B 328 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7585 (mm-30) REVERT: B 433 ARG cc_start: 0.8264 (mtt180) cc_final: 0.7678 (mtt90) REVERT: B 500 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7616 (mtp85) REVERT: B 575 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7943 (mtt180) REVERT: B 725 LYS cc_start: 0.8653 (tttt) cc_final: 0.7979 (mtpp) REVERT: C 429 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7940 (mtt-85) REVERT: C 433 ARG cc_start: 0.8361 (mtt180) cc_final: 0.7781 (mtt90) REVERT: C 500 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7644 (mtp-110) REVERT: C 553 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7744 (mp) REVERT: C 725 LYS cc_start: 0.8629 (mttt) cc_final: 0.7892 (mtpp) REVERT: D 274 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.5850 (tm-30) REVERT: D 328 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7559 (mm-30) REVERT: D 433 ARG cc_start: 0.8300 (mtt180) cc_final: 0.7724 (mtt90) REVERT: D 500 ARG cc_start: 0.7845 (mtt180) cc_final: 0.7456 (mtp85) REVERT: D 725 LYS cc_start: 0.8597 (mttt) cc_final: 0.8038 (mtpp) outliers start: 51 outliers final: 36 residues processed: 266 average time/residue: 0.7039 time to fit residues: 207.9636 Evaluate side-chains 271 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 228 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 429 ARG Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 723 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: [14, 235, 52, 168, 103, 132, 115, 37, 202, 232, 109] chunk 14 optimal weight: 1.9990 chunk 235 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 chunk 232 optimal weight: 0.3980 chunk 109 optimal weight: 0.3980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 411 HIS B 692 GLN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS D 692 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.109016 restraints weight = 19979.683| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.00 r_work: 0.2863 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19968 Z= 0.112 Angle : 0.487 10.786 26950 Z= 0.254 Chirality : 0.036 0.232 3044 Planarity : 0.003 0.041 3314 Dihedral : 12.868 144.116 3029 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.68 % Allowed : 16.69 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.17), residues: 2324 helix: 2.37 (0.13), residues: 1418 sheet: 1.62 (0.59), residues: 72 loop : -0.86 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 557 TYR 0.020 0.001 TYR D 554 PHE 0.014 0.001 PHE C 305 TRP 0.014 0.001 TRP D 698 HIS 0.006 0.001 HIS B 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (19961) covalent geometry : angle 0.48707 / 0.25 (26950) hydrogen bonds : bond 0.05258 / 3.49 ( 1078) hydrogen bonds : angle 3.63425 / 2.55 ( 3108) Misc. bond : bond 0.00311 / 0.15 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8377.85 seconds wall clock time: 142 minutes 46.37 seconds (8566.37 seconds total)